Conditions: Lupus Nephritis
Allocation: RANDOMIZED | Intervention model: PARALLEL
Enrollment: 43
Healthy volunteers: no

Brief summary:
In this experimental study, researchers will try to find out if treatment of lupus nephritis with a combination of rituximab and cyclophosphamide (CTX), or a combination of rituximab and CTX followed by treatment with belimumab is safe and if this drug combination can block the immune system attacks.

Detailed description:
Lupus nephritis is a severe form of systemic lupus erythematosus (SLE) with active disease in the kidneys. SLE is a complex disease in which the body's own immune system attacks some of the body parts: the skin, the joints, the kidneys, the nervous system, the heart, the lungs and the blood. The cause of SLE is not known. Treatment for SLE usually involves drugs that are designed to block the immune system attacks. When SLE affects the kidneys (nephritis), stronger immune suppressing treatment is usually needed.

The drugs used in treatment of lupus nephritis often do not cure the disease and can cause serious side effects, including lowering the immune system too much. When the immune system is too low, a person is at a higher risk of getting infections. Therefore, research into new treatments with fewer serious side effects is needed for lupus nephritis.

Arms:
arm 1: Prednisone taper to 10 mg/day by week 12 and continue prednisone 10 mg/day to week 96. arm 2: 1. Belimumab (10 mg/kg IV) at weeks 4, 6, 8, and every 4 weeks to week 48.
2. Prednisone taper to 10 mg/day by week 12, and continue prednisone 10 mg/day to week 96.

Interventions: intervention 1: Rituximab intervention 2: Cyclophosphamide intervention 3: Prednisone intervention 4: Methylprednisolone intervention 5: Diphenhydramine intervention 6: Acetaminophen intervention 7: Rituximab intervention 8: Cyclophosphamide intervention 9: Prednisone intervention 10: Methylprednisolone intervention 11: Diphenhydramine intervention 12: Acetaminophen intervention 13: Belimumab
Intervention descriptions: intervention 1: Rituximab 1000mg intravenously (IV) at week 0 and week 2 intervention 2: Cyclophosphamide (750 mg) intravenously (IV) at week 0 and week 2. intervention 3: * Week 0 and Week 2: Prednisone (40 mg/day; taper to 10 mg/day by week 12)
* Continue prednisone 10 mg/day to week 96 intervention 4: Week 0 and Week 2:

Solumedrol (100 mg) IV intervention 5: Diphenhydramine (50 mg, or equivalent dose of similar antihistamine) will be given orally 1 hour (plus or minus 15 minutes) before each infusion of rituximab. intervention 6: Acetaminophen (650 mg) will be given orally 1 hour (plus or minus 15 minutes) before each infusion of rituximab. intervention 7: Rituximab 1000mg intravenously (IV) at week 0 and week 2. intervention 8: Cyclophosphamide (750 mg) intravenously (IV) at week 0 and week 2. intervention 9: * Week 0 and Week 2: Prednisone (40 mg/day; taper to 10 mg/day by week 12)
* Continue prednisone 10 mg/day to week 96 intervention 10: Week 0 and Week 2: Solumedrol (100 mg) IV intervention 11: Diphenhydramine (50 mg, or equivalent dose of similar antihistamine) will be given orally 1 hour (plus or minus 15 minutes) before each infusion of rituximab. intervention 12: Acetaminophen (650 mg) will be given orally 1 hour (plus or minus 15 minutes) before each infusion of rituximab. intervention 13: The RCB Group will receive IV belimumab 10mg/kg at weeks 4, 6, 8, and then every 4 weeks through week 48

Protocol document:
Prot_000.pdf: 
 
 
Rituximab Plus Cyclophosphamide Followed by Belimumab  
for the Treatment of Lupus Nephritis 
Protocol ITN055AI 
Version 2.0 (October 9, 2015) 
 
[IND 117212] 
 
This clinical study is supported and conducted by the Immune Tolerance Network, which is 
sponsored by the National Institute of Allergy and Infectious Diseases. 
Protocol Co-Chair 
Betty Diamond, MD 
Professor of Medicine  
Feinstein Institute 
North Shore Hospital 
350 Community Drive 
Manhasset, NY 11030 
Tel: 516-562-3830    Fax: 516-562-2537 
Email: bdiamond@nshs.edu 
 
Protocol Co-Chair 
David Wofsy, MD 
Professor of Medicine & 
Microbiology/Immunology 
Division of Rheumatology  
University of California, San Francisco 
533 Parnassus Avenue, Box 0633 
San Francisco, CA 94143 
Tel:  415-750-2104      Fax: 415-750-6920 
Email: wofsyd@medsch.ucsf.edu 
 
Protocol Co-Chair 
Cynthia Aranow, MD 
Investigator 
Feinstein Institute 
North Shore Hospital 
350 Community Drive 
Manhasset, NY 11030 
Tel: 516-562-3837    Fax: 516-562-2537 
Email: caranow@nshs.edu 
 
Protocol Co-Chair 
Maria Dall’Era, MD 
Associate Professor of Clinical Medicine 
Division of Rheumatology 
University of California, San Francisco 
533 Parnassus Avenue, Box 0633 
San Francisco, CA 94143 
Tel:  415-476-0783      Fax: 415-502-0888 
Email: maria.dallera@ucsf.edu 
 
ITN Clinical Trial Physician 
Dawn Smilek, MD, PhD 
Associate Director, Clinical Development 
Clinical Trials Group 
Immune Tolerance Network 
185 Berry St. Suite 3515 
San Francisco, CA 94107 
Tel: 415-353-4308     Fax: 415-343-4404 
E-mail: dsmilek@immunetolerance.org 
NIAID Medical Monitor 
Linna Ding, MD, PhD  
Medical Officer 
Division of Allergy, Immunology, and 
Transplantation  
National Institute of Allergy and Infectious 
Diseases 
5601 Fishers Lane Room 7D46 
Rockville, MD, 20852 
Tel: 240-627-3524      Fax: 301-402-2571  
Email: linnad@niaid.nih.gov 
 


ITN Clinical Operations Manager 
Kristin Ryker, MPH, CCRP 
Clinical Trials Group 
Immune Tolerance Network 
185 Berry St. Suite 3515 
San Francisco, CA 94107 
Tel: 415-353-4405     Fax: 415-353-4404 
Email: kryker@immunetolerance.org 
 
 
NIAID Project Manager 
Wendy Gao, BSN, MS 
Project Manager 
Division of Allergy, Immunology, and 
Transplantation  
National Institute of Allergy and Infectious 
Diseases  
5601 Fishers Lane Room 7D37 
Rockville, MD, 20852 
Tel: 240-627-3471       Fax: 301-480-1450 
Email: gaowe@niaid.nih.gov 
 
ITN Lead Biologist 
Fred Karnell, PhD 
Associate Director 
Biomarker and Discovery Research 
Immune Tolerance Network 
7500 Old Georgetown Road, Suite 800 
Bethesda, MD 20814 
Tel: 240-235-6175     Fax: 240-235-6197 
Email: fkarnell@immunetolerance.org 
 
 
NIAID Regulatory Affairs 
Lyudmila Lyakh, MD, PhD 
Regulatory Affairs Officer 
Division of Allergy, Immunology, and 
Transplantation  
National Institute of Allergy and Infectious 
Diseases  
5601 Fishers Lane Room 7B39 
Rockville, MD, 20852 
Tel: 240-627-3530        Fax: 301-480-1537 
Email: lyudmill@niaid.gov 
  
Rho Senior Statistician 
James Rochon, PhD 
Rho, Inc. 
6330 Quadrangle Drive 
Chapel Hill, NC 27517 
Tel: 919-595-6857     Fax: 919-408-0999 
Email: james_rochon@rhoworld.com 
 
 
 
Confidentiality Statement 
This document is confidential. It is provided for review only to investigators, potential 
investigators, consultants, study staff, and applicable independent ethics committees or 
institutional review boards. It is understood that the contents of this document will not be 
disclosed to others without written authorization from ITN and NIAID unless it is necessary to 
obtain informed consent from potential study participants. 
 
 
 
 


Protocol Approval 
Protocol No: ITN055AI 
Protocol Version: 2.0 
Dated: October 9, 2015 
IND#: 117212 
Protocol Chairs:  Betty Diamond, MD; David Wofsy, 
MD; Cynthia Aranow, MD; Maria Dall’Era, MD 
Short Title: Rituximab and Belimumab for Lupus Nephritis  
 
I confirm that I have read the above protocol in the latest version. I understand it, and I will 
work according to the principles of good clinical practice (GCP) as described in the US Code of 
Federal Regulations (CFR)—45 CFR part 46 and 21 CFR parts 50, 56, and 312, and in the 
International Conference on Harmonization (ICH) document Guidance for Industry: E6 Good 
Clinical Practice: Consolidated Guidance dated April 1996. Further, I will conduct the study in 
keeping with local legal and regulatory requirements. 
As the principal investigator, I agree to carry out the study by the criteria written in the 
protocol and understand that no changes can be made to this protocol without written permission 
of the NIAID. 
_______________________________ 
Principal Investigator (Print) 
_______________________________                                 _______________ 
Principal Investigator (Signature)                                                      Date 


Immune Tolerance Network  
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Protocol ITN055AI 
Version 2.0 
October 9, 2015 
 
Synopsis 
Title 
Rituximab Plus Cyclophosphamide followed by Belimumab  
for the Treatment of Lupus Nephritis 
 
Short Title 
Rituximab and Belimumab for Lupus Nephritis 
Sponsor 
NIAID 
Conducted By 
Immune Tolerance Network 
Protocol Chairs  
Betty Diamond, MD; David Wofsy, MD; Cynthia Aranow, MD;  
Maria Dall’Era MD 
 
Accrual Objective 
40 participants 
Study Treatment 
Study treatment will be rituximab, cyclophosphamide (CTX), and 
Solumedrol. This treatment will be followed by prednisone and 
belimumab in one group, and by prednisone without belimumab in the 
other group. 
 
Study Design 
This trial will be conducted as a prospective randomized phase 2 open 
label multicenter study in individuals with active lupus nephritis age 18 
and older. There will be two treatment arms with 1:1 randomization of a 
total of 40 participants. 
During the treatment phase, all participants will receive infusions of 
Solumedrol 100mg, rituximab 1000mg, and CTX 750mg intravenously 
(IV) at week 0 and week 2. Prednisone 40 mg per day will be 
administered with a guided steroid taper to 10mg per day by week 12.  
Participants will be randomized at week 4 to either the 
Rituximab/Cyclophosphamide (RC) Group or the 
Rituximab/Cyclophosphamide/Belimumab (RCB) Group. 
The RC Group will be maintained on prednisone. The RCB Group will 
receive IV belimumab 10mg/kg at weeks 4, 6, 8, and then every 4 weeks 
through week 48 in addition to prednisone.  
During the tolerance assessment phase, intravenous study medication 
will be discontinued after week 48, and all participants will be 
maintained on prednisone through week 96 of the study. 
Study Duration 
Total study duration will be 200 weeks. The enrollment period for this 
study will be 104 weeks. Study participation period will be 96 weeks, 
which includes a treatment phase of 48 weeks and a tolerance assessment 
phase of 48 weeks. 
 
 
 


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Primary Objective 
The primary objective of the study is to assess the safety of belimumab 
administration following treatment with rituximab and CTX, in terms of 
infectious adverse events. 
Primary Endpoint 
The primary endpoint is the proportion of participants who experience at 
least one Grade 3 or higher infectious adverse event at or prior to week 
48. 
Secondary 
Endpoints 
1. Proportion of participants who experience at least one Grade 3 or 
higher infectious adverse event at or prior to week 24, and at or prior 
to week 96. 
2. Proportion of participants with B cell reconstitution at week 24, 48, 
and 96, defined as the participant’s baseline B cell count, or the 
lower limit of normal, whichever is lower. 
3. Proportion of participants with Grade 4 hypogammaglobulinemia at 
or before week 24, 48, and 96. 
4. Proportion of participants with a complete response at week 24. 
Complete response is defined as meeting all of the following 
criteria: 
 Urine protein-to-creatinine ratio (UPCR) < 0.5, based on a 24-
hour collection. 
 Estimated glomerular filtration rate (eGFR) ≥120 ml/min/1.73m2 
calculated by the CKD-EPI formula or, if <120 ml/min/1.73m2, 
then >80% of eGFR at entry. 
 Prednisone dose tapered to 10 mg/day, or as specified in section 
5.5.2. 
5. Proportion of participants with an overall response (complete or 
partial response) at week 24. A partial response is defined as 
meeting all of the following criteria: 
 > 50% improvement in the UPCR from study entry, based on a 
24-hour collection. 
 Estimated glomerular filtration rate (eGFR) ≥120 ml/min/1.73m2 
calculated by the CKD-EPI formula or, if < 120 ml/min/1.73m2, 
then >80% of eGFR at entry. 
 Prednisone dose tapered to 10 mg/day, or as specified in section 
5.5.2. 
6. Proportion of participants with complete response at week 48. 


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7. Proportion of participants with an overall response (complete or 
partial response) at week 48. 
8. Proportion of participants with complete response at week 96 
(cumulative complete response). 
9. Proportion of participants with sustained complete response at week 
96 (representing “clinical tolerance”). Sustained complete response 
is defined as a complete response measured at 48 and 96 weeks. 
10. Proportion of participants with an overall response (complete or 
partial response) at week 96. 
11. Proportion of participants with treatment failure at or before week 
24, 48, and 96, as defined by withdrawal from the protocol due to 
worsening nephritis, infection, or study medication toxicity.  
12. Frequency of non-renal flares at or before week 24, 48, and 96, 
defined by the British Isles Lupus Assessment Group (BILAG) 
criteria. 
13. Anti-dsDNA antibodies and C3, C4 levels at week 24, 48, and 96 
14. Frequency of the following specific AEs: 
 Any event leading to death. 
 Grade 2 or greater leukopenia or thrombocytopenia. 
 Premature ovarian failure.  
 Malignancy. 
 Venous thromboembolic event (deep venous thrombosis or 
pulmonary embolism). 
 Disease- or study medication-related event leading to 
hospitalization. 
 Infusion reactions (within 24 hours of infusion) that result in the 
cessation of further infusions (including cytokine-release allergic 
reaction). 
Inclusion Criteria 
1. Diagnosis of Systemic Lupus Erythematosus (SLE) by American 
College of Rheumatology (ACR) criteria or Systemic Lupus 
International Collaborating Clinics (SLICC) criteria. 
2. Positive antinuclear antibody (ANA) or positive anti-ds DNA test 
results at visit -1 or any time within 14 days before visit -1. 


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Protocol ITN055AI 
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3. Age 18 years or older. 
4. Active proliferative lupus nephritis, as defined by either of the 
following: 
a. Kidney biopsy documentation within the last 3 months of 
ISN/RPS proliferative nephritis:  Class III, Class IV, or Class V 
in combination with Class III or IV. 
b. Kidney biopsy documentation within the last 18 months of 
ISN/RPS proliferative nephritis:  Class III, Class IV, or Class V 
in combination with Class III or IV, associated with at least one 
of the following:  
i. Active urinary sediment as defined by any one of 
the following:  
a. >4 RBC/hpf in the absence of menses and 
infection; 
b. >5 WBC/hpf in the absence of infection; or  
c. cellular casts limited to RBC or WBC casts. 
ii. UPCR ≥3 based on a 24-hour collection at visit -1 
or any time within 14 days before visit -1. 
iii. Confirmed increase in UPCR compared to a prior 
UPCR determination within 3 months of study 
entry. An increase in proteinuria will be considered 
to be confirmed if present on 2 consecutive 
assessments, or if increase led to a change in 
treatment. Increase in UPCR is defined as: 
a. UPCR to >1 if prior UPCR was ≤0.2; 
b. UPCR >2 if prior UPCR was ≤1 but >0.2; 
c. UPCR >double the prior UPCR if prior 
UPCR was >1. 
5. UPCR >1 based on a 24-hour collection at visit -1 or any time 
within 14 days before visit -1. 
6. Ability to provide informed consent. 
Exclusion Criteria 
1. 
New onset lupus nephritis, defined as lupus nephritis for which the 
participant has not yet been treated with either mycophenolate 
mofetil or cyclophosphamide. 
2. 
Neutropenia (absolute neutrophil count <1500/mm3). 
3. Thrombocytopenia (platelets <50,000/mm3). 


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4. Moderately severe anemia (Hgb <8 mg/dL). 
5. Positive QuantiFERON – TB Gold test results. PPD tuberculin test 
may be substituted for QuantiFERON – TB Gold test. 
6. Pulmonary fibrotic changes on chest radiograph consistent with prior 
healed tuberculosis. 
7. Active bacterial, viral, fungal, or opportunistic infections. 
8. Evidence of infection with human immunodeficiency virus (HIV), 
hepatitis B (as assessed by HBsAg and anti-HBc) or hepatitis C. 
9. Hospitalization for treatment of infections, or parenteral (IV or IM) 
antibacterials, antivirals, anti-fungals, or anti-parasitic agents within 
the past 60 days. 
10. Chronic infection that is currently being treated with suppressive 
antibiotic or antiviral therapy, including but not limited to 
tuberculosis, pneumocystis, cytomegalovirus, herpes simplex virus, 
herpes zoster, and atypical mycobacteria. 
11. History of significant infection or recurrent infection that, in the 
investigator’s opinion, places the participant at risk by participating 
in this study. 
12. Receipt of a live-attenuated vaccine within 3 months of study 
enrollment. 
13. End-stage renal disease (eGFR <20 mL/min/1.73m2) 
14. Concomitant malignancies or a history of malignancy, with the 
exception of adequately treated basal and squamous cell carcinoma 
of the skin, or carcinoma in situ of the cervix. 
15. History of transplantation.  
16. History of primary immunodeficiency. 
17. Pregnancy. 
18. Breastfeeding. 
19. Unwillingness to use an FDA-approved form of birth control 
(including but not limited to a diaphragm, an intrauterine device, 
progesterone implants or injections, oral contraceptives, the double-
barrier method, or a condom). 
20. Use of cyclophosphamide within the past 6 months. 
21. Use of anti-TNF medication, other biologic medications, or non-
biologic experimental therapeutic agents within the past 90 days, or 
5 half-lives prior to screening, whichever is greater. 


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22. Intravenous immunoglobulin (IVIG), plasmapheresis, or 
leukopheresis within the past 90 days. 
23. Use of an investigational biologic agent within the past 6 months. 
24. Prior treatment with rituximab. 
25. Treatment with other biologic B cell therapy within the past 12 
months. 
26. Liver function test (aspartate aminotransferase [AST], alanine 
aminotransferase [ALT], or alkaline phosphatase) results that are ≥2 
times the upper limit of normal.  
27. Severe, progressive, or uncontrolled renal, hepatic, hematological, 
gastrointestinal, pulmonary, cardiac, or neurological disease, either 
related or unrelated to SLE, with the exception of active lupus 
nephritis (or, in the investigator’s opinion, any other concomitant 
medical condition that places the participant at risk by participating 
in this study). 
28. Comorbidities requiring corticosteroid therapy, including those 
which have required three or more courses of systemic 
corticosteroids within the previous 12 months. 
29. Current substance abuse or history of substance abuse within the past 
year. 
30. History of severe allergic or anaphylactic reactions to chimeric or 
fully human monoclonal antibodies.  
31. History of anaphylactic reaction to parenteral administration of 
contrast agents. 
32. Lack of peripheral venous access. 
33. History of severe depression or severe psychiatric condition. 
34. History of suicidal thoughts within the past 2 months or suicidal 
behavior within the past 6 months, or a significant suicide risk in the 
investigator’s opinion. 
35. Inability to comply with study and follow-up procedures. 
 


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Table of Contents 
1. 
BACKGROUND AND RATIONALE ........................................................................................ 18 
1.2.1 
The Role of B Cells in Autoimmunity and in Systemic Lupus Erythematosus ......... 19 
1.2.2 
Rationale for Combining Rituximab, Cyclophosphamide, and Belimumab to Treat 
Lupus Nephritis .......................................................................................................... 20 
1.2.3 
Rationale for Conducting a Safety Pilot Study with Rituximab, Cyclophosphamide, 
and Belimumab .......................................................................................................... 21 
1.3.1 
Preclinical Studies ...................................................................................................... 22 
1.3.2 
Clinical Studies .......................................................................................................... 23 
1.4.1 
Risks Associated with Rituximab .............................................................................. 27 
1.4.2 
Risks Associated with Belimumab ............................................................................ 29 
1.4.3 
Risks Associated with Cyclophosphamide ................................................................ 30 
1.4.4 
Risks Associated with Corticosteroids ....................................................................... 31 
1.4.5 
Risks of Sequential Therapy with Rituximab and Belimumab .................................. 31 
1.4.6 
Risks Associated with Modified Maintenance Immunosuppression ......................... 33 
1.4.7 
Induction of Tolerance and Other Potential Benefits ................................................. 33 
2. 
OBJECTIVES ....................................................................................................................... 33 
3. 
STUDY DESIGN .................................................................................................................. 34 
3.3.1 
Primary Endpoint ....................................................................................................... 35 
3.3.2 
Secondary Endpoints ................................................................................................. 35 
3.3.3 
Study Population ........................................................................................................ 37 
3.3.4 
Definition of Renal and Non-Renal Flare .................................................................. 37 
3.5.1 
Ongoing Review ........................................................................................................ 38 
3.5.2 
Stopping Rules ........................................................................................................... 39 
4. 
ELIGIBILITY ....................................................................................................................... 42 
1.1 
Background ....................................................................................................................... 18 
1.2 
Scientific Rationale ........................................................................................................... 19 
1.3 
Preclinical and Clinical Experience ................................................................................... 22
1.4 
Summary of Known and Potential Risks and Benefits for Human Participants ............... 27
2.1 
Primary Objective .............................................................................................................. 33 
2.2 
Secondary Objectives ........................................................................................................ 34 
2.3 
Exploratory Objectives ...................................................................................................... 34 
3.1 
Description ........................................................................................................................ 34 
3.2 
Study Duration .................................................................................................................. 35 
3.3 
Study Endpoints ................................................................................................................ 35 
3.4 
Rationale for Selection of Route, Dose, and Regimen ...................................................... 38 
3.5 
Premature Termination or Suspension of the Trial ........................................................... 38 
4.1 
Inclusion Criteria ............................................................................................................... 42 
4.2 
Exclusion Criteria .............................................................................................................. 43 
4.3 
Premature Termination of a Participant from the Study .................................................... 44 


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5. 
STUDY MEDICATIONS ........................................................................................................ 44 
5.1.1 
Formulation, Packaging, and Labeling ...................................................................... 44 
5.1.2 
Preparation, Administration, and Dosage .................................................................. 45 
5.1.3 
Stability and Storage .................................................................................................. 46 
5.1.4 
Toxicity Management for Rituximab ......................................................................... 46 
5.2.1 
Formulation, Packaging, and Labeling ...................................................................... 46 
5.2.2 
Preparation, Administration, and Dosage .................................................................. 47 
5.2.3 
Recommended Storage Conditions ............................................................................ 47 
5.2.4 
Toxicity Management for Belimumab ....................................................................... 47 
5.3.1 
Dosage, Preparation, and Administration .................................................................. 48 
5.3.2 
Toxicity Management for Cyclophosphamide ........................................................... 49 
5.4.1 
Dosage, Preparation, and Administration .................................................................. 49 
5.4.2 
Recommended Storage Conditions ............................................................................ 50 
5.5.1 
Dosage for All Participants ........................................................................................ 50 
5.5.2 
Dose Modification for Participants with Non-Renal Flare ........................................ 51 
5.5.3 
Discontinuation of Prednisone for Participants with Non-Renal Flare ...................... 51 
5.7.1 
Prophylactic Medications........................................................................................... 52 
5.7.2 
Permitted Medications ............................................................................................... 53 
5.7.3 
Prohibited Medications .............................................................................................. 53 
5.7.4 
Contraception Use ...................................................................................................... 54 
6. 
STUDY PROCEDURES ......................................................................................................... 54 
6.1.1 
Scheduled Visits ........................................................................................................ 54 
6.1.2 
Unscheduled Visits .................................................................................................... 55 
6.2.1 
Enrollment ................................................................................................................. 55 
6.2.2 
Randomization ........................................................................................................... 55 
6.2.3 
Blinding ..................................................................................................................... 55 
5.1 
Investigational Study Medication:  Rituximab .................................................................. 44
5.2 
Investigational Study Medication:  Belimumab ................................................................ 46
5.3 
Additional Study Medications:  Cyclophosphamide ......................................................... 48
5.4 
Additional Study Medication:  Solumedrol ....................................................................... 49
5.5 
Additional Study Medication:  Prednisone ........................................................................ 50
5.6 
Discontinuation of Study Medication ................................................................................ 51 
5.7 
Concomitant Medications .................................................................................................. 52 
5.8 
Drug Accountability .......................................................................................................... 54 
5.9 
Assessment of Compliance with Study Medication .......................................................... 54 
6.1 
Visit Windows ................................................................................................................... 54
6.2 
Enrollment, Randomization and Blinding ......................................................................... 55


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7. 
MECHANISTIC PLAN .......................................................................................................... 57 
7.2.1 
Detection of Autoreactive B Cells ............................................................................. 58 
7.2.2 
Multi-Parameter Flow Cytometry (MFC) .................................................................. 58 
7.2.3 
Gene Expression in Peripheral Blood ........................................................................ 59 
7.2.4 
Serum Cytokine Assays ............................................................................................. 59 
7.2.5 
Genotype Analysis ..................................................................................................... 59 
7.2.6 
Antibodies to John Cunningham Virus ...................................................................... 59 
7.3.1 
Individual Based Longitudinal Profiling ................................................................... 60 
7.3.2 
Exploratory Analysis ................................................................................................. 60 
8. 
ADVERSE EVENTS .............................................................................................................. 62 
8.2.1 
Adverse Event ............................................................................................................ 62 
8.2.2 
Study-Specific Adverse Events.................................................................................. 62 
8.2.3 
Adverse Reaction and Suspected Adverse Reaction .................................................. 63 
8.2.4 
Serious Adverse Event or Serious Suspected Adverse Reaction ............................... 63 
8.2.5 
Adverse Events of Special Interest (AESIs) .............................................................. 63 
8.2.6 
Unexpected Suspected Adverse Reaction .................................................................. 64 
8.3.1 
Methods of Collection ............................................................................................... 64 
8.3.2 
Specific Instructions for Recording Adverse Events ................................................. 64 
8.3.3 
Collection Period for Adverse Events and Serious Adverse Events .......................... 65 
8.3.4 
Recording Method ..................................................................................................... 66 
8.4.1 
Grading of Hypogammaglobulinemia ....................................................................... 66 
8.4.2 
Grading Criteria ......................................................................................................... 66 
8.4.3 
Attribution Definitions ............................................................................................... 67 
8.5.1 
Reporting SAEs to the IND Sponsor ......................................................................... 67 
6.3 
General Assessments ......................................................................................................... 55 
6.4 
Clinical Laboratory Assessments ...................................................................................... 55 
6.5 
Lupus Assessments ............................................................................................................ 57 
6.6 
Clinical Pathology Assessment ......................................................................................... 57 
7.1 
Rationale ............................................................................................................................ 57 
7.2 
Planned Mechanistic Assays ............................................................................................. 58 
7.3 
Overview of Data Analysis ............................................................................................... 60
7.4 
Future / Unplanned Studies ............................................................................................... 61 
7.5 
Specimen Logistics ............................................................................................................ 61 
7.6 
Specimen Tracking Procedures ......................................................................................... 61 
7.7 
Specimen Storage .............................................................................................................. 61 
8.1 
Overview ........................................................................................................................... 62 
8.2 
Definitions ......................................................................................................................... 62 
8.3 
Collecting and Recording Adverse Events ........................................................................ 64
8.4 
Grading and Attribution of Adverse Events ...................................................................... 66
8.5 
Reporting Serious Adverse Events .................................................................................... 67


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8.5.2 
Reporting AESIs to the IND Sponsor ........................................................................ 68 
8.5.3 
Reporting SAEs to Health Authorities ....................................................................... 68 
8.5.4 
Reporting SAEs to IRBs and Ethics Committees ...................................................... 69 
8.5.5 
Reporting SAEs to the DSMB ................................................................................... 69 
8.5.6 
Reporting SAEs and AESIs to Genentech ................................................................. 69 
8.5.7 
Reporting Pregnancy .................................................................................................. 70 
9. 
STATISTICAL CONSIDERATIONS AND ANALYTICAL PLAN ................................................ 71 
9.1.1 
Study Milestones ........................................................................................................ 71 
9.1.2 
Analysis Populations .................................................................................................. 71 
9.2.1 
Primary Endpoint ....................................................................................................... 72 
9.2.2 
Secondary Endpoints ................................................................................................. 72 
9.2.3 
Endpoint Analysis by Race ........................................................................................ 74 
9.2.4 
Baseline Characteristics and Demographics .............................................................. 74 
9.2.5 
Safety Analysis .......................................................................................................... 74 
9.2.6 
Medical History ......................................................................................................... 75 
9.2.7 
Use of Medications .................................................................................................... 75 
10. 
ACCESS TO SOURCE DATA/DOCUMENTS........................................................................... 77 
11. 
QUALITY CONTROL AND ASSURANCE ............................................................................... 77 
12. 
ETHICAL CONSIDERATIONS AND COMPLIANCE WITH GOOD CLINICAL PRACTICE ........... 77 
13. 
PUBLICATION POLICY ........................................................................................................ 78 
14. 
REFERENCES ...................................................................................................................... 79 
APPENDIX 1. SCHEDULE OF EVENTS ............................................................................................. 86 
 
9.1 
Analysis Samples............................................................................................................... 71
9.2 
Analysis of Endpoints........................................................................................................ 72
9.3 
Sample Size ....................................................................................................................... 75 
9.4 
Reporting Deviations from the Statistical Plan ................................................................. 76 
12.1 Statement of Compliance .................................................................................................. 77 
12.2 Informed Consent .............................................................................................................. 78 
12.3 Privacy and Confidentiality ............................................................................................... 78 


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List of Figures 
Figure 1 Study Schema .................................................................................................................. 35 
 
List of Tables 
Table 1 Qualifying thresholds for flare rate after week 24 and continuing through week 48 ....... 41 
Table 2 Qualifying thresholds for flare rate after week 48 ............................................................ 41 
Table 3 Management of cyclophosphamide-related toxicity ........................................................ 49 
Table 4 Prednisone tapering schedule ........................................................................................... 50 
Table 5 Attribution of adverse events ........................................................................................... 67 
Table 6 Secondary endpoints and analysis samples ...................................................................... 73 
Table 7 95% confidence limits for proportions of AEs in pilot study ........................................... 76 
Table 8 Power to detect between-group differences in the proportion of grade 3+ infection AEs 76 
 
 
 
 
 


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Abbreviations 
ACEi 
ACE inhibitor 
ACLS 
Advance Cardiac Life Support 
ACR 
American College of Rheumatology 
AE 
adverse event 
AESI 
adverse event of special interest 
ALT 
alanine aminotransferase 
AST 
aspartate aminotransferase 
ANA 
antinuclear antibody 
ANCOVA 
analysis of covariance 
AR 
adverse reaction 
ARB 
angiotensin receptor blocker 
AZA 
Azathioprine 
BAFF 
B-cell activating factor 
BILAG 
British Isles Lupus Assessment Group 
BLyS 
B-lymphocyte stimulator 
BR3-Fc 
BAFF receptor-3 Fc 
CBC 
complete blood count 
CFR 
U. S. Code of Federal Regulations 
cGCP 
current good clinical practice 
CKD-EPI 
Chronic Kidney Disease Epidemiology Collaboration 
CRF 
case report form 
CRO 
contract research organization 
CPR 
cardiopulmonary resuscitation 
CTX 
cyclophosphamide 
DAIT 
Division of Allergy, Immunology, and Transplantation 
dsDNA 
double-stranded DNA 
DSMB 
Data and Safety Monitoring Board 


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eCRF 
electronic case report form 
EDC 
electronic data capture 
eGFR 
estimated glomerular filtration rate 
ELISA 
enzyme-linked immunosorbent assay 
ELISPOT 
enzyme-linked immunospot 
ENA 
extractable nuclear antigen 
FDA 
U.S. Food and Drug Administration 
GCP 
good clinical practice 
HEp-2 
human epithelial type 2 
HIV 
human immunodeficiency virus 
HLA 
human leukocyte antigen 
ICH 
International Conference on Harmonisation 
ISN/RPS 
International Society of Nephrology/Renal Pathology Society (classification) 
IgA 
immunoglobulin A 
IgG 
immunoglobulin G 
IgM 
immunoglobulin M 
IND 
Investigational New Drug Application 
IPEX 
immunodysregulation polyendocrinopathy enteropathy X-linked syndrome 
IRB 
institutional review board 
ITN 
Immune Tolerance Network 
ITT 
intent to treat 
IV 
Intravenous 
JC 
John Cunningham 
LN 
lupus nephritis 
MedDRA 
Medical Dictionary for Regulatory Activities 
MMF 
mycophenolate mofetil 
NCI-CTCAE 
National Cancer Institute Common Terminology Criteria for Adverse Events 
NIAID 
National Institute of Allergy and Infectious Diseases 


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NSAID 
nonsteroidal anti-inflammatory drug 
PCR 
polymerase chain reaction 
PML 
progressive multifocal leukoencephalophathy 
PO 
per os (by mouth) 
PP 
per protocol 
RC 
Rituximab/Cyclophosphamide 
RCB 
Rituximab/Cyclophosphamide/Belimumab 
RNA 
ribonucleic acid 
RNP 
ribonucleoprotein 
SAE 
serious adverse event 
SAP 
statistical analysis plan 
SAR 
serious adverse reaction 
SELENA-
SLEDAI 
Safety of Estrogens in Lupus Erythematosus National Assessment - Systemic 
Lupus Erythematosus Disease Activity Index 
SCG 
Standard of Care Treatment Group 
SLE 
systemic lupus erythematosus 
SLICC 
Systemic Lupus International Collaborating Clinics 
Sm 
Smith antigen 
SMX/TMP 
sulfamethoxazole-trimethoprim 
SOC 
standard of care 
SS 
safety sample 
SUSAR 
Serious and unexpected suspected adverse reaction 
TNF 
tumor necrosis factor 
UCSF 
University of California, San Francisco 
ULN 
Upper limit of normal range 
UPCR 
urine protein-to-creatinine ratio 
WBC 
white blood cell 
WHO 
World Health Organization 
 


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1. 
BACKGROUND AND RATIONALE 
1.1 
BACKGROUND 
Systemic lupus erythematosus (SLE) is an autoimmune disease that affects multiple 
organ systems and has numerous clinical presentations [1]. Women are affected 
predominantly, including young women of child-bearing age, with peak age of onset 
between late teens and early 40s. SLE is characterized by autoantibodies, including 
antibodies to dsDNA, and by abnormal B cell activation and differentiation [2], 
indicating that B cell depleting and modulating therapies could be beneficial in treating 
SLE. Belimumab, an inhibitor of B-cell activating factor (BAFF), has recently been 
FDA-approved for the treatment of SLE [3], and rituximab, a B-cell depleting agent, has 
been recommended for treatment of lupus nephritis (LN) that is refractory to standard 
immunosuppression [4]. 
SLE is a chronic illness, and can be life-threatening when major organ systems are 
involved. Proliferative lupus nephritis is a severe manifestation of SLE requiring 
aggressive treatment. As many as 60% of adults with SLE will develop lupus nephritis 
during the first 10 years of disease, with approximately 35% having clinical evidence of 
nephritis at the time of diagnosis [5-8] . Treatment of lupus nephritis remains one with 
imperfect response and excessive toxicity, and this manifestation of SLE continues to 
have significant impact on quality of life, mortality, and cost. Though approved for the 
treatment of many manifestations of SLE, belimumab has not been carefully examined in 
patients with lupus nephritis. 
The current standard of care for lupus nephritis is a two-step approach with induction of 
renal response followed by maintenance therapy [4]. Although there is no FDA approved 
agent for treatment of lupus nephritis, standard of care (SOC) for induction of response is 
considered to be treatment with mycophenolate mofetil (MMF) plus corticosteroids or 
cyclophosphamide (CTX) plus corticosteroids. Although the majority of patients in the 
Euro-Lupus Nephritis Trial achieved a renal response with the Euro-Lupus CTX regimen 
[9], complete response rates at 6 months in a recent large, international, randomized, 
controlled trial were 8% using MMF and 8% using CTX (ALMS) [10]. Other studies 
have suggested a better response rate with MMF [11, 12]. However meta-analysis failed 
to demonstrate clear superiority of either therapy [13]. 
The variation in response rates reflects, at least in part, differences in patient populations, 
duration of treatment, and definition of response. In addition to these unacceptably low 
success rates and considerable toxicity, maintenance therapy requires continued 
immunosuppression with MMF or azathioprine (AZA), in combination with 
corticosteroids, for a minimum of 2 years, typically longer. There is little evidence that 
either CTX or MMF succeeds in resetting peripheral B cell tolerance as renal relapse is 
common [14]. Thus, an efficacious treatment with minimal toxicity and sustained clinical 
and immunologic response remains an unmet need for lupus nephritis. 


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1.2 
SCIENTIFIC RATIONALE 
1.2.1 The Role of B Cells in Autoimmunity and in Systemic Lupus 
Erythematosus 
Autoimmune diseases, including SLE, can be defined as clinical syndromes caused by 
inappropriate activation of self-reactive B cells or T cells [2]. For most autoimmune 
diseases, the earliest trigger remains elusive. Many factors, including genetic 
susceptibility and environmental influence, culminate in the breakdown of B-cell or T-
cell tolerance. In addition, antibody-independent pathogenic B cell functions, mediated 
through antigen presentation, co-simulation and cytokine production, result in the 
activation of autoreactive memory T helper cells and dendritic cells, the inhibition of T 
regulatory cells, and the induction of pathogenic Th1 and Th17 cells [15, 16]. 
There is abundant evidence that elevated levels of autoreactive B cells are associated with 
a number of autoimmune diseases, including type 1 diabetes, rheumatoid arthritis, 
Sjogren’s syndrome, multiple sclerosis, and IPEX syndrome [17-25]. Elevated levels of 
autoreactive B cells have also been observed in apparently healthy individuals when the 
known autoimmune susceptibility allele PTPN22 is present [17]. In some autoimmune 
diseases, both central and peripheral B cell tolerance appear to be dysregulated , while in 
others elevated levels of autoreactive B cells appear only in the periphery [17, 20]. In 
IPEX, elevated levels of autoreactive B cells are associated with a defect in regulatory T 
cells [21]. Interestingly, disease modifying tumor necrosis factor (TNF)-inhibitors and 
methotrexate do not reduce the level of B cell autoreactivity in rheumatoid arthritis, 
indicating that these agents exert their effect by alternative mechanisms of action [26].  
The role of B cells in lupus pathogenesis has been highlighted because of their ability to 
generate pathogenic autoantibodies. Lupus nephritis, for example, is characterized by 
immune complex deposition, inflammation, and scarring in the glomeruli and the 
tubulointerstitium [27-29]. Studies of B cell subsets in human SLE have demonstrated 
evidence of expansion of the immature transitional B cells, memory B cells, and plasma 
cells, with decreased numbers of circulating naïve B cells [30]. Additionally, sequence 
analysis has demonstrated increased numbers of autoreactive mature naïve B cells in SLE 
patients compared to healthy controls, suggesting a breach within the tolerance 
checkpoint between transitional and mature naïve B cell compartments [23, 24, 31-33]. 
Some SLE patients have abnormally increased autoreactivity in the transitional B cell 
compartment, possibly due to defects in receptor editing, deletion and anergy within the 
bone marrow. Similar to the results observed with anti-TNF agents and methotrexate in 
rheumatoid arthritis, elevated levels of autoreactive B cells persist in SLE despite 
treatment with immunosuppressive agents such as corticosteroids and CTX [33]. The 
results indicate that these immunosuppressives exert their effect by alternative 
mechanisms, and suggest that a therapeutic approach specifically targeting autoreactive B 
cells could lead to improved clinical outcomes in SLE.  
Additional evidence for an important role of B cells in the pathogenesis of SLE comes 
from studies that link expression levels of BAFF, also known as B-lymphocyte stimulator 
(BLyS), to the survival of mature peripheral B cells, antibody production, and 


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autoimmune disease [34-39]. BAFF, a crucial homeostatic cytokine, maintains B cell 
numbers and regulates B cell selection. Newly formed and mature primary B cells require 
BAFF for survival through signals imposed at the transitional B cell stage of 
differentiation that rescue developing B cells from apoptosis [40, 41]. There is evidence 
that excess levels of BAFF allow autoreactive B cells to escape elimination at the 
transitional stage [42-44]. Transgenic mice that overexpress BAFF develop autoimmune 
manifestations that are similar in some respects to SLE and Sjogren’s syndrome [45], and 
there is evidence of increased circulating levels of BAFF in patients with SLE [46]. 
1.2.2 Rationale for Combining Rituximab, Cyclophosphamide, and Belimumab 
to Treat Lupus Nephritis 
Given their role in the pathophysiology of lupus and lupus nephritis, autoreactive B cells 
are attractive therapeutic targets. However, two recent randomized, placebo controlled 
studies of B cell depletion with rituximab (anti-CD20), in combination with MMF, did 
not meet their primary endpoints and thus failed to demonstrate efficacy in either active 
extra-renal lupus (EXPLORER trial) or lupus nephritis (LUNAR trial) [12, 47]. This is in 
contrast to several case series of patients with refractory lupus or lupus nephritis who 
have been successfully treated with rituximab in combination with CTX [48-55].  
Although the reason for this discrepancy is not known, a number of explanations have 
been discussed in detail [12, 47, 53]. The authors of the EXPLORER trial note that the 
criteria for their endpoints were very stringent, so that some benefit from rituximab could 
have been overlooked in the study. The LUNAR study may have been underpowered to 
convincingly demonstrate benefit. Also, the study populations in the randomized 
controlled trials were not considered to be refractory to standard immunosuppression, and 
participants with relatively mild disease were included. In contrast, participants in the 
open label case series generally had severe disease, and were said to be refractory to 
standard therapy. The effect of background therapy with MMF and corticosteroids may 
have obscured a treatment benefit from rituximab in the EXPLORER and LUNAR 
studies. It is also possible that CTX plays a critical role compared to MMF as background 
immunosuppression in combination with rituximab through its effect on infiltrating 
inflammatory cells in the kidney which may need to be eradicated for renal improvement. 
A recently published study analyzed the relationships between B cell reconstitution, 
baseline anti-dsDNA antibody levels and time to flare in 61 SLE patients with refractory 
active disease treated with rituximab and CTX [56]. This study provides important 
preliminary data on the importance of B cell reconstitution and B cell subsets in disease 
relapse. The results suggest: 1) early B cell repopulation is associated with clinical 
relapse, and 2) sustained lowering of anti-dsDNA antibody titers correlates with 
remission. Frequencies of autoreactive B cells in the B cell repertoire were not assessed 
in this study. 
Existing data from murine studies however, suggests that reconstitution of the B cell 
repertoire following treatment with CTX preferentially selects for more potentially 


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pathogenic autoreactive B cells [57]. BAFF levels are known to be elevated following B 
cell depletion, and high BAFF levels have been associated with an increased risk of 
recurrent disease flare [58, 59]. It is likely that the circulating high BAFF levels that exist 
following B cell depletion permit the maturation of autoreactive B cells, allowing them to 
bypass tolerance checkpoints and enter the immunocompetent repertoire. B cell 
reconstitution in the absence of high levels of BAFF might be expected to result in a 
tolerized B cell repertoire without autoreactivity, and a sustained clinical response. If this 
is the case, then treatment of proliferative lupus nephritis with rituximab and CTX 
followed by BAFF inhibition with belimumab will result in reduced selection of 
autoreactive B cells in the reconstituted B cell repertoire, and this reduction in 
autoreactive B cells may result in clinical benefit. 
1.2.3 Rationale for Conducting a Safety Pilot Study with Rituximab, 
Cyclophosphamide, and Belimumab  
Although there is strong scientific rationale for combining B cell depleting agents in 
lupus nephritis, the safety of such a strategy has yet to be established. B cell depletion 
and transient hypogammaglobulinemia are both generally well tolerated, with few 
infectious complications [53, 54, 60-62], although exceptions have been reported [63, 
64]. Standard of care for individuals with active lupus nephritis includes 
immunosuppression, and infections are common in this population. For example, in the 
ALMS study, which compared MMF and CTX for induction therapy in 370 participants 
with active lupus nephritis, the most commonly reported adverse events (AEs) and 
serious adverse events (SAEs) were infections in both treatment groups [10]. Infectious 
AEs were reported in 65% of participants, and infectious SAEs were reported in 11%. A 
total of 9 deaths were attributed to infection in this study. 
In the setting of active lupus nephritis, prolonged B cell depletion following repeated 
cycles of rituximab has been associated with more favorable clinical outcomes, while 
early B cell reconstitution correlates with disease flares [52, 54]. Despite these 
encouraging results, it is possible that combining rituximab and belimumab in lupus 
nephritis may result in more profound and prolonged B cell depletion and 
hypogammaglobulinemia than observed when these agents are administered separately, 
which could theoretically increase the risk of infectious complications. For this reason, 
we are conducting a study to prospectively assess the safety and feasibility of sequential 
administration of rituximab and cyclophosphamide followed by belimumab in a small 
carefully monitored group of individuals with lupus nephritis. 
Participants with active lupus nephritis will undergo B cell depletion with one cycle of 
rituximab and CTX in combination with corticosteroids, in accordance with the induction 
regimen that has been described [50, 52]. Belimumab administration according to 
standard dosing for SLE will begin four weeks after initiation of rituximab and 
cyclophosphamide, at a time when B cell depletion is expected to be nearly complete, and 
B cell reconstitution is expected to begin. Sequential rather than simultaneous 
administration of these B cell depleting agents will provide a wash-out period for prior 


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immunosuppressives such as MMF before belimumab is added. Participants will be 
followed closely for adverse events and disease activity. According to the rationale 
discussed in section 1.2.2, belimumab is predicted to favor reconstitution of non-
autoreactive B cells. Laboratory assessment of the autoreactive B cell repertoire will be 
undertaken in order to explore the effect of belimumab on the reconstituting B cell 
repertoire in a preliminary fashion. However, the primary objective of this study is to 
assess the safety of sequential administration of rituximab and belimumab for lupus 
nephritis in terms of infectious adverse events.  
1.3 
PRECLINICAL AND CLINICAL EXPERIENCE 
1.3.1 Preclinical Studies 
1.3.1.1 Preclinical Studies with Rituximab 
In vivo preclinical studies have shown that rituximab depletes B cells from the peripheral 
blood, lymph nodes, and bone marrow of cynomolgus monkeys; this depletion occurs 
presumably through complement- and cell-mediated processes [65, 66]. In high-dose 
safety studies performed in cynomolgus monkeys, no serious adverse clinical events were 
observed, and laboratory and histopathological abnormalities, such as white blood cell 
(WBC) reduction and lymphoid atrophy, were limited. 
1.3.1.2 Preclinical Studies with Belimumab 
In early studies in mice, belimumab was shown to block the expansion of splenic B cells 
induced by administration of recombinant human BAFF [67]. In cynomolgus monkeys, 
belimumab administration resulted in decreased peripheral blood CD20+ B cells (35-41% 
of baseline) after 13 weeks of treatment every other week, without affecting total 
lymphocyte numbers [68]. Following discontinuation of belimumab after 26 weeks, the 
decrease in B cells numbers persisted through at least 39 weeks, and even longer in some 
monkeys. In general, B cell numbers returned to normal by week 60. Belimumab 
appeared to be safe and well-tolerated in the monkeys, with no treatment-related 
infections observed. 
1.3.1.3 Preclinical Studies with Belimumab Combined with Rituximab 
There are no published studies of the belimumab and rituximab combination in 
preclinical model systems as neither of them cross-react with the rodent orthologue 
molecules. However, preclinical studies have been undertaken with surrogate biologics 
similar in action to belimumab (BAFF receptor-3 Fc) in combination with a mouse anti-
mouse CD20 (surrogate for Rituxan). Murine studies demonstrate superior efficacy of 
anti-CD20 B cell depletion combined with BAFF inhibitor therapy in NZB/W mice 
compared to control, either drug alone or CTX [69]. Combination therapy resulted in 
improved renal scores, prolonged B cell depletion, hypogammaglobulinemia, and 
reduced autoantibody levels. 
 


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1.3.2 Clinical Studies 
1.3.2.1 Overview of Clinical Studies with Rituximab for Approved Indications 
Rituximab is a chimeric monoclonal antibody with specificity for CD20, and is approved 
for treatment of non-Hodgkin’s lymphoma, chronic lymphocytic leukemia, rheumatoid 
arthritis, and ANCA-associated vasculitis. 
http://www.gene.com/gene/products/information/pdf/rituxan-prescribing.pdf 
CD20 is a transmembrane protein located on pre-B and mature B lymphocytes, but is not 
found on hematopoietic stem cells, pro-B-cells, normal plasma cells, or other normal 
cells. In autoimmune disease, rituximab may act by interfering with multiple steps of the 
autoimmune/inflammatory process, such as production of rheumatoid factor, antigen 
presentation, T-cell activation, and/or proinflammatory cytokine production. According 
to the rituximab prescribing information, rituximab rapidly induces near complete 
depletion of peripheral B cells in the majority of patients with rheumatoid arthritis and 
ANCA-associated vasculitis. Sustained B cell depletion persists for approximately 6 
months, followed by gradual recovery in most patients, although prolonged B cell 
depletion can occur, lasting more than 3 years. Immunoglobulin levels can be reduced 
following rituximab treatment, especially IgM, although the clinical consequences of 
such reductions are unclear. 
The efficacy of rituximab combined with methotrexate was demonstrated in a 520 
patient, multicenter, randomized, placebo-controlled phase 3 trial known as REFLEX, in 
rheumatoid arthritis refractory to anti-tumor necrosis factor therapy [70]. This study met 
its primary and secondary endpoints, with all American College of Rheumatology (ACR) 
response parameters significantly improved in the rituximab-treated patients. Safety 
measures were generally similar between the rituximab and the placebo groups. This trial 
and others [71, 72] support the use of rituximab for the treatment of rheumatoid arthritis. 
Rituximab was also shown to be efficacious as induction therapy in ANCA-associated 
vasculitis in the 197 patient randomized, double-blind, non-inferiority RAVE trial 
conducted by the ITN with NIAID sponsorship [73, 74]. At 6 months, 64% of 
participants in the rituximab group versus 52% of participants in the standard of care 
CTX group met the primary endpoint of clinical remission, which was maintained at 18 
months in 39% of the rituximab group and 33% of the CTX group. The results met pre-
specified criteria for non-inferiority of rituximab to CTX. Safety measures were similar 
in the two groups, and rituximab was FDA-approved for the treatment of ANCA-
associated vasculitis on the basis of this trial. 
1.3.2.2 Overview of Clinical Studies in Systemic Lupus Erythematosus with 
Rituximab 
Rituximab has been evaluated for efficacy in SLE in combination with standard 
immunosuppressive agents [12, 47-49, 51-54, 75-79]. Due to mixed results and 
limitations in the design of some of the trials, it has not been fully established whether 
patients with SLE benefit from the addition of rituximab to standard immunosuppression. 
Results were disappointing from placebo controlled trials with rituximab administered on 


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a background of standard immunosuppression with azathioprine, MMF, or methotrexate 
(LUNAR and EXPLORER) [12, 47]. Nevertheless, many patients with SLE have been 
reported to improve following open label treatment with rituximab and CTX [48-52]. 
1.3.2.2.1 
Clinical Studies in Systemic Lupus Erythematosus with Rituximab 
Combined with Azathioprine, Mycophenolate Mofetil, or Methotrexate 
B cell depletion with rituximab for SLE was compared to placebo on a background of 
standard immunosuppression in 2 randomized, controlled trials [12, 47]. The first trial, 
known as EXPLORER, was conducted in 257 patients with moderate-severe active SLE 
who received azathioprine, MMF, or methotrexate in addition to rituximab and 
corticosteroids [47]. This study failed to meet its primary and secondary endpoints of 
complete or partial clinical response assessed by BILAG scores in rituximab versus 
placebo-treated patients. In pre-planned subgroup analysis, however, a higher proportion 
of the African-American/Hispanic population achieved a complete or partial clinical 
response with rituximab versus placebo (p=0.0408). Safety outcomes, including 
infectious adverse events, were similar overall between the rituximab and the placebo 
groups. 
The second trial, known as LUNAR, was conducted in 144 patients with active 
proliferative lupus nephritis, who received either rituximab or placebo in combination 
with MMF and corticosteroids [12]. This trial also failed to meet its primary endpoint, 
defined as combined complete or partial renal response at week 52. The overall response 
rate was higher in the rituximab group compared to the control group (57% vs. 46%), but 
statistical significance was not achieved. Overall, the incidence of adverse events, 
including infectious adverse events, was similar in the rituximab and placebo groups. 
Similar to the EXPLORER results, pre-planned subgroup analysis in LUNAR suggested 
a better renal response to rituximab plus MMF compared to placebo plus MMF in black 
participants. Although the results are intriguing, the number of black participants in 
LUNAR was too small to support any conclusion regarding preferential benefit. 
Moreover, in other studies black ethnicity has been associated with non-responsiveness 
and failure to achieve B-cell depletion, suggesting the possibility of ethnic variation [54, 
75, 80, 81]. Genetic polymorphisms of FcγRIIb and FcγIIIb have been suggested to 
explain ethnic variation of response to rituximab, but this hypothesis is not supported by 
clinical data [54, 82-84].  
There are a number of possible explanations for the failed primary endpoint in LUNAR, 
including concomitant medication use and definition of renal response.  Recent 
publications have shown that variation in renal response definition can impact the 
interpretation of clinical trial results in lupus nephritis [85, 86].  Moreover, inclusion of 
hematuria in renal response definitions, such as that utilized in LUNAR, interferes with 
the predication of good long-term renal outcomes [87]. 


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1.3.2.2.2 
Clinical Studies in Systemic Lupus Erythematosus with Rituximab and 
Cyclophosphamide 
Several recent uncontrolled case series examined the effect of B cell depletion with 
rituximab in combination with CTX and corticosteroids in SLE patients who had been 
found to be refractory to treatment with standard immunosuppressive therapy. The 
various regimens were administered in open label fashion in each of the studies.  
In the first study, retrospective analysis undertaken in 50 patients with refractory SLE 
(including 34 patients with renal involvement) showed complete or partial remission in 
80% of patients after 6 months of follow-up following one cycle of open label rituximab, 
CTX, and corticosteroids [50]. Improvement in BILAG scores was observed in all organ 
systems. Median time to B cell repletion was 6 months, though approximately a third of 
the patients experienced prolonged B cell depletion (>12 months). Based on this study 
and others, the American College of Rheumatology concluded that rituximab can be used 
in some patients with lupus nephritis who fail to improve following standard induction 
therapy with either CTX or MMF [4]. There were 5 serious adverse events reported in 
this study, including one death from adult respiratory distress syndrome attributed to an 
idiosyncratic reaction to CTX infusion. Two of the serious adverse events were attributed 
to rituximab, including an infusion reaction responsive to steroids, and pneumococcal 
pneumonia and sepsis from which the patient recovered. A more recently published study 
from the same group suggests that repeated courses of rituximab and CTX may produce a 
long-lasting clinical effect in SLE [52]. 
In the second study, limited analysis of pooled data was undertaken from 43 patients with 
refractory lupus nephritis treated with open label rituximab, CTX, and corticosteroids 
[49]. Overall increase in serum albumin and decrease in proteinuria was observed in both 
proliferative lupus nephritis and membranous lupus nephritis.  
In a third case series, 8 patients with refractory SLE were treated with rituximab, CTX, 
and corticosteroids, and followed prospectively for a response [48]. Profound B cell 
depletion was prolonged in these patients (>12 months) following 6 doses of rituximab 
given over approximately 3 months. Proteinuria improved in the 5 patients with renal 
involvement, and SLEDAI scores improved in all patients. 
In a recently published long term study, 25 lupus nephritis patients were treated with 
rituximab, cyclophosphamide, and corticosteroids and were followed for a mean of 36 
months (range 9-95 months) [55]. A renal response was observed in 22/25 participants 
after a median of 12 months, and most demonstrated histologic improvement on renal 
biopsy. Participants did equally well whether or not they received traditional maintenance 
therapy (MMF or AZA) versus steroids alone after the reappearance of B cells in the 
circulation. 
Of note, therapy with rituximab and cyclophosphamide has been investigated in new 
onset lupus nephritis using oral steroid-sparing regimens in which MMF or AZA is 
administered following B cell depletion with rituximab and cyclophosphamide [78, 79]. 
However, there is little published data in new onset lupus nephritis patients using low 


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dose prednisone maintenance therapy following B cell depletion. For this reason, new 
onset lupus nephritis patients will be excluded from this study.  
1.3.2.2.3 
Clinical Studies in Lupus Nephritis with Rituximab – Pooled Results 
A recent analysis pooled the results for efficacy of rituximab in European cohorts with 
biopsy-proven lupus nephritis [51]. Results were included for 164 patients treated with 
rituximab in combination with corticosteroids (162 patients), MMF (55 patients), and 
CTX (58 patients). The analysis was conducted retrospectively, and did not include 
control patients who were not treated with rituximab. Nevertheless, a favorable 
therapeutic response was said to be observed in 67% of patients. Responses were more 
common in patients with type III and mixed type LN, and least common in pure type V 
and type IV LN. Baseline features that were prognostic of a favorable response included 
lower proteinuria, higher albumin, and lower frequency of nephrotic syndrome and renal 
failure. Common adverse events noted in the analysis included infusion reactions and 
infections, and three patients died (from septic shock, brain hemorrhage, and disease 
progression, respectively). The results suggest that rituximab in combination with other 
immunosuppressive agents may be beneficial, but further illustrate the need for 
randomized control trials. 
1.3.2.3 Clinical Studies in Systemic Lupus Erythematosus with Belimumab 
Belimumab is a fully human monoclonal IgG1 antibody that inhibits the binding of 
soluble, biologically active B-lymphocyte stimulator (BLyS), otherwise known as B-cell 
activating factor (BAFF), to its receptor on B cells [67]. Belimumab does not bind to B 
cells directly, but inhibits the survival of B cells and reduces differentiation of B cells 
into immunoglobulin-producing plasma cells. Belimumab is approved for the treatment 
of active, autoantibody-positive SLE. 
http://www.hgsi.com/images/Benlysta/pdf/benlysta_pi.pdf.  
In a phase 1 study in mild to moderate SLE, belimumab was shown to reduce peripheral 
CD20+ B cell numbers and was well-tolerated [88]. A randomized controlled phase 2 
study with belimumab administered on a background of SOC immunosuppression in SLE 
(which did not include patients with lupus nephritis) failed to meet its co-primary 
efficacy endpoints [89]. However, subgroup analysis showed that patients who were 
seropositive for ANA and/or anti-dsDNA antibodies had a significantly better clinical 
response to belimumab at 52 weeks compared to the placebo group.  
In this phase 2 study, belimumab was administered at days 0, 14, 28, and then every 28 
days for 52 weeks, resulting in 63-71% depletion of naïve, activated, and plasmacytoid 
CD20+ B cells. In contrast, peripheral blood plasma cells were not reduced overall. A 
long-term open label extension of the study confirmed that belimumab preferentially 
reduced the naïve and transitional B cell compartments, suggesting that newly formed B 
cells are more dependent on BAFF than memory B cells and plasma cells [90].  
Belimumab was evaluated for efficacy in seropositive active SLE in two phase 3 trials 
[91, 92]. Both trials met their primary endpoint, which was the rate of response at week 


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52. In BLISS-52, belimumab was administered on a background of standard of care 
immunosuppression [91]. Patients with lupus nephritis were included in the trial, but only 
11.9% had renal BILAG scores of A or B at baseline. Patients with severe active lupus 
nephritis were excluded. A significantly greater number of responses were observed at 
week 52 in the belimumab 10 mg/ml (58%) and the belimumab 1 mg/ml (51%) groups 
compared to placebo (44%). The rate of severe flares was significantly reduced in the 10 
mg/ml belimumab group, prednisone usage was significantly reduced, and a number of 
other secondary efficacy endpoints were met. Adverse events and serious adverse events 
were similar in the belimumab and placebo groups. 
The study design of BLISS-76 was similar to BLISS-52. The primary endpoint was met 
at 52 weeks, with 43.2% responding in the belimumab 10 mg/ml group, significantly 
more than 33.5% in the placebo group. [92]. Multivariate analysis of the pooled results 
from BLISS-52 and BLISS-76 identified several baseline disease characteristics 
associated with an increased response to belimumab [93]. These include SELENA-
SLEDAI score >10, anti-dsDNA positivity, low complement levels, and steroid usage at 
baseline. Post hoc analysis of pooled results from the two BLISS trials showed that 
belimumab improved overall disease activity in most musculoskeletal and 
mucocutaneous organ domains, and resulted in less worsening in hematological, 
immunological, and renal domains [94]. 
1.4 
SUMMARY OF KNOWN AND POTENTIAL RISKS AND BENEFITS 
FOR HUMAN PARTICIPANTS 
1.4.1 Risks Associated with Rituximab 
Rituximab is a chimeric monoclonal cytolytic antibody directed against CD-20, and has 
been associated with a number of adverse reactions and toxicities, both immune-mediated 
and other. Nevertheless, the safety profile of rituximab is sufficiently favorable to allow 
approval for use 1) in combination with methotrexate in moderately to severely active 
rheumatoid arthritis, 2) in combination with glucocorticoids in ANCA-associated 
vasculitis, and 3) in non-Hodgkin lymphoma and chronic lymphocytic leukemia. In 
addition, rituximab has been explored as an investigational study medication in numerous 
immune-mediated diseases, including SLE, and is frequently used “off-label” in immune-
mediated conditions for which there is no adequate FDA-approved therapy, for example 
neuromyelitis optica [95]. 
The prescribing information for rituximab carries a “black box” warning for fatal infusion 
reactions, hepatitis B virus reactivation, severe mucocutaneous reactions, and progressive 
multifocal leukoencephalopathy (PML) 
http://www.gene.com/download/pdf/rituxan_prescribing.pdf   
Common adverse reactions are infections, nausea, diarrhea, headache, muscle spasms, 
anemia, and peripheral edema. 


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1.4.1.1 Infusion Reactions with Rituximab 
Rituximab can cause severe infusion reactions, including fatal reactions, typically during 
the first infusion, with an onset of 30-120 minutes. Patients must be premedicated with 
acetaminophen and antihistamine and, in some cases, 100 mg Solumedrol. Reactions 
include urticaria, angioedema, hypotension, hypoxia, bronchospasm, pulmonary 
infiltrates, acute respiratory distress syndrome, myocardial infarction, ventricular 
fibrillation, cardiogenic shock, anaphylactoid events, or death. Because of the possibility 
of infusion reactions, rituximab must be administered in a monitored setting with access 
to resuscitative drugs, monitoring devices, and cardiopulmonary resuscitation (CPR) 
equipment. 
1.4.1.2 Infections Associated with Rituximab 
Consistent with its B-cell depleting properties, rituximab has been associated with a 
number of infections, the most serious of which is progressive multifocal 
leukoencephalophathy (PML). PML is a rare, debilitating, frequently fatal, opportunistic 
central nervous system infection caused by the John Cunningham (JC) virus. Patients 
typically have a history of concurrent or past chemotherapy or immunosuppressive 
therapy. Most cases of PML were diagnosed within 12 months of the last infusion of 
rituximab. A recent study estimated the risk of PML in rituximab-treated patients with 
rheumatoid arthritis at approximately 5 per 100,000 exposed patients, or extremely rare 
[96]. PML has occurred rarely in SLE patients treated with rituximab, and also in SLE 
patients who have not been treated with rituximab [96, 97], so it is unclear whether 
rituximab confers an increased risk of PML in this population [54]. The most common 
signs and symptoms of PML include visual disturbances, ocular movements, ataxia, and 
mental status changes such as disorientation or confusion. Clinical signs and symptoms 
of PML and SLE can be similar; therefore participants will be carefully monitored for 
this and other infectious complications.  
Other serious bacterial, fungal, and new or reactivated viral infections can occur during 
or subsequent to rituximab therapy. Reactivated hepatitis B virus can result in fulminant 
hepatitis, hepatic failure, and death, and participants with evidence of hepatitis B virus 
will be excluded from the study. Other new or reactivated viral infections include 
cytomegalovirus, herpes simplex virus, parvovirus B19, varicella zoster virus, West Nile 
virus, and hepatitis C. 
Neutropenia events, including severe and persistent late onset neutropenia have been 
reported [98]. In a recent study, late onset neutropenia was observed at a rate of 0.6/100 
patient-years in rheumatoid arthritis and 1.5/100 patient-years in other autoimmune 
disease following rituximab treatment [99]. Although these events are uncommon and 
usually mild, some have been associated with fatal infections. 


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1.4.1.3 Cardiovascular Symptoms, Severe Mucocutaneous Reactions, Tumor 
Lysis Syndrome, Renal Toxicity, Bowel Perforation, and Bone Marrow 
Suppression 
Patients with preexisting cardiac conditions, including arrhythmias and angina, have had 
recurrences of these events during rituximab therapy. Severe mucocutaneous reactions, 
some having a fatal outcome, have been observed in patients treated with rituximab. 
Though not applicable in this trial, patients with hematologic malignancy have 
experienced tumor lysis syndrome, with severe renal toxicity that in some cases led to 
death. Abdominal pain, bowel obstruction, and perforation have also been reported. 
Because rituximab targets all CD20-positive B lymphocytes, complete blood counts 
(CBC) should be obtained from participants at regular intervals during rituximab therapy 
and more frequently from participants who develop cytopenias. The duration of 
cytopenias caused by rituximab can extend well beyond the treatment period. 
1.4.1.4 Immunization in the Setting of Rituximab 
Live viral vaccine administration following rituximab therapy has not been studied for 
safety and is not recommended. It is recommended that non-live vaccines be 
administered at least 4 weeks prior to rituximab. Rituximab was found to interfere with 
the development of an immune response to pneumococcal and influenza vaccines in RA 
patients [100, 101], and lymphoma patients failed to develop a protective immune 
response to influenza vaccination [102]. 
1.4.2 Risks Associated with Belimumab 
Belimumab, a monoclonal antibody that targets BAFF, has a generally favorable toxicity 
profile. It has been recently approved for active, autoantibody-positive SLE, to be used in 
combination with standard immunosuppression. It has not been approved for active lupus 
nephritis, or severe active central nervous system lupus. It has not been studied in 
combination with other biologics or with CTX. Long term toxicity of belimumab is not 
fully known. http://www.hgsi.com/images/Benlysta/pdf/benlysta_pi.pdf.  
Common adverse reactions reported in the prescribing information include nausea, 
diarrhea, pyrexia, nasopharyngitis, bronchitis, insomnia, pain in extremity, depression, 
migraine, and pharyngitis. 
1.4.2.1 Infections Associated with Belimumab 
In clinical trials, the overall incidence of infections with belimumab was 71%, compared 
to 67% of patients treated with placebo. Serious infections, including pneumonia, urinary 
tract infection, cellulitis, and bronchitis occurred in 6% of patients treated with 
belimumab and 5.2% of patients treated with placebo, while infections resulting in death 
occurred in 0.3% of belimumab patients versus 0.1% of placebo patients. 
PML resulting in neurological deficits, including fatal cases, has been reported in SLE 
patients receiving immunosuppressant pharmacotherapy, including belimumab. A 
diagnosis of PML should be considered in any participant presenting with new-onset or 
deteriorating neurological signs and symptoms. The participant will be referred to a 


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neurologist or other appropriate specialist for evaluation. If PML is confirmed, study 
agent will be discontinued and consideration should be given to stopping 
immunosuppression. 
1.4.2.2 Infusion Reactions and Hypersensitivity Reactions Associate with 
Belimumab 
In clinical trials, infusion reactions and hypersensitivity reactions were reported. Infusion 
reactions occurred more frequently on the first two infusion days and tended to decrease 
with subsequent infusions. Delay in the onset of hypersensitivity reactions has been 
observed, as well as recurrence of clinically significant reactions after initial resolution of 
symptoms. Therefore, participants in this study will be monitored and made aware of the 
potential risks. It was not possible to distinguish between hypersensitivity and infusion 
reactions in all cases due to overlap of signs and symptoms. Anaphylaxis was observed in 
0.6% (9/1458) of participants receiving belimumab in the trials, and 0.4% (3/675) of 
participants receiving placebo. 
1.4.2.3 Depression and Mortality Associated with Belimumab 
There were more deaths in belimumab treated patients (0.75%) than placebo treated 
patients (0.44%) in three clinical trials with belimumab. Causes of death included 
infection, cardiovascular disease, and suicide, with no predominate cause. 
In the trials, psychiatric events were reported more frequently with belimumab (16%) 
than with placebo (12%). Most of these events were depression-related, insomnia, and 
anxiety, and they usually were observed in participants with a history of psychiatric 
conditions. Two suicides occurred in participants treated with belimumab. For this 
reason, participants in this study will be instructed to contact the investigator for new or 
worsening depression or suicidal thoughts. 
1.4.3 Risks Associated with Cyclophosphamide  
CTX is an alkylating agent indicated for the treatment of a large number of malignancies, 
including lymphomas, multiple myeloma, leukemia, and breast carcinoma. It is also 
indicated in selected cases of pediatric minimal change nephrotic syndrome. CTX is 
widely used, either alone or in combination with other immunosuppressive agents, in a 
variety of autoimmune conditions including lupus nephritis, for which adequate approved 
therapy does not exist or disease has proven refractory.  
CTX is associated with a number of serious adverse events and toxicities, including 
suppression of the immune system, infections, hemorrhagic cystitis, secondary 
malignancies, fetal harm, infertility, cardiac toxicity, interstitial pneumonitis, 
anaphylactic reactions, and death. Permanent ovarian failure occurs in over 50% of 
women after one year's exposure and is age related; male infertility has been less well 
studied. According to the current package insert, other common adverse events include 
nausea and vomiting, abdominal discomfort or pain, diarrhea, skin rash, alopecia, 
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1.4.4 Risks Associated with Corticosteroids 
Side effects of Solumedrol include convulsions, headache, vertigo, mood swings, 
psychosis, congestive heart failure, hypertension, salt and water retention, increased 
potassium excretion, Cushing syndrome, menstrual irregularities, hyperglycemia, GI 
irritation, peptic ulcer, weight gain. Dermatologic effects may include thin skin, 
petechiae, ecchymosis, facial erythema, poor wound healing, hirsutism and urticaria. 
Muscle weakness, loss of muscle mass and osteoporosis may also occur. Ophthalmologic 
complications may include increased intraocular pressure, glaucoma, exophthalmos, and 
cataracts. Other complications may include immunosuppression and increased 
susceptibility to infection.  
For further information about the risks associated with Solumedrol, please refer to the 
Solu-Medrol® package insert at the following website: 
http://labeling.pfizer.com/ShowLabeling.aspx?id=648 
The major short-term adverse effects of prednisone are salt and water retention, 
hypertension, hyperglycemia, central nervous system stimulation, peptic ulceration, and 
immunosuppression. While such effects are reversible, the additional adverse effects of 
prolonged prednisone use include osteoporosis, subcapsular cataracts, skin fragility, 
myopathy, Cushingoid facies, hirsutism, alopecia, fat redistribution, and striae. 
1.4.5 Risks of Sequential Therapy with Rituximab and Belimumab 
There is no prior experience with the use of rituximab and belimumab in the same 
patient. Thus, this trial constitutes the first effort to examine the rituximab and 
belimumab combination in a small number of closely monitored participants. As 
discussed in section 1.2.2, there is a strong biologic rationale for examining this 
approach. However, there is also a risk that two anti-B cell therapies may cause more 
profound and prolonged B cell depletion than either agent alone.  
To date, the best evidence that we have to assess this risk comes from the profound and 
prolonged B cell depletion that occurs in patients treated with repeated cycles of 
rituximab. Extensive experience in humans treated with repeated cycles of rituximab, 
including people with SLE, indicates that the infection risk is low [60]. Moreover, in 
SLE, the patients with the most profound and prolonged B cell depletion have tended to 
do best [52, 54]. These data are reassuring, but they may not accurately predict the 
consequences of combining rituximab and belimumab. In addition, some of the 
participants will have been exposed to immunosuppressives such as MMF, azathioprine, 
and corticosteroids prior to initiation of B cell depleting therapy in this trial.  
Therefore, we are taking the following precautions: (i) limiting the number of participants 
in each group to 20 in order to get a foundation of safety data before proceeding to a 
larger efficacy trial; (ii) initiating rituximab first, and then adding belimumab four weeks 
after participants have discontinued all prior immunosuppressive therapy, to minimize 
overlap effects and provide a washout period for prior immunosuppressive agents; (iii) 


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providing for safety follow-up of B-cell depleted participants throughout the course of the 
trial; and (iv) incorporating stopping rules and pre-planned safety analyses. 
There is also a risk that prolonged hypogammaglobulinemia could occur when B cell 
depletion therapy with rituximab is followed by multiple doses of belimumab. 
Belimumab has been shown to reduce immunoglobulin levels over a long treatment 
period, although immunoglobulin levels in the majority of subjects remained in the 
normal range [90, 103]. Rituximab treatment can cause hypogammaglobulinemia, but 
this is not generally associated with an increased risk of infection [52, 104]. Infections 
associated with hypogammaglobulinemia in the setting of treatment with rituximab and 
cyclophosphamide for ANCA-associated vasculitis were reported in one study [64], but 
no association was observed in another [105]. A recent phase 2/3 trial with atacicept in 
lupus nephritis was halted after only six participants were enrolled, when severe 
infections occurred in the setting of hypogammaglobulinemia, even though a correlation 
between IgG level and infection could not be established with such a small sample [106]. 
In contrast, hypogammaglobulinemia was not associated with an increased risk of 
infections when rituximab and atacicept were administered sequentially in rheumatoid 
arthritis [62].  
A recent study of rituximab-associated hypogammaglobulinemia in multi-system 
autoimmune disease showed that hypogammaglobulinemia occurred in 56% of 243 
subjects treated with rituximab; however, the nadir IgG level was not sustained in half of 
those with moderate to severe hypogammaglobulinemia [107]. Moreover, during a mean 
of 42 months of follow-up, IgG replacement was undertaken in only a small number of 
subjects (4.2%) due to recurrent infection [107, 108]. In lupus nephritis, 
hypogammaglobulinemia has been shown to correlate inversely with proteinuria [109, 
110]. In these studies, hypogammaglobulinemia was not associated with an increased risk 
of infection, and IgG levels increased in parallel with improvement in proteinuria 
following treatment. Thus, in lupus nephritis, hypogammaglobulinemia present at 
baseline is expected to improve as proteinuria resolves.  Hypogammaglobulinemia 
present at baseline was associated with nephrotic range proteinuria and recurrent lupus 
nephritis [111].   
Persistent trough levels of immunoglobulin G (IgG) < 400 mg/dL in patients with 
common variable immunodeficiency and X-linked agammaglobulinemia have been 
associated with increased risk of infection, pneumonia in particular [112]. Sustained very 
low levels of IgG < 100 mg/dL are associated with the highest risk of infection, while 
transient or less severe hypogammaglobulinemia is tolerated in most subjects [61].  Since 
it is possible that combined B cell therapy with rituximab and belimumab could interfere 
with IgG recovery following treatment of lupus nephritis, IgG levels will be monitored 
throughout the treatment phase of the study and hypogammaglobulinemia with IgG < 150 
mg/dL will trigger suspension of belimumab administration. In addition, belimumab will 
be suspended for Grade 3 or greater infectious adverse events in the setting of IgG < 300 
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1.4.6 Risks Associated with Modified Maintenance Immunosuppression 
Patients with lupus nephritis usually receive some form of maintenance therapy to reduce 
the risk of flare after achieving disease response with induction [4, 113]. The current trial 
proposes that participants, who receive rituximab and CTX, or rituximab and CTX 
followed by belimumab, will not receive maintenance immunosuppression except 
corticosteroids. These participants could be at an increased risk for flare compared with 
patients who receive induction therapy with CTX followed by maintenance 
immunosuppression with SOC azathioprine. Renal flare is a risk factor for developing 
end-stage renal disease.  
This risk will be mitigated by including relatively few participants in each experimental 
group and by closely following them for evidence of flare. Participants who flare will be 
discontinued from the study and treated according to standard practice. Moreover, case 
series with rituximab and CTX have shown that patients receiving this regimen generally 
do well without maintenance immunosuppression [48-50]. In a recent observational study 
of rituximab and cyclophosphamide in lupus nephritis, participants did equally well 
whether or not they received ongoing maintenance therapy [55]. A renal response was 
observed in 22/25 participants by 12 months. Four renal flares occurred in the responders 
at 10, 17, 60, and 64 months. It is even possible that exposure to rituximab and CTX, or 
rituximab and CTX followed by belimumab, as proposed in the current trial, may reduce 
later risk of flare. Addressing this question in a prospective randomized fashion is one of 
the aims of the current trial. 
1.4.7 Induction of Tolerance and Other Potential Benefits 
As discussed in section 1.1, there is no FDA approved agent for the treatment of lupus 
nephritis. Current SOC is considered induction of response with MMF or CTX plus 
corticosteroids, but complete response rates are unacceptably low with these regimens 
[10-12]. Moreover, ongoing immunosuppression is required. The combination of 
rituximab and CTX is being used as an alternative to SOC in contemporary management 
of refractory lupus nephritis [4], and case series suggest this combination is beneficial 
[48-50, 52]. 
Therefore, participants may have a benefit in terms of disease response to combination 
treatment with rituximab and CTX. Moreover, participants who are treated with 
belimumab following rituximab and CTX may experience a long-lasting disease 
remission, since belimumab is expected to preferentially limit the expansion of 
autoreactive pathogenic B cells during B cell reconstitution following depletion with 
rituximab. The participants might also benefit from not being exposed to maintenance 
immunosuppressive therapy. 
2. 
OBJECTIVES 
2.1 
PRIMARY OBJECTIVE 
The primary objective of the study is to assess the safety of belimumab administration 
following treatment with rituximab and CTX, in terms of infectious adverse events. 


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2.2 
SECONDARY OBJECTIVES 
 
The combination of rituximab and CTX, with and without belimumab, will be 
evaluated for safety, in terms of B cell reconstitution, hypogammaglobulinemia, and 
all adverse events.  
 
Second, the efficacy of rituximab and CTX, with and without belimumab, will also 
be evaluated.  
 
Tolerance induction, as measured by a sustained clinical benefit without ongoing 
immunosuppression, will be assessed following discontinuation of study medications. 
2.3 
EXPLORATORY OBJECTIVES   
 
Determine whether inhibition of BAFF by belimumab will affect the level of B cell 
autoreactivity during reconstitution of the B cell compartment following treatment 
with rituximab and CTX. 
 
B cell, T cell, monocyte, and dendritic cell compartments will be assessed to 
determine the changes that these cells undergo during B cell depletion and 
subsequent reconstitution in the presence or absence of BAFF inhibition.  
 
Changes in the B cell, T cell, and dendritic cell compartments will be correlated with 
clinical measures of disease activity. 
3. 
STUDY DESIGN 
3.1 
DESCRIPTION 
This trial will be conducted as a prospective randomized phase 2 open label multicenter 
study in individuals with active lupus nephritis age 18 and older. There will be two 
treatment arms with 1:1 randomization of a total of 40 participants. 
During the treatment phase, all participants will receive infusions of Solumedrol 100mg, 
rituximab 1000mg, and CTX 750mg intravenously (IV) at week 0 and week 2. 
Prednisone 40 mg per day will be administered with a guided steroid taper to 10mg per 
day by week 12 (see section 5).  
Participants will be randomized at week 4 to either the Rituximab/Cyclophosphamide 
(RC) Group or the Rituximab/Cyclophosphamide/Belimumab (RCB) Group. 
The RC Group will be maintained on prednisone. The RCB Group will receive IV 
belimumab 10mg/kg at weeks 4, 6, 8, and then every 4 weeks through week 48 in 
addition to prednisone.  
During the tolerance assessment phase, intravenous study medication will be 
discontinued after week 48, and all participants will be maintained on prednisone through 
week 96 of the study (see section 5). 
 


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Participants (age > 18 years) with active lupus nephritis
Week 0 and Week 2:
 
Solumedrol (100 mg) IV
 
Rituximab (1000 mg) IV
 
Cyclophosphamide (750 mg) IV
 
Prednisone (40 mg/day; taper to 10 mg/day by week 12)
Randomization
Week 4
RC Group
 
Prednisone taper to 10 mg/day by week 12
 
Continue prednisone 10 mg/day to week 96
RCB Group
 
Belimumab (10 mg/kg IV) at weeks 4, 6, 8, 
and every 4 weeks to week 48
 
Prednisone taper to 10 mg/day by week 12
 
Continue prednisone 10 mg/day to week 96 
 
Figure 1 Study Schema 
 
3.2 
STUDY DURATION 
Total study duration will be 200 weeks. The enrollment period for this study will be 104 
weeks. Study participation period will be 96 weeks, which includes a treatment phase of 
48 weeks and a tolerance assessment phase of 48 weeks. 
3.3 
STUDY ENDPOINTS 
3.3.1 Primary Endpoint 
The primary endpoint is the proportion of participants who experience at least one Grade 
3 or higher infectious adverse event at or prior to week 48. 
3.3.2 Secondary Endpoints 
1. Proportion of participants who experience at least one Grade 3 or higher infectious 
adverse event at or prior to week 24, and at or prior to week 96. 
2. Proportion of participants with B cell reconstitution at week 24, 48, and 96, defined 
as the participant’s baseline B cell count, or the lower limit of normal, whichever is 
lower. 
3. Proportion of participants with Grade 4 hypogammaglobulinemia at or before week 
24, 48, and 96. 


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4. Proportion of participants with a complete response at week 24. Complete response is 
defined as meeting all of the following criteria: 
 
Urine protein-to-creatinine ratio (UPCR) < 0.5, based on a 24-hour collection 
 
Estimated glomerular filtration rate (eGFR) ≥120 ml/min/1.73m2 calculated by 
the CKD-EPI formula [114] or, if <120 ml/min/1.73m2, then >80% of eGFR at 
entry. 
 
Prednisone dose tapered to 10 mg/day, or as specified in section 5.5.2. 
5. Proportion of participants with an overall response (complete or partial response) at 
week 24. A partial response is defined as meeting all of the following criteria: 
 
> 50% improvement in the UPCR from study entry, based on a 24-hour 
collection 
 
Estimated glomerular filtration rate (eGFR) ≥120 ml/min/1.73m2 calculated by 
the CKD-EPI formula [114] or, if < 120 ml/min/1.73m2, then >80% of eGFR at 
entry. 
 
Prednisone dose tapered to 10 mg/day, or as specified in section 5.5.2. 
6. Proportion of participants with complete response at week 48. 
7. Proportion of participants with an overall response (complete or partial response) at 
week 48. 
8. Proportion of participants with complete response at week 96 (cumulative complete 
response). 
9. Proportion of participants with sustained complete response at week 96 (representing 
“clinical tolerance”). Sustained complete response is defined as a complete response 
measured at 48 and 96 weeks. 
10. Proportion of participants with an overall response (complete or partial response) at 
week 96. 
11. Proportion of participants with treatment failure at or before week 24, 48, and 96, as 
defined by withdrawal from the protocol due to worsening nephritis, infection, or 
study medication toxicity  
12. Frequency of non-renal flares at or before week 24, 48, and 96, defined by the British 
Isles Lupus Assessment Group (BILAG) criteria [115]. 
13. Anti-dsDNA antibodies and C3, C4 levels at week 24, 48, and 96 
14. Frequency of the following specific AEs: 
 
Any event leading to death. 


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 
Grade 2 or greater leukopenia or thrombocytopenia. 
 
Premature ovarian failure.  
 
Malignancy. 
 
Venous thromboembolic event (deep venous thrombosis or pulmonary 
embolism). 
 
Disease- or study medication-related event leading to hospitalization. 
 
Infusion reactions (within 24 hours of infusion) that result in the cessation of 
further infusions (including cytokine-release allergic reaction). 
3.3.3 Study Population 
Adult female and male participants with active lupus nephritis will be recruited from a 
collaborative group of sites in the United States. Participants who meet eligibility criteria 
will be enrolled without regard to age, gender, or race. 
3.3.4 Definition of Renal and Non-Renal Flare 
3.3.4.1 Renal Flare 
Two successive evaluations at least one week apart must be performed before a 
determination is made based on any of the following definitions: 
 
 
For participants who attain a complete response at week 12 or anytime thereafter, 
either of the following: 
1. UPCR > 1 based on a 24-hour collection. 
2. new hematuria defined as  > 8 RBC/hpf and  > the level of hematuria observed at 
complete response, in the absence of menses and infection, and accompanied by 
either an 800 mg increase of urine protein or new RBC casts. 
 
 
For all others, any one of the three following criteria which occur after week 6: 
1. Increasing serum creatinine and persistent proteinuria, defined as 
a) serum creatinine above the upper limit of normal range, and 
b) serum creatinine at least 25% higher than the value at visit -1 or visit 0, 
whichever is higher, and 
c) UPCR based on a 24-hour collection which is at least 75% of the value at 
visit -1. 
 
2. Worsening proteinuria, defined as: 
a) UPCR > 1 based on a 24-hour collection, and 
b) doubling of the UPCR compared with the lowest previous value. 
The lowest previous value must be based on a 24-hour urine collection. The 
first evaluation showing a doubling may be detected by a spot or 24-hour 
urine collection. The second evaluation confirming the doubling must be 
based on a 24-hour urine collection.  
 


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3. New hematuria defined as >8 RBC/hpf and > the lowest prior level of hematuria, 
in the absence of menses and infection, and accompanied by either an 800 mg 
increase of urine protein or new RBC casts. 
3.3.4.2 Non-Renal Flare 
Using the British Isles Lupus Assessment Group (BILAG)-2004 guidelines [115], a non-
renal flare is any new A finding in a non-renal organ system. BILAG “A finding” 
represents a significant increase in, or a new manifestation of, disease activity.  
3.4 
RATIONALE FOR SELECTION OF ROUTE, DOSE, AND REGIMEN 
The rituximab and CTX regimen for the RC and the RCB Groups was selected based on the 
suggested dosage and administration for rituximab in rheumatoid arthritis outlined in the 
package insert http://www.gene.com/download/pdf/rituxan_prescribing.pdf, on published 
clinical studies with rituximab and CTX in lupus nephritis [50, 52], and on current clinical 
practice at UCSF. In the RCB Group, this same regimen of rituximab and CTX is followed 
by belimumab, according to the recommended dose and frequency described for SLE in the 
package insert http://us.gsk.com/products/assets/us_benlysta.pdf. Belimumab administration 
will begin four weeks after initiation of rituximab and cyclophosphamide, at a time when B 
cell depletion is expected to be nearly complete, and B cell reconstitution is expected to 
begin.  
3.5 
PREMATURE TERMINATION OR SUSPENSION OF THE TRIAL 
3.5.1 Ongoing Review 
The progress of the study will be monitored by the NIAID Data and Safety Monitoring 
Board (NIAID DSMB). The NIAID autoimmune DSMB will be chartered to review 
safety data and to make recommendations regarding continuation, termination, or 
modification of the study. Based on a 104-week recruitment period and an additional 
study period of at least 96 weeks, the DSMB will formally review the safety data 
approximately 6 months after study enrollment begins. Following this initial review, the 
DSMB will subsequently review the safety data at least yearly. The discontinuation of 
study treatment will also be periodically reported to the DSMB. 
A safety analysis of grade 3 or greater infection will take place when 10 participants have 
been followed for 24 weeks. An additional analysis will take place when a total of 20 
participants have been followed for 24 weeks. 
In addition, safety data will be reviewed by the DSMB when an event occurs that is of 
sufficient concern to the NIAID medical monitor or protocol co-chairs to warrant review, 
or when an event occurs that could contribute to a stopping rule listed in section 3.5.2. 
The DSMB will also review the results and conclusions of the analyses described in 
section 3.5.2. Findings will be reported to IRBs and health authorities. 


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3.5.2 Stopping Rules 
3.5.2.1 Study-related Adverse Events  
If any of the following events occur, the DSMB chair will be notified and a review of 
safety data will be performed to determine if enrollment in the study should be stopped 
and/or administration of investigational study medication should be halted: 
1. Any death that is at least possibly related to use of the investigational study 
medication.  
2. Two or more of the same Preferred Term grade 4 AE, other than leukopenia, 
lymphopenia, neutropenia, or hypogammaglobulinemia involving different 
participants that are at least possibly related to use of the investigational study 
medication. 
3. Two or more life-threatening infusion reactions during infusion of study medication 
or within the observation period after study medication that lead to permanent 
discontinuation of infusion in the first 20 participants. 
4. One case of PML. 
5. Two or more Grade 4 hypogammaglobulinemia events (section 8.4.1) involving 
different participants. 
3.5.2.2 Incidence of Renal Flares after Week 24 
If the renal flare rate exceeds the acceptable value in either the RC group or the RCB 
group, the DSMB chair will be notified and a review of safety data will be performed to 
determine if enrollment in the study should be stopped and/or administration of 
investigational study medication should be halted.  
Both experimental groups will undergo B cell depletion with rituximab and CTX, and 
then will be maintained on prednisone, as described in section 3.1. Participants in the RC 
group may be at risk for renal flare upon subsequent B cell reconstitution, which is 
expected to occur after 24 weeks for most participants [50, 53]. Participants in the RCB 
group are expected to be at lower risk for flare upon B cell reconstitution, according to 
the hypothesis that belimumab will inhibit the re-emergence of autoreactive cells in the 
reconstituting B cell compartment. Nevertheless, it is important to assess the rate of renal 
flare in both experimental groups, compared to the rate of renal flare that would be 
expected with standard of care therapy. Renal flare is defined in section 3.3.4.1.  
We assume that an acceptable rate of renal flare is 0.20 after week 24, and 0.25 after 
week 48. This is a somewhat higher rate of renal flare than observed in previous lupus 
nephritis experience in patients receiving standard of care [116]. This rate is chosen, 
however, based on the assumption that there is a potential benefit to freedom from 
maintenance therapy, and most patients who have a flare respond to reinstitution of 
treatment [14]. Moreover, since new onset lupus nephritis patients have been excluded, 
the expected flare rate for this study may be higher than observed in previous studies that 
included new onset lupus nephritis among the participants [116]. 


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The renal flare rate is the number of participants with a renal flare observed after week 24 
of the study, divided by the total number of evaluable participants at week 24 who have 
not been discontinued from the protocol at or prior to week 24 (discontinuation criteria 
are specified in section 5.6). The renal flare rate will be calculated separately for each 
experimental group. Rate of renal flare will be monitored according to the following 
guideline:    
Evidence that the true renal flare rate exceeds the acceptable value will be assessed by 
calculating a one-sided 80% confidence interval around the renal flare rate after 5 
participants have completed week 24 of the study. The confidence interval will be 
calculated using the Clopper-Pearson (exact) method for binomial proportions. This will 
be done each time a renal flare occurs. If the lower bound of the 80% confidence interval 
is above the acceptable rate, this will be considered evidence that the renal flare rate is 
too high. Table 1 illustrates the threshold number of flares after week 24 and continuing 
through week 48 per a given number of evaluable participants that would lead to DSMB 
review of the safety data. Table 2 illustrates the threshold number of flares after week 48 
per a given number of evaluable participants that would lead to DSMB review of the 
safety data.  


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Table 1 Qualifying thresholds for flare rate after week 24 and continuing through week 48 
Flares 
Participants 
Observed 
Rate 
80% One-Sided CI 
Bound 
3 
5 
0.60 
0.33 
3 
6 
0.50 
0.27 
3 
7 
0.43 
0.23 
4 
8 
0.50 
0.30 
4 
9 
0.44 
0.27 
4 
10 
0.40 
0.24 
4 
11 
0.36 
0.22 
5 
12 
0.42 
0.27 
5 
13 
0.38 
0.25 
5 
14 
0.36 
0.23 
5 
15 
0.33 
0.21 
6 
16 
0.38 
0.25 
6 
17 
0.35 
0.24 
6 
18 
0.33 
0.22 
6 
19 
0.32 
0.21 
6 
20 
0.30 
0.20 
 
Table 2 Qualifying thresholds for flare rate after week 48 
Flares 
Participants 
Observed 
Rate 
80% One-Sided CI Bound 
3 
5 
0.60 
0.33 
3 
6 
0.50 
0.27 
4 
7 
0.57 
0.35 
4 
8 
0.50 
0.30 
4 
9 
0.44 
0.27 
5 
10 
0.50 
0.33 
5 
11 
0.45 
0.30 


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Flares 
Participants 
Observed 
Rate 
80% One-Sided CI Bound 
5 
12 
0.42 
0.27 
6 
13 
0.46 
0.32 
6 
14 
0.43 
0.29 
6 
15 
0.40 
0.27 
6 
16 
0.38 
0.25 
7 
17 
0.41 
0.29 
7 
18 
0.39 
0.27 
7 
19 
0.37 
0.26 
8 
20 
0.40 
0.29 
4. 
ELIGIBILITY 
4.1 
INCLUSION CRITERIA 
1. Diagnosis of Systemic Lupus Erythematosus (SLE) by American College of 
Rheumatology (ACR) criteria or Systemic Lupus International Collaborating Clinics 
(SLICC) criteria. 
2. Positive antinuclear antibody (ANA) or positive anti-ds DNA test results at visit -1 or 
any time within 14 days before visit -1. 
3. Age 18 years or older. 
4. Active proliferative lupus nephritis, as defined by either of the following: 
a. Kidney biopsy documentation within the last 3 months of ISN/RPS proliferative 
nephritis:  Class III, Class IV, or Class V in combination with Class III or IV. 
b. Kidney biopsy documentation within the last 18 months of ISN/RPS proliferative 
nephritis:  Class III, Class IV, or Class V in combination with Class III or IV, 
associated with at least one of the following:  
i. 
Active urinary sediment as defined by any one of the following:  
a. >4 RBC/hpf in the absence of menses and infection; 
b. >5 WBC/hpf in the absence of infection; or  
c. cellular casts limited to RBC or WBC casts. 
ii. UPCR ≥ 3 based on a 24-hour collection at visit -1 or any time within 14 
days before visit -1. 
iii. Confirmed increase in UPCR compared to a prior UPCR determination 
within 3 months of study entry. An increase in proteinuria will be 
considered to be confirmed if present on 2 consecutive assessments, or if 
increase led to a change in treatment. Increase in UPCR is defined as: 
a. UPCR to > 1 if prior UPCR was ≤ 0.2; 
b. UPCR > 2 if prior UPCR was ≤ 1 but > 0.2; 


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c. UPCR > double the prior UPCR if prior UPCR was > 1. 
5. UPCR >1 based on a 24-hour collection at visit -1 or any time within 14 days before 
visit -1. 
6. Ability to provide informed consent. 
4.2 
EXCLUSION CRITERIA 
1. New onset lupus nephritis, defined as lupus nephritis for which the participant has 
not yet been treated with either mycophenolate mofetil or cyclophosphamide. 
2. Neutropenia (absolute neutrophil count <1500/mm3). 
3. Thrombocytopenia (platelets <50,000/mm3). 
4. Moderately severe anemia (Hgb <8 mg/dL). 
5. Positive QuantiFERON – TB Gold test results. PPD tuberculin test may be 
substituted for QuantiFERON – TB Gold test. 
6. Pulmonary fibrotic changes on chest radiograph consistent with prior healed 
tuberculosis. 
7. Active bacterial, viral, fungal, or opportunistic infections. 
8. Evidence of infection with human immunodeficiency virus (HIV), hepatitis B (as 
assessed by HBsAg and anti-HBc) or hepatitis C. 
9. Hospitalization for treatment of infections, or parenteral (IV or IM) antibacterials, 
antivirals, anti-fungals, or anti-parasitic agents within the past 60 days. 
10. Chronic infection that is currently being treated with suppressive antibiotic or 
antiviral therapy, including but not limited to tuberculosis, pneumocystis, 
cytomegalovirus, herpes simplex virus, herpes zoster, and atypical mycobacteria. 
11. History of significant infection or recurrent infection that, in the investigator’s 
opinion, places the participant at risk by participating in this study. 
12. Receipt of a live-attenuated vaccine within 3 months of study enrollment. 
13. End-stage renal disease (eGFR <20 mL/min/1.73m2) 
14. Concomitant malignancies or a history of malignancy, with the exception of 
adequately treated basal and squamous cell carcinoma of the skin, or carcinoma in 
situ of the cervix.  
15. History of transplantation. 
16. History of primary immunodeficiency. 
17. Pregnancy. 
18. Breastfeeding. 
19. Unwillingness to use an FDA-approved form of birth control (including but not 
limited to a diaphragm, an intrauterine device, progesterone implants or injections, 
oral contraceptives, the double-barrier method, or a condom). 
20. Use of cyclophosphamide within the past 6 months. 
21. Use of anti-TNF medication, other biologic medications, or experimental non-
biologic therapeutic agents within the past 90 days, or 5 half-lives prior to screening, 
whichever is greater. 
22. Intravenous immunoglobulin (IVIG), plasmapheresis, or leukopheresis within the 
past 90 days. 
23. Use of investigational biologic agent within the past 6 months. 


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24. Prior treatment with rituximab. 
25. Treatment with other biologic B cell therapy within the past 12 months.  
26. Liver function test (aspartate aminotransferase [AST], alanine aminotransferase 
[ALT], or alkaline phosphatase) results that are ≥2 times the upper limit of normal.  
27. Severe, progressive, or uncontrolled renal, hepatic, hematological, gastrointestinal, 
pulmonary, cardiac, or neurological disease, either related or unrelated to SLE, with 
the exception of active lupus nephritis (or, in the investigator’s opinion, any other 
concomitant medical condition that places the participant at risk by participating in 
this study). 
28. Comorbidities requiring corticosteroid therapy, including those which have required 
three or more courses of systemic corticosteroids within the previous 12 months. 
29. Current substance abuse or history of substance abuse within the past year. 
30. History of severe allergic or anaphylactic reactions to chimeric or fully human 
monoclonal antibodies. 
31. History of anaphylactic reaction to parenteral administration of contrast agents. 
32. Lack of peripheral venous access. 
33. History of severe depression or severe psychiatric condition. 
34. History of suicidal thoughts within the past 2 months or suicidal behavior within the 
past 6 months, or a significant suicide risk in the investigator’s opinion. 
35. Inability to comply with study and follow-up procedures. 
4.3 
PREMATURE TERMINATION OF A PARTICIPANT FROM THE 
STUDY 
Withdrawal of consent. Participants who withdraw consent will be asked to complete all 
the assessments listed for visit 18 in Appendix 1. 
Failure to return. Participants who do not return for visits and who do not respond to 
repeated attempts by the site staff to have them return will be considered lost to follow-
up.  
Participants who prematurely terminate from the study will be replaced if they withdraw 
prior to randomization, but will not be replaced if they withdraw after randomization.  
5. 
STUDY MEDICATIONS 
5.1 
INVESTIGATIONAL STUDY MEDICATION:  RITUXIMAB 
5.1.1 Formulation, Packaging, and Labeling 
Rituximab is a sterile, clear, colorless, preservative-free liquid concentrate for 
intravenous administration. Rituximab is supplied at a concentration of 10 mg/mL in 
either 100 mg/10 mL or 500 mg/50 mL single-use vials. The product is formulated in 
polysorbate 80 (0.7 mg/mL), sodium citrate dihydrate (7.35 mg/mL), sodium chloride (9 
mg/mL) and water for Injection. The pH is 6.5. The vials provided to the pharmacy will 
have study-specific investigational agent labels. 


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Rituximab will either be purchased or donated by the manufacturer for use in this trial. 
Rituximab will be distributed by a designated drug distributor under contract to NIAID.  
5.1.2 Preparation, Administration, and Dosage 
Rituximab will be administered as an intravenous infusion of 1000 mg at week 0 and 
week 2. Rituximab should never be administered as an IV push or bolus. Solumedrol and 
CTX will be administered on the same days as rituximab. The study medications will be 
administered in the following order:   
1. Diphenhydramine (or equivalent) and acetaminophen 60 minutes prior to rituximab 
(see section 5.1.2.2.2) 
2. Solumedrol 30 minutes prior to rituximab (see section 5.4) 
3. Rituximab 
4. CTX (see section 5.3) 
5.1.2.1 Preparation   
Rituximab will be prepared for administration according to the manufacturer’s 
instructions. Reconstituted rituximab is stable at 2C to 8C (36F to 46F) for 24 hours. 
Because rituximab solution does not contain a preservative, diluted solution should be 
stored refrigerated (2–8°C). http://www.gene.com/gene/products/information/pdf/rituxan-
prescribing.pdf.  
5.1.2.2 Administration 
5.1.2.2.1 
Monitoring 
Infusions will occur in a setting with access to ACLS certified personnel, resuscitative 
drugs, monitoring devices, and CPR equipment. Vital signs must be assessed prior to the 
infusion. During the infusions, vital signs will be assessed every 15 minutes for 1 hour 
and then every 30 minutes until the infusion is complete. The participant’s vital signs 
must be checked 1 hour after the completion of the infusion. Rituximab must not be 
administered as an intravenous push or bolus because hypersensitivity reactions may 
occur. After infusion, the IV line should remain in the participant for at least 1 hour to 
enable the administration of drugs, if necessary.  
5.1.2.2.2 
Premedication 
Diphenhydramine (50 mg, or equivalent dose of similar antihistamine) and 
acetaminophen (650 mg) will be given orally 1 hour (plus or minus 15 minutes) before 
each infusion of rituximab. Study medication Solumedrol 100 mg intravenously should 
be administered 30 minutes prior to rituximab (see section 5.4). Because transient 
hypotension may occur during rituximab infusion, no antihypertensive medications 
should be administered at least 12 hours before an infusion. Concomitant angiotensin 
converting enzyme inhibitor or angiotensin receptor blocker should be with-held on the 
days of rituximab infusion. 
5.1.2.2.3 
First Infusion at Visit 0 
The rituximab solution for infusion should be administered intravenously using infusion 
pumps at an initial rate of 50 mg/hour. Rituximab should not be mixed or diluted with 


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other drugs. If hypersensitivity or infusion-related events do not occur, escalate the 
infusion rate in 50 mg/hour increments every 30 minutes, to a maximum of 400 mg/hour. 
Rituximab infusion should be interrupted should severe infusion reactions occur. In most 
cases of mild to moderate reactions, the infusion can be resumed at a 50% rate reduction 
(e.g., from 100 mg/hour to 50 mg/hour) when all symptoms have completely improved 
and are no longer deemed a threat to the participant’s well-being. Institute medical 
management (e.g., corticosteroids, epinephrine, bronchodilators, or oxygen) for infusion 
reactions as needed. Rituximab infusion should be discontinued for severe and life-
threatening reactions. 
5.1.2.2.4 
Second Infusion at Visit 1 
If no reactions occur with the first infusion, the second rituximab infusion can be 
administered at an initial rate of 100 mg/hour and then increased by 100 mg/hour every 
30 minutes, to a maximum of 400 mg/hour as tolerated. Interrupt or slow the infusion for 
infusion reactions, and continue at one-half the previous rate upon improvement of 
symptoms. Rituximab infusion should be discontinued for severe and life-threatening 
reactions. 
5.1.3 Stability and Storage 
Rituximab vials are stable at 2°C to 8°C (36°F to 46°F) and have a proposed shelf life of 
30 months. Once reconstituted into IV bags, rituximab is chemically stable for up to 24 
hours at 2°C to 8°C (36° to 46°F). Rituximab vials should be protected from direct 
sunlight. 
5.1.4 Toxicity Management for Rituximab 
Suspend rituximab if any of the following occurs: 
 
An infection or other AE that the investigator judges to be significant. 
 
A grade 3 or greater AE that the investigator judges to be probably or definitely 
related to rituximab. 
 
A grade 3 or greater infusion reaction. 
5.2 
INVESTIGATIONAL STUDY MEDICATION:  BELIMUMAB 
5.2.1 Formulation, Packaging, and Labeling 
Belimumab is supplied as a sterile, white to off-white, preservative-free, lyophilized 
powder for intravenous infusion. Single-use vials of belimumab lyophilized powder for 
injection are supplied in 5 ml vials with 120 mg per vial and in 20 ml vials with 400 mg 
per vial. Upon reconstitution with Sterile Water for Injection, USP, according to the 
instructions in section 5.2.2.1, each single-use vial delivers 80 mg/mL belimumab in 0.16 
mg/mL citric acid, 0.4 mg/mL polysorbate 80, 2.7 mg/mL sodium citrate, and 80 mg/mL 
sucrose, with a pH of 6.5. 
Belimumab is a marketed drug and will be purchased for the study from commercial 
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5.2.2 Preparation, Administration, and Dosage 
Belimumab will be administered as an intravenous infusion at a dose of 10 mg/kg at 
weeks 4, 6, and 8 and then every 4 weeks through week 48 to the RCB group as 
described in section 3.1 
5.2.2.1 Reconstitution and Dilution of Belimumab 
Belimumab will be reconstituted by a healthcare professional according to the 
manufacturer’s package insert instructions: 
http://www.accessdata.fda.gov/drugsatfda_docs/label/2012/125370s016lbl.pdf 
5.2.2.2 Administration Instructions 
5.2.2.2.1 
Infusion 
The diluted solution of belimumab should be administered by intravenous infusion only, 
over a period of 1 hour. The infusion rate may be slowed or interrupted if the participant 
develops an infusion reaction. Belimumab should be administered by healthcare 
providers prepared to manage anaphylaxis. Belimumab should not be infused 
concomitantly in the same intravenous line with other agents. Belimumab infusion should 
be discontinued immediately for serious hypersensitivity reactions or for severe and life-
threatening reactions. 
5.2.2.2.2 
Monitoring 
Infusions will occur in a setting with access to ACLS certified personnel, resuscitative 
drugs, monitoring devices, and CPR equipment. Vital signs must be assessed prior to the 
infusion. During the infusions, vital signs will be assessed every 15 minutes. After 
infusion, the IV line should remain in the participant for at least 2 hours following the 
first two infusions of belimumab, and for at least 1 hour following subsequent infusions 
of belimumab, to enable the administration of drugs, if necessary. The participant’s vital 
signs must be checked 1 hour after completion of the infusion. 
5.2.3 Recommended Storage Conditions 
Store vials of belimumab refrigerated between 2o to 8º C (36º to 46º F). Vials should be 
protected from light and stored in the original carton until use. Do not freeze. Avoid 
exposure to heat. Do not use beyond the expiration date. 
The reconstituted solution of belimumab, if not used immediately, should be stored 
protected from direct sunlight and refrigerated at 2o to 8o C (36o to 46o F). Solutions of 
belimumab diluted in normal saline may be stored at 2o to 8o C (36o to 46o F) or room 
temperature. The total time from reconstitution of belimumab to completion of infusion 
should not exceed 8 hours. 
5.2.4 Toxicity Management for Belimumab 
5.2.4.1 Toxicity Management of Belimumab for Hypogammaglobulinemia 
Suspend belimumab if, at the previously scheduled or unscheduled visit, the IgG level is 
< 150 mg/dL. 


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Belimumab administration will be restarted at the next scheduled visit after IgG level is 
found to be ≥ 150 mg/dL.  
Suspend belimumab if the participant develops Grade 4 hypogammaglobulinemia 
(section 8.4.1). If the infection resolves, belimumab may be restarted at the next 
scheduled dose. 
 
5.2.4.2 Additional Toxicity Management for Belimumab 
Suspend belimumab administration if the participant develops an infection or other AE 
that the investigator judges to be significant. If the infection or AE resolves, belimumab 
may be restarted at the next scheduled dose.  
Discontinue belimumab if any of the following occurs: 
 
A grade 3 or greater AE other than infection or hypogammaglobulinemia that the 
investigator judges to be probably or definitely related to belimumab. 
 
A grade 3 or greater infusion reaction. 
 
A diagnosis of PML should be considered in any subject presenting with new-onset or 
deteriorating neurological signs and symptoms. The subject should be referred to a 
neurologist or other appropriate specialist for evaluation. If PML is confirmed, study 
medication should be discontinued and consideration should be given to stopping 
immunosuppression. 
 
If PML is suspected, this should be immediately reported to the NIAID Medical 
Monitor. The appropriateness of continuing study medication, while the case is being 
assessed, should be discussed. 
 
Participants will be assessed at each visit for new or worsening depression, and for 
suicidal thoughts or behavior. Participants will be instructed to contact the investigator if 
any of these occur between study visits. Belimumab may be suspended for this reason at 
the discretion of the investigator. 
5.3 
ADDITIONAL STUDY MEDICATIONS:  CYCLOPHOSPHAMIDE 
5.3.1 Dosage, Preparation, and Administration 
All participants will receive CTX at week 0 and week 2 at the doses described in section 
3.1. CTX will be administered on the same days as Solumedrol and rituximab, in the 
exact order described in section 5.1.2.  
Hematology results must be obtained before the second infusion of CTX (visit 1, study 
week 2). These results will be obtained within 7 days prior to the infusion. For additional 
information on the administration of CTX, as well as its handling and storage, please 
refer to the package insert for Cytoxan®, which can be found at this website: 


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http://www.accessdata.fda.gov/drugsatfda_docs/label/2013/012141s090,012142s112lbl.p
df 
5.3.2 Toxicity Management for Cyclophosphamide 
Toxicity related to cyclophosphamide will be managed according to the directives in 
Table 3. 
Table 3 Management of cyclophosphamide-related toxicity 
Toxicity 
Actiona 
Moderate Toxicities: 
 Marrow suppression (WBC < 3,000/mm3, 
Hgb  8 g/dl,  or platelets < 100,000/mm3) 
 Liver function test abnormality (AST or ALT 
>2 times ULN but  3 times ULN) 
 Other intolerable adverse effects that may be 
reversible 
Reduce CTX to 500 mg. 
Severe Toxicities: 
 Marrow suppression (neutrophils  < 
1,000/mm3, Hgb  6.5 g/dl, or platelets < 
75,000/mm3) 
 Liver function test abnormality (AST or ALT 
>3 times ULN) 
 Severe infection 
 Malignancy 
 Hemorrhagic cystitis (gross or  microscopic 
hematuria; cystoscopy shows bleeding, 
atrophy, pallor, telangiectasia, or contracture 
of the bladder mucosa) 
 Pneumonitis that cannot be attributed to 
causes other than cyclophosphamide 
Suspend administration of CTX. 
a Note: If clinical and laboratory abnormalities are related to lupus disease activity 
and treatment is not a contributing factor, the dose should not be modified. 
5.4 
ADDITIONAL STUDY MEDICATION:  SOLUMEDROL 
5.4.1 Dosage, Preparation, and Administration 
Solumedrol 100 mg will be administered intravenously at week 0 and week 2. 
http://labeling.pfizer.com/ShowLabeling.aspx?id=648 
Solumedrol will be administered on the same days as rituximab and CTX, and in the 
exact order described in section 5.1.2. 


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5.4.2 Recommended Storage Conditions 
Protect from light. Store unreconstituted product at controlled room temperature 20° to 
25°C (68° to 77°F). Store solution at controlled room temperature 20° to 25°C (68° to 
77°F). Use solution within 48 hours after mixing. 
5.5 
ADDITIONAL STUDY MEDICATION:  PREDNISONE 
5.5.1 Dosage for All Participants 
All participants will receive prednisone 40 mg/day for the first 2 weeks. Participants less 
than 40 kg may receive 1 mg/kg/day based on the principal investigator’s judgment. 
Prednisone will then be tapered until study week 12 to a dose of 10 mg/day. This dose will 
be continued until week 48 unless the participant has a prednisone-related toxicity that in 
the judgment of the principal investigator requires further reduction. However, the dose 
should not be tapered below 5 mg/day. Dose schedule will depend on the principal 
investigator preference with total dose either administered as once daily or twice daily (e.g., 
20 mg qd or 10 mg bid). Dose reductions will be made each study week as listed in Table 4. 
Participants weighing greater than 40 kg may receive 1 mg/kg per day (maximum 60 mg 
per day) for the first two weeks at the discretion of the principal investigator. Prednisone 
dose in these participants must be tapered to 30 mg per day by week 6, and the remainder 
of the prednisone taper will be followed according to Table 4. 
If a participant deviates from the prednisone tapering regimen, he or she will be instructed 
to return to the scheduled dose before the deviation occurred within 1 week, unless the 
participant refuses or the investigator determines it is not in the participant’s best interest. 
Table 4 Prednisone tapering schedule 
Study Week 
Reduced Dose 
(mg/day) 
Weeks 1-2 
40 
Week 3 
35 
Week 4 
35 
Week 5 
30 
Week 6 
30 
Week 7 
25 
Week 8 
20 
Week 9 
17.5 


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Study Week 
Reduced Dose 
(mg/day) 
Week 10 
15 
Week 11 
12.5 
Week 12 
10 
 
Between week 48 and week 96, prednisone may be further tapered. However, the rate of 
taper should not be greater than 1 mg every month, and the dose should not be tapered 
below 5 mg/day. 
5.5.2 Dose Modification for Participants with Non-Renal Flare 
Prednisone dosing and administration may be modified as follows: 
Prednisone may be increased once during the study for non-renal flares of SLE and once 
for conditions unrelated to SLE based on the principal investigator’s judgment. The dose 
may be increased for a period of 14 days at a dose up to double the current dose, not to 
exceed 40 mg/day. 
 
For participants with non-renal flares of SLE, the tapering regimen should then be 
resumed from the new dose level as prescribed. 
 
For participants with conditions unrelated to SLE, the prednisone taper may be done 
more quickly than specified in Table 2 based on clinical judgment. The determination 
that a condition is unrelated to SLE will be made by the principal investigator in 
consultation with the protocol chairs. 
5.5.3 Discontinuation of Prednisone for Participants with Non-Renal Flare 
Prednisone dosing and administration according to study specification should be 
discontinued if any the following occurs: 
 
Participant has a non-renal flare or other condition and needs additional steroid 
therapy that would be given at a higher dose than 40 mg, or given for a longer period 
than 14 days. 
 
Participant fails to resume steroid taper after the investigator initiates an increase. 
If prednisone dosing and administration according to study specification is discontinued, 
the procedures in section 5.6 should be followed. 
5.6 
DISCONTINUATION OF STUDY MEDICATION 
Study treatment, defined as the dosing and administration of study medication according 
to study specification, will be discontinued for an individual participant if any of the 
following occurs: 
 
A discontinuation criterion is met for prednisone (section 5.5.3). 


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 
The participant does not receive at least one full dose of rituximab. 
 
The participant does not receive at least one full dose of cyclophosphamide. 
 
The participant experiences a renal flare (see definition in section 3.3.4.1). 
 
A second occurrence of non-renal flare (see definition in section 3.3.4.2). 
 
At week 24, the participant demonstrates < 25% improvement in urine protein to 
creatinine ratio compared to the urine protein to creatinine ratio at visit -1, based on a 
24-hour urine collection. 
 
The investigator determines that it is in the participant’s best interest to discontinue 
treatment for any reason (including non-compliance). 
 
The participant requests that treatment be halted. 
 
The participant becomes pregnant. 
Further care will be provided according to the judgment and practice of the principal 
investigator. 
At this time the participant will complete all assessments listed for visit 18 in Appendix 
1. The participant will have one additional visit 30 days later, which will comprise all the 
assessments listed for visit U in Appendix 1. The participant will be asked to have 
additional visits at week 24, 36, 48, 72, and 96, if these visits have not already occurred, 
for safety follow up. 
If study treatment is discontinued, the NIAID medical monitor should be notified. 
Participants will be replaced if they discontinue the protocol prior to randomization, but 
will not be replaced if they discontinue after randomization. 
5.7 
CONCOMITANT MEDICATIONS 
5.7.1 Prophylactic Medications 
5.7.1.1 Required 
The following medications will be used during the treatment phase. 
All participants will receive Pneumocystis pneumonia prophylaxis through week 24 using 
one of the following approaches: 
 
Sulfamethoxazole-trimethoprim (SMX/TMP): 1 double-strength tablet PO Monday, 
Wednesday, and Friday. 
 
Dapsone (for those allergic to sulfa medications): 100 mg/day PO. 
 
Other appropriate Pneumocystis pneumonia prophylaxis.  
Pneumocystis pneumonia prophylaxis may be continued until week 48 at the discretion of 
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5.7.1.2 Allowed 
Measures to prevent and to treat osteoporosis are strongly encouraged during this trial. 
These measures may include any or all of the following: calcium carbonate or citrate 
(1500 mg/day), vitamin D (up to 2000 IU/day), and bisphosphonates.  
During treatment with CTX, anti-emetics may be administered, mesna may be used to 
prevent bladder toxicity, and leuprolide acetate may be used as prophylaxis against 
gonadal toxicity. 
At the discretion of the site investigator, participants may be treated with a cholesterol-
lowering agent such as a statin.  
Treatment with an antimalarial agent such as hydroxychloroquine is encouraged unless 
contraindicated. 
All participants not already on either an ACE inhibitor (ACEi) or an angiotensin receptor 
blocker (ARB) may be started on such an agent unless contraindicated. Doses should be 
adjusted in an attempt to achieve a targeted systolic blood pressure less than 130 mmHg. 
A combination of medications that may include an ACEi, ARB, calcium channel blocker, 
or beta-blocker may also be used if a single agent does not control systolic blood pressure 
adequately. 
5.7.2 Permitted Medications   
It is recommended that nonsteroidal anti-inflammatory drugs (NSAIDs) not be initiated 
during the trial due to the possible adverse effect on renal function. They may be used, 
however, if necessary for the control of symptoms.  
The use of NSAIDs or other prescription or over-the-counter medications used for control 
of symptoms will be recorded at each visit. Participants will be asked whether these are 
being used for lupus-related symptoms or for symptoms not related to lupus. 
Treatment of hypogammaglobulinemia in participants with infectious AEs is permitted at 
the discretion of the site investigator, in consultation with the protocol chair and the 
medical monitor. 
5.7.3 Prohibited Medications 
Participants may not use immunosuppressive agents except as specified by the protocol. 
Prohibited immunosuppressive agents include but are not limited to mycophenolate 
mofetil preparations and azathioprine. Participants are required to discontinue 
immunosuppressive agents before enrollment.  
The use of any investigational drug or treatment other than those specified in the protocol 
is prohibited during study participation. 
The use of live-attenuated vaccines is prohibited during treatment with study medications 
and for 12 weeks after treatment. 


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It is suggested that the participant refrain from using any herbal remedies without 
consulting the investigators. 
5.7.4 Contraception Use 
All female participants of childbearing age must use a medically acceptable form of 
contraception during both the treatment phase and the tolerance assessment  phase of the 
trial and must continue its use for 12 months after receiving their last dose of rituximab 
and 6 months after receiving their last dose of belimumab.  
http://www.fda.gov/ForConsumers/ByAudience/ForWomen/FreePublications/ucm313215.htm 
5.8 
DRUG ACCOUNTABILITY 
Under federal regulations (21CFR 312.62) an investigator is required to maintain 
adequate records of the disposition of the investigational product, including the date and 
quantity of drug that was received, the participants to whom drug was dispensed 
(participant by participant accounting), and an account of any drug accidentally or 
deliberately destroyed. 
Records for receipt, storage, use, and disposition of the study drug will be maintained by 
the study sites. A drug-dispensing log will be kept current for each participant and will 
contain the identification of each participant and the date and quantity of drug dispensed. 
All records regarding disposition of the investigational product will be available for 
inspection by the clinical trial monitor. 
5.9 
ASSESSMENT OF COMPLIANCE WITH STUDY MEDICATION 
Rituximab, CTX, belimumab, and Solumedrol will be administered intravenously by 
trained medical staff; compliance, therefore, will be monitored by the medical staff and 
documented on the electronic case report form (eCRF). Prednisone compliance will be 
monitored by patient self-report and documented on the eCRF. 
6. 
STUDY PROCEDURES 
6.1 
VISIT WINDOWS 
6.1.1 Scheduled Visits 
Appendix 1 presents the schedule of assessments for this trial. Visit 0 must occur within 
21 days of visit -1. All other scheduled study visits must occur within the time limits 
specified below: 
Visits 1 through 4: 
±2 days 
Visits 5 through 14:  
±7 days  
Visits 15 through 18:  
±14 days 


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6.1.2 Unscheduled Visits 
Unscheduled visits will be performed for the collection of clinical assessments required 
to document a flare or to evaluate adverse events. Assessments for an unscheduled visit 
are listed in Appendix 1. Some of the assessments may be omitted if they are not 
indicated for the purposes of the study. 
6.2 
ENROLLMENT, RANDOMIZATION AND BLINDING 
6.2.1 Enrollment 
Participants who meet the eligibility criteria will be enrolled at study visit 0. 
6.2.2 Randomization 
Participants will be randomly assigned at week 4 to either of the experimental groups. 
Participants will be randomly assigned to their treatment group utilizing a centralized, 
automated randomization system. Randomization will not be stratified. 
6.2.3 Blinding 
All study medications will be administered open label, and the study treatment 
assignments will not be blinded.  
6.3 
GENERAL ASSESSMENTS 
Informed consent. Written informed consent will be obtained before any study 
assessments or procedures are performed. 
Randomization.  
Medical history. A history will be taken to determine if the participant has had any 
clinically significant diseases or medical procedures other than the disease under study. 
Lupus history. A history will be taken to determine both dates of diagnosis of disease and 
onset of lupus nephritis. 
Adverse events. Participants will be assessed for AEs. 
Concomitant medications. All concomitant medications will be recorded. 
Comprehensive physical examination. 
Limited physical examination. A physical examination focused on participant’s current 
complaints and clinical status at the study visit will be conducted.  
Vital signs. Weight, temperature, blood pressure, respiration, and pulse will be obtained 
at all visits. Refer to section 5 for details of vital sign assessments prior to, during, and 
after infusions. 
6.4 
CLINICAL LABORATORY ASSESSMENTS 
Hematology (CBC, differential and platelet count). 


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Serum creatinine. 
Serum chemistry (AST, ALT, bilirubin, and alkaline phosphatase). 
Serum albumin. 
Serum urea nitrogen.  
Serum pregnancy. 
Spot urine for protein and creatinine, protein-to-creatinine ratio, and albumin-to-
creatinine ratio. If a doubling of the protein-to-creatinine ratio compared with the lowest 
previous value is detected, a 24-hour collection should be performed. 
24-hour urine for protein and creatinine and protein-to-creatinine ratio. 
Urinalysis. 
STAT urine pregnancy. 
ANA. 
HIV. Unless test has been performed within 30 days of visit -1 and documented test 
results are available. 
Hepatitis B (surface antibody, core antibody, and surface antigen). Unless test has been 
performed within 30 days of visit -1 and documented test results are available. 
Hepatitis C (RNA or antibody). Unless test has been performed within 30 days of visit -1 
and documented test results are available. 
Chest x-ray. Unless x-ray has been performed within 30 days of visit -1 and documented 
test results are available.  
Anti-dsDNA. 
C3, C4. 
CD19. 
Anticardiolipin antibodies (IgA, IgG, and IgM). 
Quantitative serum immunoglobulins (IgA, IgG, and IgM). 
Anti-ENA (anti-Sm and anti-RNP). 
QuantiFERON – TB Gold test. Unless test has been performed within 30 days of visit -1 
and documented test results are available. (PPD tuberculin test may be substituted for 
QuantiFERON – TB Gold test). 


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6.5 
LUPUS ASSESSMENTS 
BILAG 2004 [115] 
SELENA-SLEDAI [117] 
SLICC Damage Index [118] 
6.6 
CLINICAL PATHOLOGY ASSESSMENT 
Kidney biopsy (if clinically indicated) 
7. 
MECHANISTIC PLAN 
7.1 
RATIONALE  
Given the significant role of B cells in the pathogenesis of SLE, this trial is focused on B 
cell depletion and reconstitution for the induction of tolerance in severe LN patients. Our 
hypothesis is that treatment with belimumab will inhibit the reconstitution of autoreactive 
B cells in patients with LN following B cell depletion with rituximab and 
cyclophosphamide. Belimumab blocks BAFF, which is a cytokine that belongs to the 
TNF receptor ligand family that may promote the maturation and survival of B cells, 
including autoreactive B cells. BAFF, which is present at higher than normal levels in 
lupus, increases temporarily following B cell depletion, raising the possibility that it may 
allow for the positive selection of autoreactive B cells and prevent disease control.  
An exploratory endpoint of this clinical trial will center on the regulation of a peripheral 
tolerance checkpoint between the transitional and mature naïve B cell compartments. 
This tolerance checkpoint is defective in patients with lupus, resulting in the enhanced 
selection of mature naïve B cells with autoreactivity.  Therefore, the mechanistic studies 
will focus on the enumeration of the autoreactive cells in the mature naïve B cell 
compartment at week 48 when the recovery of blood B cells is adequate to perform this 
analysis. These mechanistic studies will increase our understanding of disease 
pathogenesis by evaluating the transitional, naïve, and memory B cell compartments in 
LN patients; identifying immunologic indicators of disease resolution; and evaluating the 
effects of B cell depletion and BAFF blockade on immunological pathways. Whole blood 
will be collected with the objective of analyzing circulating cytokine levels, circulating 
cell populations, and potentially genetic signatures of disease and tolerance. It is 
hypothesized that tolerance can be induced by depleting B cells and inhibiting 
autoreactive B cell reconstitution in patients treated with the combination of rituximab, 
cyclophosphamide and belimumab. We expect that participants with active lupus 
nephritis receiving therapy with rituximab, cyclophosphamide and belimumab (RCB) 
will have fewer autoreactive mature naïve peripheral blood B cells at week 48 than 
participants receiving rituximab plus cyclophosphamide (RC). 


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7.2 
PLANNED MECHANISTIC ASSAYS 
7.2.1 Detection of Autoreactive B Cells 
It is hypothesized that treatment with rituximab and CTX followed by belimumab will 
significantly reduce the levels of autoreactive mature naïve B cells. Whole blood will be 
collected from enrolled participants to evaluate changes in autoreactive mature naïve B 
cell and autoantibody levels. A single B cell cloning assay described by Nussenzweig and 
colleagues may be used to evaluate the mature naïve B cell compartment and test cloned 
antibodies for reactivity with self-antigens [17, 19, 23, 24, 33, 119]. We hypothesize that 
the percent of mature naïve autoreactive B cells will be reduced at week 48 in 
participants who are B-cell depleted with rituximab and CTX followed by belimumab 
(RCB) compared to B-cell depletion without subsequent belimumab (RC). 
Since the isolation of monoclonal antibodies from single B cells is both labor-intensive 
and costly, other assays are under development to address this hypothesis in a more cost-
effective manner. Some of these assays are based on flow cytometry and allow for the 
enumeration of ANA positive and 9G4+ cells [120-123]. 9G4 is an idiotype expressed by 
a clinically relevant subset of autoreactive B cells in lupus, while ANA positivity is the 
serological hallmark of lupus.  In addition, ELISPOT assays have been developed that 
can quantify ANA reactive cells and may be useful for detecting B cells with reactivity 
towards nuclear antigens.    
A limitation of the above assays is that they only identify B cells with reactivity against a 
restricted subset of autoreactive B cells, for example 9G4+ B cells or those that bind 
nuclear antigens.  Current research has been focused on developing a method of 
expanding single B cells in culture, yielding micrograms of antibodies, which in turn, 
may be tested by ELISA using Luminex-bead technology to measure their reactivity 
against a large panel of candidate autoantigens. This assay, and perhaps others in 
development, may be utilized to evaluate the effects of belimumab quantify the 
percentage of autoreactive B cells in the mature naïve B cell compartment, as well as the 
transitional B cell compartment. 
7.2.2 Multi-Parameter Flow Cytometry (MFC) 
Treatment paradigms outlined in this protocol focus on depletion of B cells through the 
administration of rituximab and the inhibition of autoreactive B cell reconstitution 
through administration of belimumab. Therefore, the B cell reconstitution kinetics will be 
evaluated by measuring the transitional, mature, memory, and regulatory B cell 
compartments following treatment.  
Due to the multifactorial nature of LN and the documented involvement of T cells and 
dendritic cells, circulating T cells and monocytes will be evaluated in peripheral blood. 
Frozen flow cytometry experiments will use banked specimens to investigate longitudinal 
changes in B cells, T cells, monocytes, and dendritic cells. Levels of circulating cells will 
be compared between the baseline and time points following treatment. Additional 
comparisons will be made between treatment groups to evaluate effectiveness of 
treatment. 


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7.2.3 Gene Expression in Peripheral Blood  
Systemic treatment of patients with biologics has been shown to modulate gene 
expression in SLE; therefore whole blood will be collected and may be used to evaluate 
changes in the periphery due to immunomodulation of the disease or the systemic nature 
of the treatment.  
Whole blood will be collected from enrolled participants to evaluate changes in gene 
expression following therapeutic treatment. Global changes in gene expression may be 
evaluated at the end of the study using Illumina or Affymetrix technology. Gene 
expression of selected cytokines and other immune regulatory molecules may be further 
evaluated using quantitative PCR. Whole blood may be compared pre- and post-treatment 
to determine the effect of treatment on the global gene expression in participants with 
LN. Comparisons at baseline will be important to demonstrate that all participants have 
similar inflammatory signatures prior to treatment. 
Differential expression comparisons may be made at baseline among the two groups and 
for changes from baseline within each group. For the time-series data where varying rates 
of depletion need to be accounted for, expression values may be normalized by adjusting 
for frequency of specific cell counts. Candidate gene lists will be defined in advance and 
included as part of the statistical analysis plan avoiding any penalty for multiple testing 
corrections. De novo discovery analysis approaches will be applied after testing for 
candidate genes with and without testing corrections. 
7.2.4 Serum Cytokine Assays 
Participant serum/plasma will be collected and analyzed for circulating levels of 
cytokines and inflammatory mediators.  
Serum levels for individual cytokines and inflammatory mediators will be compared 
between the baseline and time points following treatment. Additionally, levels of 
cytokines and inflammatory mediators could be evaluated for correlations with absolute 
counts and activation status of circulating B cell, T cell, and monocyte populations. 
Finally, comparisons will be made between treatment groups to evaluate effectiveness of 
the therapeutic intervention on circulating levels of inflammatory mediators.  
7.2.5 Genotype Analysis 
Genetic differences may, in part, determine response to B cell depletion followed by 
BAFF blockade. Therefore, DNA will be collected at baseline from all consenting 
participants. Banked DNA may be used to allow HLA typing for specific alleles and 
single nucleotide polymorphism analysis for genes with reported associations to SLE or 
drug related effects.  
7.2.6 Antibodies to John Cunningham Virus 
PML is a rare opportunistic infection of the nervous system that is caused by the John 
Cunningham (JC) virus, and occurs in the setting of immunodeficiency or 
immunosuppression. Cases of PML have occurred in SLE patients who have been treated 


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with rituximab, in SLE patients who have been treated with belimumab, and also in SLE 
patients who have not been treated with either of these agents [96, 97].  
The presence of JC virus seropositivity has been useful in predicting PML risk in 
multiple sclerosis patients who receive the immunosuppressive agent natalizumab, a 
monoclonal antibody to α4-integrin [124]. However, the clinical significance of JC virus 
seropositivity in SLE has not been established. SLE patients typically demonstrate many 
abnormal antibody reactivities, and the prevalence of JC virus seropositivity in SLE is 
unknown. Therefore, participants in this study will be tested for seropositivity to JC virus 
at baseline, in order to gain preliminary data about prevalence of JC virus seropositivity 
in patients with lupus nephritis.  
7.2.7 Analysis of Urine 
Urinary lymphocytes and podocytes in lupus nephritis and other renal diseases have been 
associated with an inflammatory cell signature and identification of biomarkers of disease 
activity [125, 126]. Urinary mRNA podocyte damage markers can be used for monitoring 
risk for progression and response to therapy [127].  Urinary biomarkers of renal response 
to therapy would be especially useful since it is not feasible for subjects to undergo serial 
biopsy of the lupus nephritis target tissue (kidney).  In addition, the autoreactive profile 
of urinary B cells may reflect a renal response to therapy more accurately than peripheral 
blood.  Therefore, urine specimens will be collected, and hematopoietic and non-
hematopoietic cell populations may be analyzed by flow cytometry, RNA-seq, 
assessment of autoreactivity, and other analytic techniques. Urine proteomics may also be 
assessed. 
7.3 
OVERVIEW OF DATA ANALYSIS 
This study is designed to assess the ability of combination therapy to statistically reduce 
the percent of autoreactive transitional and naïve B cells. Mechanistic data collected will 
be analyzed as both cohort and individual participant-based longitudinal profiling which 
includes graphic plotting and descriptive statistics etc.  
7.3.1 Individual Based Longitudinal Profiling  
Mechanistic samples from participants enrolled in this study will be assayed as described 
above with the aim to identify specific cell phenotypes, intracellular responses and /or 
gene sets (peripheral blood) that correlate with successful disease 
remission/improvement. Graphic plots and descriptive statistics will facilitate 
longitudinal monitoring of relevant cellular populations, immune cell repertoire, and gene 
expression etc., in conjunction with the treatment process, adverse events and clinical 
outcomes. Descriptive statistics will be provided as appropriate. 
7.3.2 Exploratory Analysis 
The primary objective of exploratory analysis is to discover cellular and immunogenetic 
patterns among the participants at clinical milestones during the study that may provide 
insights into potential association with the suppression of the inflammatory process and 


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disease remission/improvement. Pattern recognition methods including hierarchical 
clustering and principal component analysis may be used for the analysis. The 
exploratory analysis will be conducted on individual assay datasets (flow cytometry, gene 
expression, etc.) as well as integrated multi-assay data. 
7.4 
FUTURE / UNPLANNED STUDIES 
Specimens stored during the trial may be used in future assays to reevaluate biological 
responses as research tests are developed over time. Additionally, samples may be used 
for assays/ experiments outside the scope of this proposal, such as investigation of 
differences in the B cell receptor repertoire as evaluated by sequencing, proteomics or 
other assays that may emerge and be compelling. Re-evaluations or new assays will only 
be performed on samples of participants who have consented for future research. The 
ITN sample sharing policy will apply for the provision of samples to study or outside 
investigators (www.immunetolerance.org).  
7.5 
SPECIMEN LOGISTICS 
The clinical sites will be trained in collection, processing, shipment, and tracking of 
mechanistic research specimens. The ITN will monitor specimen quality, shipping 
compliance and retrain the clinical site if not producing optimum quality mechanistic 
samples. Mechanistic samples will be shipped to ITN repositories/ core labs, per ITN 
standard procedures. All shipping will conform to Department of Transportation 
regulations (49 CFR 173.199) for Diagnostic Specimens. 
7.6 
SPECIMEN TRACKING PROCEDURES 
The ITN will track all mechanistic specimens until the final disposition of all material is 
known. Samples will remain in the ITN repository until used for assays or destroyed. 
7.7 
SPECIMEN STORAGE 
Samples sent to the ITN repository will be stored under specific conditions to maintain 
long-term sample integrity, as well as specimen tracking from receipt to shipment to 
alternate locations. The ITN specimen tracking system will be used to track date of 
shipment, location shipped to, carrier, items shipped, amount shipped, barcode numbers, 
protocol number and associated comments about each individual specimen. Storage 
temperature, location, processing, aliquoting, and freeze/thaw events may also be 
recorded. 
If the study participant consents to storage, the participant’s specimens will be stored 
indefinitely. The participant can change their mind at any time and have their stored 
specimens destroyed by notifying the study physician in writing. In such cases, the site 
coordinator would send all requests for sample destruction to the ITN. The site will 
receive confirmation that the specimen was destroyed as requested. If the participant’s 
samples have already been analyzed, then the data will be used as part of the overall 
analysis. The participant can only request to have samples destroyed if they still exist, i.e. 
have not already been used in an experiment. 


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Specimens at the ITN core or repository can only be transferred to another destination 
with appropriate authorization per ITN standard procedures. Purpose for 
accessing/transferring the specimen (within study assay as defined by the protocol or 
future studies), evaluation of participant consent for the purpose provided, verification of 
specimen identifiers, and quality and quantity of the specimen are some of the items 
checked prior to authorization. 
8. 
ADVERSE EVENTS 
8.1 
OVERVIEW 
The investigator is responsible for the detection and documentation of events meeting the 
criteria and definition of an AE, AR, SAE, or SAR as described in sections 8.2.1, 8.2.2, 
and 8.2.3 in this protocol. All AEs and SAEs will be recorded in the source documents 
and on the appropriate electronic CRF(s). All data will be reviewed periodically by the 
DSMB, which may provide recommendations to NIAID about withdrawing any 
participant and/or terminating the study because of safety concerns. 
Adverse events that are classified as serious according to the definition of health 
authorities must be reported promptly and appropriately to the NIAID, ITN, principal 
investigators in the trial, IRBs, and health authorities. This section defines the types of 
AEs and outlines the procedures for appropriately collecting, grading, recording, and 
reporting them. Information in this section complies with 21CFR 312; ICH Guideline 
E2A: Clinical Safety Data Management: Definitions and Standards for Expedited 
Reporting; and ICH Guideline E-6: Guidelines for Good Clinical Practice; and applies the 
standards set forth in the National Cancer Institute (NCI), Common Terminology Criteria 
for Adverse Events, Version 4.03 (referred to herein as the “NCI-CTCAE manual”). 
Additional information and a printable version of the NCI-CTCAE manual are found at 
this website:  http://ctep.cancer.gov/reporting/ctc.html. 
8.2 
DEFINITIONS 
8.2.1 Adverse Event 
An adverse event is any occurrence or worsening of an undesirable or unintended sign, 
symptom, laboratory finding, or disease that occurs during participation in the trial 
whether or not considered trial related [From OHRP "Guidance on Reviewing and 
Reporting Unanticipated Problems Involving Risks to Subjects or Others and Adverse 
Events (1/15/07)" http://www.hhs.gov/ohrp/policy/advevntguid.html]. An adverse event 
will be followed until it resolves or until 30 days after a participant terminates from the 
study, whichever comes first. All AEs will be recorded as specified in section 8.3.3.1 
whether they are or are not related to disease progression or study participation. 
8.2.2 Study-Specific Adverse Events 
 
For purposes of this study, B cell depletion will not be considered an adverse event. 
 
Hypogammaglobulinemia will be graded according to the scale in section 8.4.1. 


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8.2.3 Adverse Reaction and Suspected Adverse Reaction 
An adverse reaction (AR) means any adverse event caused by a drug. Adverse reactions 
are a subset of all suspected adverse reactions for which there is reason to conclude that 
the drug caused the event. 
Suspected adverse reaction (SAR) means any adverse event for which there is a 
reasonable possibility that the drug caused the adverse event. For the purposes of safety 
reporting, ‘reasonable possibility’ means there is evidence to suggest a causal relationship 
between the drug and the adverse event. A suspected adverse reaction implies a lesser 
degree of certainty about causality than an adverse reaction, which means any adverse 
event caused by a drug (21 CFR 312.32(a)). 
8.2.4 Serious Adverse Event or Serious Suspected Adverse Reaction 
An AE or SAR is considered “serious” if, in the view of either the investigator or the 
sponsor, it results in any of the following outcomes: 
 
Death:  A death that occurs during the study or that comes to the attention of the 
investigator during the protocol-defined follow-up period must be reported to the 
sponsor whether it is considered treatment related or not. 
 
A life-threatening event:  An AE or SAR is considered “life-threatening” if, in the 
view of the investigator or the sponsor, its occurrence places the participant at 
immediate risk of death. It does not include an AE or SAR that, had it occurred in a 
more severe form, might have caused death. 
 
Inpatient hospitalization or prolongation of existing hospitalization. 
 
Persistent or significant incapacity or substantial disruption of the ability to conduct 
normal life functions. 
 
An event that requires intervention to prevent permanent impairment or damage. An 
important medical event that may not result in death, be life threatening, or require 
hospitalization may be considered an SAE when, based on appropriate medical 
judgment, it may jeopardize the participant and may require medical or surgical 
intervention to prevent one of the outcomes listed above. 
 
Congenital anomaly or birth defect. 
If an event meets any of the above definitions, regardless of the relationship of the event 
to study drug, the event must be reported to the sponsor as described in section 8.5.1. 
8.2.5 Adverse Events of Special Interest (AESIs)  
Adverse Events of Special Interest (AESIs) are identified for rituximab and will be 
collected and reported to Genentech in this trial. 
 
Hepatic Events, including elevated hepatic transaminase levels [ALT/AST levels 
>3xULN]  or  total bilirubin > 3 mg/dL 
 
Progressive Multifocal Leukoencephalopathy 
 
Posterior Reversible Encephalopathy Syndrome 


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 
Malignancy 
 
Adverse Events of Special Interest (AESIs) are identified for belimumab and will be 
collected in this trial. 
 
Serious hypersensitivity or infusion reactions 
 
Serious infections, including herpes zoster and opportunistic infections  
 
Malignancy 
 
Suicidal thought, intent, or behavior 
 
Grade 4 hypogammaglobulinemia 
If an adverse event meets any of the above AESI categories, regardless of the relationship 
of the event to study drug or severity, the event must be reported to the IND sponsor as 
described in Section 8.5.2. 
8.2.6 Unexpected Suspected Adverse Reaction 
With regards to reporting to the Health Authority, a SAR is considered “unexpected” 
when its nature (specificity), severity, or rate of occurrence is not consistent with 
applicable product information as described in the safety information provided in the 
package insert or investigator’s brochure. For this study expectedness will be determined 
by the package insert for Rituxan or the investigator’s brochure for rituximab; in the 
package insert for Benlysta; the package insert for Cytoxan®; the package insert for 
Solumedrol; and the prescribing information for prednisone. A serious and unexpected 
suspected adverse reaction is referred to as a SUSAR. 
8.3 
COLLECTING AND RECORDING ADVERSE EVENTS 
8.3.1 Methods of Collection 
Adverse events may be collected as follows: 
 
Observing the participant. 
 
Questioning the participant in an objective manner. 
 
Receiving an unsolicited complaint from the participant. 
An abnormal value or result from a clinical or laboratory evaluation (e.g., a radiograph, 
an ultrasound, or an electrocardiogram) can also indicate an adverse event if it is 
determined by the investigator to be clinically significant. If this is the case, it must be 
recorded in the source document and as an adverse event on the appropriate adverse event 
form(s). The evaluation that produced the value or result should be repeated until that 
value or result returns to normal or can be explained and the participant’s safety is not at 
risk. 
8.3.2 Specific Instructions for Recording Adverse Events 
Correct medical terminology/concepts should be used when reporting AEs and SAEs. 
Avoid colloquialisms and abbreviations. 
 
Diagnosis vs. Signs and Symptoms 


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If known at the time of reporting, a diagnosis should be reported rather than 
individual signs and symptoms (e.g., record only liver failure or hepatitis rather than 
jaundice, asterixis, and elevated transaminases). However, if a constellation of signs 
and/or symptoms cannot be medically characterized as a single diagnosis or 
syndrome at the time of reporting, it is ok to report the information that is currently 
available. If a diagnosis is subsequently established, it should be reported as follow-
up information. 
 
Deaths 
All deaths that occur during the protocol-specified AE reporting period (see Section 
8.3.3), regardless of attribution, will be reported to the appropriate parties. When 
recording a death, the event or condition that caused or contributed to the fatal 
outcome should be reported as the single medical concept. If the cause of death is 
unknown and cannot be ascertained at the time of reporting, report “Unexplained 
Death.” 
 
Preexisting Medical Conditions 
A preexisting medical condition is one that is present at the start of the study. Such 
conditions should be reported as medical and surgical history. A preexisting medical 
condition should be re-assessed throughout the trial and reported as an AE or SAE 
only if the frequency, severity, or character of the condition worsens during the 
study. When reporting such events, it is important to convey the concept that the 
preexisting condition has changed by including applicable descriptors (e.g., “more 
frequent headaches”). 
 
Hospitalizations for Medical or Surgical Procedures 
Any AE that results in hospitalization or prolonged hospitalization should be 
documented and reported as an SAE. If a subject is hospitalized to undergo a medical 
or surgical procedure as a result of an AE, the event responsible for the procedure, 
not the procedure itself, should be reported as the SAE. For example, if a subject is 
hospitalized to undergo coronary bypass surgery, record the heart condition that 
necessitated the bypass as the SAE. 
8.3.3 Collection Period for Adverse Events and Serious Adverse Events 
8.3.3.1 Adverse Events 
All AEs will be collected and recorded in the source documents from visit -1 until the 
time the participant completes the study (visit 18), or prematurely withdraws from the 
study. Only ≥ grade 2 AEs will be recorded in the clinical database for the same time 
period. 
8.3.3.2 Serious Adverse Events 
All serious adverse events will be collected from visit -1 until 30 days after the 
participant completes the study (visit 18), or prematurely withdraws from the study. If a 
participant has received belimumab and prematurely withdraws from the study, serious 


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adverse events will be collected from visit -1 until 16 weeks after the last infusion of 
belimumab, or 30 days after termination from the study, whichever is longer.  
8.3.4 Recording Method 
8.3.4.1 Adverse Events 
Throughout the study, the investigator will record AEs on the appropriate eCRF 
regardless of their severity or relation to study participation. The investigator will treat 
participants experiencing AEs appropriately and observe them at suitable intervals until 
their symptoms resolve or their status stabilizes. 
8.3.4.2 Serious Adverse Events 
Serious adverse events will be recorded on the adverse event eCRF and on the SAE 
eCRF, and health authorities will be notified as outlined in section 8.5. 
8.4 
GRADING AND ATTRIBUTION OF ADVERSE EVENTS 
8.4.1 Grading of Hypogammaglobulinemia  
For this study hypogammaglobulinemia events will be graded as follows. 
 
Grade 1: 450-690 mg/dL IgG 
 
Grade 2: 300-449 mg/dL IgG 
 
Grade 3: < 300 mg/dL IgG 
 
Grade 4: < 300 mg/dL IgG associated with Grade 3 or greater infectious AE 
8.4.2 Grading Criteria 
The study site will grade the severity of AEs experienced by study participants according 
to the criteria set forth in the National Cancer Institute’s Common Terminology Criteria 
for Adverse Events Version 4.03 (NCI-CTCAE manual). This document provides a 
common language to describe levels of severity, to analyze and interpret data, and to 
articulate the clinical significance of all AEs. Please refer to the NCI-CTCAE manual for 
the desired event and specific grading for that event. If the event is not listed in the NCI-
CTCAE manual, please refer to the general guidelines for grading listed below. 
Adverse events will be graded on a scale from 1 to 5 according to the following standards 
in the NCI-CTCAE manual: 
Grade 1 = mild adverse event. 
Grade 2 = moderate adverse event. 
Grade 3 = severe and undesirable adverse event. 
Grade 4 = life-threatening or disabling adverse event. 
Grade 5 = death. 


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For additional information and a printable version of the NCI-CTCAE manual, go to 
http://ctep.cancer.gov/reporting/ctc.html   
8.4.3 Attribution Definitions 
Adverse events will be categorized for their relation to one or more of the following 
study medications: 
 
Belimumab; 
 
Rituximab; or 
 
Cyclophosphamide, methylprednisolone, and prednisone. 
The relation, or attribution, of an adverse event to study participation will be reported by 
the site investigator. The site investigator will also record the determination of attribution 
on the appropriate eCRF and/or SAE reporting form. The sponsor’s determination of 
attribution will be used for reporting to the appropriate health authorities. The relation of 
an adverse event to study participation will be determined using the descriptors and 
definitions provided in Table 5. 
Table 5 Attribution of adverse events 
Code 
Descriptor 
Definition 
Unrelated Category  
1 
Unrelated 
The adverse event is clearly not related. 
2 
Unlikely 
The adverse event is doubtfully related. 
Related Categories  
3 
Possible 
The adverse event has a reasonable possibility to be 
related; that is, there is evidence to suggest a causal 
relationship. 
4 
Probable 
The adverse event is likely related. 
5 
Definite 
The adverse event is clearly related. 
8.5 
REPORTING SERIOUS ADVERSE EVENTS 
8.5.1 Reporting SAEs to the IND Sponsor 
The following process for reporting an SAE ensures compliance with 21CFR 312 and 
ICH guidelines. After learning that a participant has experienced an SAE, the investigator 
or designee is responsible for reporting the SAE via the electronic SAE report form (SAE 
eCRF) within 24 hours of becoming aware of the event. Initial SAE eCRF should include 
as much information as possible, but at a minimum must include the following: 
 
SAE term. 
 
Relationship to study medications. 
 
Reason why the event is serious. 


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 
Supplementary eCRF pages that are current at the time of SAE reporting: medical 
history, concomitant medications, demographics, study drug administration, death.  
As additional details become available, the SAE eCRF should be updated and submitted. 
Every time the SAE eCRF is submitted, it should be electronically signed by the 
investigator or sub-investigator.  
For additional information regarding SAE reporting, contact Rho Product Safety: 
Rho Product Safety  
6330 Quadrangle Drive, Suite 500 
Chapel Hill, NC  27517 
Toll-free: 1-888-746-7231 
SAE Fax Line: 1-888-746-3293 
Email: rho_productsafety@rhoworld.com 
8.5.2 Reporting AESIs to the IND Sponsor 
After learning that a participant has experienced an AESI, the investigator or designee is 
responsible for reporting the AESI via electronic case report form (eCRF) within 24 
hours of becoming aware of the event. Initial eCRF should include as much information 
as possible, but at a minimum must include the following: 
 
AESI term. 
 
Relationship to study medications. 
 
Whether or not the event meets serious criteria. 
 
Supplementary eCRF pages that are current at the time of AESI reporting: medical 
history, concomitant medications, demographics, study drug administration, death.  
As additional details become available, the eCRF should be updated and submitted. 
Every time the eCRF is submitted, it should be electronically signed by the investigator 
or sub-investigator.  
For additional information regarding SAE reporting, contact Rho Product Safety as noted 
in section 8.5.1. 
8.5.3 Reporting SAEs to Health Authorities 
After the SAE has been reported by the site investigator and assessed by the IND 
sponsor, there are two options for the IND sponsor to report an event to the appropriate 
health authorities: 
Standard reporting (report in the IND annual report). This option applies if the adverse 
event is classified as one of the following: 
 
Serious, suspected adverse reaction per section 8.2.3 and 8.2.4, and not unexpected 
per section 8.2.6. 
 
Serious and not a suspected adverse reaction per section 8.2.3 and 8.2.4. 


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Expedited reporting is required (report in the IND safety report). This option applies if 
the adverse event is classified as one of the following: 
 
1. 
Serious and unexpected suspected adverse reaction (SUSAR) per sections 8.2.3, 
8.2.4, and 8.2.6. 
The sponsor must report any suspected adverse reaction that is both serious and 
unexpected. The sponsor must report an adverse event as a suspected adverse reaction 
only if there is evidence to suggest a causal relationship between the study drug and the 
adverse event, such as: 
 
A single occurrence of an event that is uncommon and known to be strongly 
associated with drug exposure (e.g., angioedema, hepatic injury, or Stevens-Johnson 
Syndrome); 
 
 
One or more occurrences of an event that is not commonly associated with drug 
exposure, but is otherwise uncommon in the population exposed to the drug (e.g., 
tendon rupture); 
 
 
An aggregate analysis of specific events observed in a clinical trial (such as known 
consequences of the underlying disease or condition under investigation or other 
events that commonly occur in the study population independent of drug therapy) 
that indicates those events occur more frequently in the drug  treatment group than in 
a concurrent or historical control group. 
 
2. Any findings from other studies: The sponsor must report any findings from other 
epidemiological studies, pooled analysis of multiple studies, or clinical studies that 
suggest a significant risk in humans exposed to the drug that would result in a safety-
related change in the protocol, informed consent, investigator brochure or other 
aspects of the overall conduct of the study. 
These events must be reported by the sponsor to the appropriate health authorities within 
15 calendar days; fatal or life-threatening events must be reported within 7 calendar days. 
8.5.4 Reporting SAEs to IRBs and Ethics Committees 
All investigators must report IND Safety Reports and related safety information to their 
respective IRBs or Ethics Committees as mandated by them. 
8.5.5 Reporting SAEs to the DSMB 
The NIAID and ITN will provide the DSMB with data of all SAEs on an ongoing basis, 
including quarterly reports of all SAEs.  
8.5.6 Reporting SAEs and AESIs to Genentech 
NIAID will report SAEs and AESIs for rituximab to Genentech as follows: 


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 
A completed MedWatch for all 7 day and 15 day IND safety reports (initial and 
follow-up reports) will be forwarded to Genentech at the same time as submission to 
FDA. All 15-day reports will include an analysis of similar events. 
 
A final report for all related SAEs and AESIs within 15 calendar days of sponsor 
notification. 
 
A final report of all unrelated SAEs to within 30 calendar days of sponsor 
notification. 
 
A quarterly line listing of all AEs. 
 
A copy of the IND annual reports at the same time as the transmission to the FDA. 
 
Final Report Format: 
o Expedited reports:  MedWatch 
o Non-expedited reports:  Medical Summary Report 
o Non-serious AEs:  Line listings 
NIAID will conduct reconciliation of SAEs and AESIs. If discrepancies are identified, 
NIAID and Genentech will cooperate in resolving the discrepancies. 
In addition, NIAID will forward the Clinical Study Report as well as any literature 
articles that are a result of the study to Genentech. 
Documents will be forwarded to Genentech drug safety in accordance with the NIAID 
Safety Management Plan, Part B. 
8.5.7 Reporting Pregnancy  
The investigator should be informed immediately of any pregnancy and all available 
pregnancy information should be entered into the electronic data capture (EDC) system 
within 24 hours of becoming aware of the event. The investigator should counsel the 
participant and discuss the risks of continuing with the pregnancy and the possible effects 
on the fetus. Monitoring of the participant should continue until the conclusion of the 
pregnancy. Follow-up information detailing the outcome of the pregnancy should be 
entered into the EDC system as it becomes available. Any premature termination of the 
pregnancy will be reported.  
While pregnancy itself is not considered to be an AE or SAE, any pregnancy 
complication or elective termination of a pregnancy for medical reasons will be recorded 
as an SAE as described in section 8.2.4. Should the pregnancy result in a congenital 
abnormality or birth defect, a separate SAE report must be submitted. 


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9. 
STATISTICAL CONSIDERATIONS AND ANALYTICAL PLAN 
9.1 
ANALYSIS SAMPLES 
9.1.1 Study Milestones 
The study analyses will take into account the major milestones that will occur during the 
course of the study. The major milestones are: 
 
Week 0: First doses of Solumedrol, rituximab, CTX and prednisone administered. 
 
Week 4: Treatment regimen change. No additional doses of Solumedrol and 
rituximab. Randomization of participants to one of the 2 treatment groups. First dose 
of belimumab administered to participants in the RCB group. 
 
Week 12: Expected completion of prednisone taper. 
 
Week 24: Week 24 assessment of clinical outcomes. 
 
Week 48: Primary endpoint assessment. No additional doses of belimumab. 
 
Week 96: Completion of tolerance assessment phase. 
9.1.2 Analysis Populations 
Modified Intent to treat (MITT) sample will be defined as all treated participants who 
receive study regimen, as defined below: 
 
Receive 1 dose of Solumedrol 
 
Receive 1 dose of rituximab 
 
Receive 1 dose of CTX 
 
Receive 1 dose of belimumab if in the RCB Group 
Per protocol (PP) samples will be defined as follows:  
PP24: Treated participants in the Modified ITT sample who receive study regimen, as 
defined below, until 24 weeks. 
 
Receive 2 doses each of Solumedrol, rituximab, and CTX 
 
Receive at least 80% of belimumab infusions if in the RCB Group 
PP48: Treated participants in the PP24 sample who receive study regimen, as defined 
below, until 48 weeks. 
 
Receive at least 80% of belimumab infusions if in the RCB Group 
PP96: Treated participants in the PP48 sample who continue in the study beyond 48 
weeks. 
Safety sample (SS) will be defined as all participants who receive at least one dose of 
study treatment. 


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9.2 
ANALYSIS OF ENDPOINTS 
9.2.1 Primary Endpoint 
The proportion of participants in the MITT analysis sample, who experience at least one 
Grade 3 or higher infectious adverse event, as defined in section 3.3.1, will be 
summarized by treatment group with 95% confidence intervals of the proportion. The 
Clopper-Pearson (exact) method for binomial proportions will be used for the calculation 
of the 95% confidence interval bounds. The 95% confidence intervals for the primary 
endpoint will also be calculated for the PP48 analysis sample. 
Although the study is not powered to detect it, a between-group comparison will be 
performed using a logistic regression model with the participant’s incidence of at least 
one Grade 3 or higher adverse event as the dependent variable and treatment as the 
independent variable. The logistic regression analysis will be performed on the MITT and 
PP48 analysis samples. 
9.2.2 Secondary Endpoints 
Clinical secondary endpoints 
1. The proportion of participants who experience at least one occurrence of 
hypogammaglobulinemia, as defined in section 3.3.2, will be analyzed for the time 
points and analysis samples indicated in Table 6 using a logistic regression model 
with the participant’s experience of hypogammaglobulinemia as the dependent 
variable and treatment as the independent variable.  
2. A similar approach will be applied to the following secondary outcomes for the time 
points and analysis samples indicated in Table 6. 
 
The proportion of participants who experience at least one Grade 3 or higher 
infectious adverse event, as defined in section 3.3.2. 
 
The proportion of participants with B cell reconstitution, as defined in section 
3.3.2 
 
The proportion of participants who achieve a complete response, as defined in 
section 3.3.2. 
 
The proportion of participants who achieve an overall response, as defined in 
section 3.3.2. 
 
The proportion of participants who achieve a sustained complete response, as 
defined in section 3.3.2. 
 
The proportion of participants who experience treatment failure, as defined in 
section 3.3.2. 
 
Serology endpoints: 
o The proportion of participants with negative anti-dsDNA. 


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o The proportion of participants who are hypocomplementemic. 
 
3. The frequency of non-renal flares, as defined in section 3.3.2, will be analyzed for the 
time points and analysis samples indicated in Table 6 using a Pearson’s chi-square 
test. For analyses with small sample sizes, Fisher’s exact test will be used in place of 
the Pearson’s chi-square test. 
Table 6 Secondary endpoints and analysis samples 
Secondary Endpoint 
Analysis Week 
MITT 
PP24 
PP48 
PP96 
Safety 
Grade 3 or higher infectious AE 
24 
X 
X 
 
 
 
 
96 
X 
 
 
X 
 
Hypogammaglobulinemia 
24 
X 
X 
 
 
 
 
48 
X 
 
X 
 
 
 
96 
X 
 
 
X 
 
B cell Reconstitution 
24 
X 
X 
 
 
 
 
48 
X 
 
X 
 
 
 
96 
X 
 
 
X 
 
Complete Response 
24 
X 
X 
 
 
 
 
48 
X 
 
X 
 
 
 
96 
X 
 
 
X 
 
Overall Response 
24 
X 
X 
 
 
 
 
48 
X 
 
X 
 
 
 
96 
X 
 
 
X 
 
Sustained Complete Response 
96 
X 
 
 
X 
 
Treatment Failure 
24 
X 
X 
 
 
 
 
48 
X 
 
X 
 
 
 
96 
X 
 
 
X 
 
Non-renal Flares 
24 
X 
X 
 
 
 
 
48 
X 
 
X 
 
 
 
96 
X 
 
 
X 
 
Serology 
24 
X 
X 
 
 
 
 
48 
X 
 
X 
 
 
 
96 
X 
 
 
X 
 
AEs of Interest 
24 
 
 
 
 
X 
 
48 
 
 
 
 
X 
 
96 
 
 
 
X 
 
Safety secondary endpoints 
 
1. The proportion of participants experiencing AEs of interest will be presented by 
treatment group and overall for the time points and analysis samples indicated in 
Table 6. The AEs of interest for analysis are: 
 
Any event leading to death. 
 
Grade 2 or greater leukopenia or thrombocytopenia. 
 
Premature ovarian failure.  


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 
Malignancy. 
 
Venous thromboembolic event (deep venous thrombosis or pulmonary 
embolism). 
 
Disease- or study medication-related event leading to hospitalization  
 
Infusion reactions (within 24 hours of infusion) that result in the cessation of 
further infusions (including cytokine-release allergic reaction). 
9.2.3 Endpoint Analysis by Race 
Summary descriptive statistics by treatment and race will be calculated for the complete 
response and overall response secondary endpoints at week 24 for the MITT and PP24 
analysis samples, at week 48 for the MITT and PP48 analysis samples and at week 96 for 
the MITT and PP96 analysis samples.  
9.2.4 Baseline Characteristics and Demographics 
Summary descriptive statistics for baseline and demographic characteristics will be 
provided for all enrolled participants. Demographic data will include age, race, sex, body 
weight, and height; these data will be presented in the following manner: 
 
Continuous data (i.e., age, body weight, and height) will be summarized descriptively 
by mean, standard deviation, median, and range. 
 
Categorical data (i.e., sex and race) will be presented as enumeration and 
percentages. 
9.2.5 Safety Analysis 
Safety analysis will be performed on the safety sample. Missing safety information will 
not be imputed. 
Safety will be analyzed in each treatment group through the reporting of AEs, vital signs, 
physical examinations, and changes in routine laboratory values.  
All AEs will be classified by body system and preferred term, according to a standardized 
thesaurus (MedDRA). The severity of AEs will be classified using the NCI-CTCAE 
toxicity scale. The total number of events and the number of participants experiencing 
AEs will be summarized by body system and preferred term for each study group and 
overall. Adverse events will also be summarized by maximum severity and relationship 
to the study drug for each study group and overall. Separate data listings will be provided 
for serious AEs, treatment-related AEs, and AEs leading to study discontinuation. 
Abnormal vital signs, physical examination results, and laboratory values that are deemed 
clinically significant by the investigators will be graded by the NCI-CTCAE toxicity 
scale and reported as AEs. 


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Change from the baseline of vital signs collected during infusions will be summarized. 
Vital signs taken during the screening procedures and during the follow-up visits will be 
summarized as well. 
For each study group and overall, physical examination results will be summarized by 
body system and visit.  
Descriptive statistics of laboratory values and the change from baseline of laboratory 
values will be presented for each study group and overall. Laboratory measurements 
include serum chemistry, urinalysis, and hematology. 
9.2.6 Medical History 
Medical history within the 12 months prior to screening — including the existence of 
current signs and symptoms — will be collected for each body system. 
9.2.7 Use of Medications 
All medications taken by or administered to study participants beginning 30 days before 
Visit -1 and continuing throughout the study will be collected. All medications used will 
be coded according to the WHO drug dictionary. The number and percentage of 
participants receiving prior and concomitant medications/therapies will be presented 
overall and by medication class. 
9.3 
SAMPLE SIZE 
The study is designed as a prospective, randomized, open label, multicenter pilot study. 
Participants are randomized to two treatment arms and exploratory comparisons between 
the two groups in the primary and secondary outcomes will be made. However, this is not 
the primary purpose of this study, and study is not powered to detect between-group 
differences. Rather, the primary endpoint in this pilot study is the proportion of 
participants in either treatment arm who experience at least one Grade 3 or higher 
infectious adverse event by Week 48. Thus, the sample size is determined by the width of 
the confidence interval surrounding the point estimate of this proportion.  
Data from ITN’s ACCESS study and a review of the literature suggested that the 
proportion could range from 0.05 to 0.35 [10, 12, 51, 55, 116]. Based on a sample size of 
20 per group, Table 7 provides the upper and lower 95% confidence limits for 
proportions in this range. As described in Section 9.2.1, the confidence limits are 
estimated using the Clopper-Pearson method for binomial proportions. 


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Table 7 95% confidence limits for proportions of AEs in pilot study 
Proportion of 
AEs* 
95% CI 
Lower 
95% CI 
Upper 
0.05 
0.001 
0.249 
0.10 
0.012 
0.317 
0.15 
0.032 
0.379 
0.20 
0.057 
0.437 
0.25 
0.087 
0.491 
0.30 
0.119 
0.543 
0.35 
0.154 
0.592 
*Proportion out of 20 participants in either treatment group 
Thus, for example, with a sample of size 20, if the proportion is observed to be 0.15, the 
corresponding 95% confidence interval would range from 0.032 to 0.379. This is 
considered adequate for a pilot study of this type. 
Although between-group comparisons are not the primary focus, they will nevertheless 
be performed in this study. Setting the sample of size to n=20 per group and the type-I 
error to α = 0.05, and assuming that the proportion of a Grade 3 or higher infectious AE 
in one treatment arm is 0.15, Table 8 shows the power with which between-group 
differences can be detected. The power was estimated using a logistic regression model 
with the treatment group as the independent variable. Thus, a difference in proportions of 
0.15 vs. 0.45 can be detected with ~ 60% power; a difference of 0.15 vs. 0.55 can be 
detected with ~80% power. 
Table 8 Power to detect between-group differences in the proportion of grade 3+ infection AEs 
Proportion 
Treatment Group 1 
Proportion 
Treatment Group 2 
Power 
0.15 
0.40 
49.0% 
0.15 
0.45 
62.7% 
0.15 
0.50 
72.9% 
0.15 
0.55 
80.3% 
0.15 
0.60 
85.5% 
9.4 
REPORTING DEVIATIONS FROM THE STATISTICAL PLAN 
The principal features of both the study design and the plan for statistical data analysis 
are outlined in this protocol and in the statistical analysis plan (SAP). Any change in 
these features requires either a protocol or an SAP amendment, which is subject to review 


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by the DSMB, the study sponsor(s), and the health authorities. These changes will be 
described in the final study report as appropriate. 
10. 
ACCESS TO SOURCE DATA/DOCUMENTS 
The investigational sites participating in this study will maintain the highest degree of 
confidentiality permitted for the clinical and research information obtained from 
participants in this clinical trial. Medical and research records should be maintained at 
each site in the strictest confidence. However, as a part of the quality assurance and legal 
responsibilities of an investigation, the investigational sites must permit authorized 
representatives of the ITN, sponsor, and health authorities to examine (and to copy when 
required by applicable law) clinical records for the purposes of quality assurance reviews, 
audits, and evaluation of the study safety and progress. Unless required by the laws 
permitting copying of records, only the coded identity associated with documents or other 
participant data may be copied (and any personally identifying information must be 
obscured). Authorized representatives as noted above are bound to maintain the strict 
confidentiality of medical and research information that may be linked to identified 
individuals. The investigational sites will normally be notified in advance of auditing 
visits. 
11. 
QUALITY CONTROL AND ASSURANCE 
The investigator is required to keep accurate records to ensure that the conduct of the 
study is fully documented. The investigator is required to ensure that all eCRFs are 
completed for every participant entered in the trial. 
The sponsor is responsible for regular inspection of the conduct of the trial, for verifying 
adherence to the protocol, and for confirming the completeness, consistency, and 
accuracy of all documented data. 
The eCRFs will be completed online via a web-based electronic data capture (EDC) 
system that has been validated and is compliant with Part 11 Title 21 of the Code of 
Federal Regulations. Study staff at the site will enter information into the electronic 
CRFs, and the data will be stored remotely at a central database. Data quality will be 
ensured through the EDC system’s continuous monitoring of data and real-time detection 
and correction of errors. All elements of data entry (i.e., time, date, verbatim text, and the 
name of the person performing the data entry) will be recorded in an electronic audit trail 
to allow all changes in the database to be monitored and maintained in accordance with 
federal regulations. 
12. 
ETHICAL CONSIDERATIONS AND COMPLIANCE WITH GOOD CLINICAL 
PRACTICE 
12.1 STATEMENT OF COMPLIANCE 
This trial will be conducted in compliance with the protocol, current Good Clinical 
Practice (GCP) guidelines—adopting the principles of the Declaration of Helsinki—and 
all applicable regulatory requirements. 


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Prior to study initiation, the protocol and the informed consent documents will be 
reviewed and approved by the sponsor and an appropriate ethics review committee or 
institutional review board (IRB). Any amendments to the protocol or consent materials 
must also be approved by the Sponsor, the IRB and submitted to FDA before they are 
implemented. 
12.2 INFORMED CONSENT 
The informed consent form is a means of providing information about the trial to a 
prospective participant and allows for an informed decision about participation in the 
study. All participants must read, sign, and date a consent form before participating in the 
study, taking the study drug, and/or undergoing any study-specific procedures. If a 
participant does not speak and read English, the consent materials must be translated into 
the appropriate language. 
The informed consent form must be updated or revised whenever important new safety 
information is available, whenever the protocol is amended, and/or whenever any new 
information becomes available that may affect participation in the trial. 
A copy of the informed consent will be given to a prospective participant for review. The 
attending physician, in the presence of a witness, will review the consent and answer 
questions. The participant will be informed that participation is voluntary and that he/she 
may withdraw from the study at any time, for any reason. 
12.3 PRIVACY AND CONFIDENTIALITY 
A participant’s privacy and confidentiality will be respected throughout the study. Each 
participant will be assigned a sequential identification number. This number, rather than 
the participant’s name, will be used to collect, store, and report participant information. 
13. 
PUBLICATION POLICY 
The ITN policy on publication of study results will apply to this study. Authorized 
participants may find details regarding the policy statement on the ITN internet website at 
http://www.immunetolerance.org. 
 


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111. 
ACCESS, The Abatacept and Cyclophosphamide Combination Efficacy and Safety Study, 
unpublished results. 
112. 
Quinti, I., et al., Effectiveness of immunoglobulin replacement therapy on clinical 
outcome in patients with primary antibody deficiencies: results from a multicenter 
prospective cohort study. J Clin Immunol, 2011. 31(3): p. 315-22. 
113. 
Buhaescu, I., A. Covic, and G. Deray, Treatment of proliferative lupus nephritis--a critical 
approach. Semin Arthritis Rheum, 2007. 36(4): p. 224-37. 
114. 
Levey, A.S., et al., A new equation to estimate glomerular filtration rate. Ann Intern 
Med, 2009. 150(9): p. 604-12. 
115. 
Isenberg, D.A., et al., BILAG 2004. Development and initial validation of an updated 
version of the British Isles Lupus Assessment Group's disease activity index for patients 
with systemic lupus erythematosus. Rheumatology (Oxford), 2005. 44(7): p. 902-6. 
116. 
Dooley, M.A., et al., Mycophenolate versus azathioprine as maintenance therapy for 
lupus nephritis. N Engl J Med, 2011. 365(20): p. 1886-95. 
117. 
Petri, M., et al., Combined oral contraceptives in women with systemic lupus 
erythematosus. N Engl J Med, 2005. 353(24): p. 2550-8. 
118. 
Romero-Diaz, J., D. Isenberg, and R. Ramsey-Goldman, Measures of adult systemic lupus 
erythematosus: updated version of British Isles Lupus Assessment Group (BILAG 2004), 
European Consensus Lupus Activity Measurements (ECLAM), Systemic Lupus Activity 
Measure, Revised (SLAM-R), Systemic Lupus Activity Questionnaire for Population 
Studies (SLAQ), Systemic Lupus Erythematosus Disease Activity Index 2000 (SLEDAI-2K), 
and Systemic Lupus International Collaborating Clinics/American College of 
Rheumatology Damage Index (SDI). Arthritis Care Res (Hoboken), 2011. 63 Suppl 11: p. 
S37-46. 
119. 
Li, Y., et al., Increased expression of FcgammaRI/CD64 on circulating monocytes parallels 
ongoing inflammation and nephritis in lupus. Arthritis Res Ther, 2009. 11(1): p. R6. 
120. 
Quach, T.D., et al., Anergic responses characterize a large fraction of human 
autoreactive naive B cells expressing low levels of surface IgM. J Immunol, 2011. 186(8): 
p. 4640-8. 
121. 
Richardson, C., et al., Molecular basis of 9G4 B cell autoreactivity in human systemic 
lupus erythematosus. J Immunol, 2013. 191(10): p. 4926-39. 
122. 
Jenks, S.A., et al., 9G4+ autoantibodies are an important source of apoptotic cell 
reactivity associated with high levels of disease activity in systemic lupus erythematosus. 
Arthritis Rheum, 2013. 65(12): p. 3165-75. 
123. 
Ching, K.H., et al., Two major autoantibody clusters in systemic lupus erythematosus. 
PLoS One, 2012. 7(2): p. e32001. 
124. 
Bloomgren, G., et al., Risk of natalizumab-associated progressive multifocal 
leukoencephalopathy. N Engl J Med, 2012. 366(20): p. 1870-80. 
125. 
Enghard, P., et al., Urinary CD4 T cells identify SLE patients with proliferative lupus 
nephritis and can be used to monitor treatment response. Ann Rheum Dis, 2014. 73(1): 
p. 277-83. 
126. 
Suthanthiran, M., et al., Urinary-cell mRNA profile and acute cellular rejection in kidney 
allografts. N Engl J Med, 2013. 369(1): p. 20-31. 
127. 
Wickman, L., et al., Urine podocyte mRNAs, proteinuria, and progression in human 
glomerular diseases. J Am Soc Nephrol, 2013. 24(12): p. 2081-95. 


Immune Tolerance Network  
CONFIDENTIAL 
 
Page 86  
 
Protocol ITN055AI 
Version 2.0 
October 9, 2015 
 
APPENDIX 1. SCHEDULE OF EVENTS 
Treatment Phase and Tolerance Assessment Phase 
 
Study Week 
 
0 
2 
4 
6 
8 
12 
16 
20 
24 
28 
32 
36 
40 
44 
48 
60 
72 
84 
96 
 
U1 
Visit Number 
-1 
0 
1 
2 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
13 
14 
15 
16 
17 
18 
U 
General Assessments 
 
Informed consent 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Randomization 
 
 
 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Medical history 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Lupus history 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Adverse events 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Concomitant 
medications 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Comprehensive 
physical 
examination 
x 
 
 
 
 
 
 
 
 
x 
 
 
 
 
 
x 
 
 
 
x 
 
Limited physical 
examination 
 
x 
x 
x 
x 
x 
x 
x 
x 
 
x 
x 
x 
x 
x 
 
x 
x 
x 
 
x 
Vital signs 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Study Drug Administration 
 
Diphenhydramine 
 
x 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Acetaminophen 
 
x 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Solumedrol 
 
x 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Rituximab  
 
x 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Cyclophosphamide  
 
x 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Belimumab2 
 
 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
 
 
 
 
 
Prednisone3 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
 
Clinical Laboratory Assessments 
 
Hematology 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Serum creatinine 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Serum chemistry 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Serum albumin 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Serum urea 
nitrogen 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Serum pregnancy 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Spot urine 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
24-hour urine 
x 
 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
 
 
 
x 
x 
Urinalysis  
x 
x 
 
x 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
STAT urine 
pregnancy 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
 
x 
 
ANA 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
x 
 
 
 
x 
 
HIV 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Hepatitis B  
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Hepatitis C 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Chest x-ray 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                          
1 U= unscheduled visit 
2 Belimumab administered only to the RCB group as outlined in section 3.1 
3 Taken daily. First dose will be administered the day following Visit 0. Methylprednisolone may be 
substituted for prednisone in equivalent doses, at the discretion of the investigator. 


Immune Tolerance Network  
CONFIDENTIAL 
Page 87 
 
Protocol ITN055AI 
Version 2.0 
October 9, 2015 
 
Study Week 
 
0 
2 
4 
6 
8 
12 
16 
20 
24 
28 
32 
36 
40 
44 
48 
60 
72 
84 
96 
 
U1 
Visit Number 
-1 
0 
1 
2 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
13 
14 
15 
16 
17 
18 
U 
Anti-dsDNA 
x 
x 
 
x 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
 
x 
C3, C4 
 
x 
 
x 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
CD19 
 
x 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
x 
x 
x 
x 
 
Anticardiolipin Ab 
(IgA, IgG, and 
IgM) 
 
x 
 
 
 
 
 
 
 
x 
 
 
 
 
 
x 
 
 
 
x 
 
Quantitative serum 
immunoglobulins 
(IgA, IgG, and 
IgM) 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
 
 
 
x 
Anti-ENA (anti-Sm 
and anti-RNP) 
 
x 
 
 
 
 
 
 
 
x 
 
 
 
 
 
x 
 
 
 
x 
 
QuantiFERON - 
TB Gold test4 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Lupus Assessments 
 
BILAG-2004 
 
x 
 
x 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
SELENA-SLEDAI 
 
x 
 
x 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
SLICC 
 
x 
 
 
 
 
 
 
 
x 
 
 
 
 
 
x 
 
x 
 
x 
 
Clinical Pathology Assessment 
 
Kidney biopsy5 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Mechanistic Laboratory Assessments6 
 
Whole blood 
autoreactive B cell 
frequency 
 
x 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
x 
x 
x 
x 
 
Whole blood flow 
cytometry panel 
staining 
 
x 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
x 
x 
x 
x 
 
Whole blood gene 
expression 
profiling 
 
x 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
x 
x 
x 
x 
 
Serum secreted 
cytokines 
 
x 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
x 
x 
x 
x 
 
Genotyping 
 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Antibody to John 
Cunningham virus 
 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Urine studies 
 
x 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
x 
x 
x 
x 
 
 
 
 
                                                          
4 PPD tuberculin test may be substituted for QuantiFERON – TB Gold test. 
5 If clinically indicated. 
6 Perform only when Hgb ≥ 8 g/dL at previous visit. 
 

SAP_001.pdf: 
 
Version:  0.5 
 
 
STATISTICAL ANALYSIS PLAN 
Final Version 1.0 
07 May 2018 
 
 
 
 
Rituximab Plus Cyclophosphamide Followed by Belimumab  
for the Treatment of Lupus Nephritis 
 
 
 
PROTOCOL NUMBER ITN055AI 
 
 
 
SPONSOR 
 
 
 
Division of Allergy, Immunology, and Transplantation 
National Institute of Allergy and Infectious Diseases – NIH 
5601 Fishers Lane 
Rockville, MD 20852 
Telephone:  (301) 496-5717 
Fax:  (301) 402-3573 
 
 
 
PREPARED BY 
 
Rho, Inc. 
6330 Quadrangle Drive 
Chapel Hill, NC 27517 
Telephone:  (919) 408-8000 
Fax:  (919) 408-0999 
 
 
 
 
 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 2 of 38 
DOCUMENT VERSION CONTROL 
Version Number 
Date 
Comments/Changes 
1.0 
07 May 2018 
Final 
 
 
 
 
 
 
 
 
 
 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 3 of 38 
APPROVALS 
Approved: 
 
Date: 
 
 
Betty Diamond, MD 
Protocol Chair 
 
 
 
 
Date: 
 
 
David Wofsy, MD 
Protocol Chair 
 
 
 
 
Date: 
 
 
Cynthia Aranow, MD 
Protocol Chair 
 
 
 
 
Date: 
 
 
Maria Dall’Era, MD 
Protocol Chair 
 
 
 
 
Date: 
 
 
Linna Ding, MD, PhD 
NIAID Medical Monitor 
 
 
 
 
Date: 
 
 
Dawn Smilek, MD, PhD 
ITN Clinical Trial Physician 
 
 
 
 
Date: 
 
 
William Barry, PhD 
Rho Scientist 
 
 
 
 
Date: 
 
 
Margie Byron, MStat 
Rho Statistician 
 
 
 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 4 of 38 
TABLE OF CONTENTS 
1. 
PROTOCOL SYNOPSIS .......................................................................................... 6 
2. 
INTRODUCTION .................................................................................................... 12 
3. 
GENERAL ANALYSIS AND REPORTING CONVENTIONS.................................. 13 
4. 
ANALYSIS SAMPLES ........................................................................................... 14 
5. 
STUDY SUBJECTS ............................................................................................... 16 
5.1 
Disposition of Subjects ................................................................................ 16 
5.2 
Demographic and Other Baseline Characteristics ....................................... 16 
6. 
STUDY OPERATIONS ........................................................................................... 17 
6.1 
Protocol Deviations ..................................................................................... 17 
6.2 
Treatment Adherence ................................................................................. 17 
6.2.1 
Rituximab/Cyclophosphamide/Solumedrol ......................................... 17 
6.2.2 
Prednisone ........................................................................................ 17 
6.2.3 
Belimumab ......................................................................................... 17 
7. 
ENDPOINT EVALUATION ..................................................................................... 19 
7.1 
Overview of Efficacy Analysis Methods ....................................................... 19 
7.1.1 
Multicenter Studies ............................................................................ 19 
7.1.2 
Assessment Time Windows ............................................................... 19 
7.1.3 
Summary of Primary and Secondary Efficacy Analysis Methods ....... 19 
7.2 
Primary Endpoint ........................................................................................ 20 
7.2.1 
Computation of the Primary Endpoint ................................................ 20 
7.2.2 
Primary Analysis of the Primary Endpoint .......................................... 21 
7.2.3 
Secondary Analyses of the Primary Endpoint .................................... 21 
7.3 
Secondary Endpoints and Analyses ............................................................ 21 
7.3.1 
Grade 3 or Higher Infectious Adverse Events .................................... 21 
7.3.2 
Hypogammaglobulinemia .................................................................. 22 
7.3.3 
B cells ................................................................................................ 23 
7.3.4 
Response to Treatment ..................................................................... 23 
7.3.5 
Treatment Failure .............................................................................. 25 
7.3.6 
Hypocomplementemia ....................................................................... 25 
7.3.7 
Anti-dsDNA ........................................................................................ 26 
7.3.8 
Non-renal Flares/BILAG ..................................................................... 27 
7.3.9 
Exploratory analyses ......................................................................... 27 
8. 
SAFETY EVALUATION ......................................................................................... 29 
8.1 
Overview of Safety Analysis Methods ......................................................... 29 
8.2 
Adverse Events ........................................................................................... 29 
8.3 
Deaths and Serious Adverse Events ........................................................... 30 
8.4 
Pregnancies ................................................................................................ 30 
8.5 
Clinical Laboratory Evaluation ..................................................................... 30 
8.6 
Vital Signs, Physical Findings, and Other Observations Related to Safety .. 31 
8.6.1 
Vital Signs .......................................................................................... 31 
8.6.2 
Physical Examinations ....................................................................... 31 
9. 
OTHER ANALYSES .............................................................................................. 32 
9.1 
Use of Medications ..................................................................................... 32 
9.2 
Medical History ........................................................................................... 32 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 5 of 38 
10. INTERIM ANALYSES AND DATA MONITORING ................................................. 33 
11. CHANGES TO THE ANALYSES PLANNED IN THE PROTOCOL ........................ 34 
11.1 
Analysis populations ................................................................................... 34 
12. REFERENCES ....................................................................................................... 35 
13. APPENDICES ........................................................................................................ 36 
13.1 
Study Flow Chart ........................................................................................ 36 
13.2 
Schedule of Events ..................................................................................... 37 
 
 
 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 6 of 38 
1. PROTOCOL SYNOPSIS 
Title 
Rituximab Plus Cyclophosphamide followed by Belimumab  
for the Treatment of Lupus Nephritis 
 
Short Title 
Rituximab and Belimumab for Lupus Nephritis 
Sponsor 
NIAID 
Conducted By 
Immune Tolerance Network 
Protocol Chairs  
Betty Diamond, MD; David Wofsy, MD; Cynthia Aranow, MD;  
Maria Dall’Era MD 
 
Accrual Objective 
40 participants 
Study Treatment 
Study treatment will be rituximab, cyclophosphamide (CTX), and 
Solumedrol. This treatment will be followed by prednisone and 
belimumab in one group, and by prednisone without belimumab in the 
other group. 
 
Study Design 
This trial will be conducted as a prospective randomized phase 2 open 
label multicenter study in individuals with active lupus nephritis age 18 
and older. There will be two treatment arms with 1:1 randomization of a 
total of 40 participants. 
During the treatment phase, all participants will receive infusions of 
Solumedrol 100mg, rituximab 1000mg, and CTX 750mg intravenously 
(IV) at week 0 and week 2. Prednisone 40 mg per day will be 
administered with a guided steroid taper to 10mg per day by week 12.  
Participants will be randomized at week 4 to either the 
Rituximab/Cyclophosphamide (RC) Group or the 
Rituximab/Cyclophosphamide/Belimumab (RCB) Group. 
The RC Group will be maintained on prednisone. The RCB Group will 
receive IV belimumab 10mg/kg at weeks 4, 6, 8, and then every 4 weeks 
through week 48 in addition to prednisone.  
During the tolerance assessment phase, intravenous study medication 
will be discontinued after week 48, and all participants will be 
maintained on prednisone through week 96 of the study. 
 
Study Duration 
Total study duration will be 200 weeks. The enrollment period for this 
study will be 104 weeks. Study participation period will be 96 weeks, 
which includes a treatment phase of 48 weeks and a tolerance assessment 
phase of 48 weeks. 
 
Primary Objective 
The primary objective of the study is to assess the safety of belimumab 
administration following treatment with rituximab and CTX, in terms of 
infectious adverse events. 
 
Primary Endpoint 
The primary endpoint is the proportion of participants who experience at 
least one Grade 3 or higher infectious adverse event at or prior to week 
48. 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 7 of 38 
Secondary 
Endpoints 
1. Proportion of participants who experience at least one Grade 3 or 
higher infectious adverse event at or prior to week 24, and at or prior 
to week 96. 
2. Proportion of participants with B cell reconstitution at week 24, 48, 
and 96, defined as the participant’s baseline B cell count, or the 
lower limit of normal, whichever is lower. 
3. Proportion of participants with Grade 4 hypogammaglobulinemia at 
or before week 24, 48, and 96. 
4. Proportion of participants with a complete response at week 24. 
Complete response is defined as meeting all of the following 
criteria: 
 Urine protein-to-creatinine ratio (UPCR) < 0.5, based on a 24-
hour collection. 
 Estimated glomerular filtration rate (eGFR) ≥120 ml/min/1.73m2 
calculated by the CKD-EPI formula or, if <120 ml/min/1.73m2, 
then >80% of eGFR at entry. 
 Prednisone dose tapered to 10 mg/day, or as specified in section 
5.5.2. 
5. Proportion of participants with an overall response (complete or 
partial response) at week 24. A partial response is defined as 
meeting all of the following criteria: 
 > 50% improvement in the UPCR from study entry, based on a 
24-hour collection. 
 Estimated glomerular filtration rate (eGFR) ≥120 ml/min/1.73m2 
calculated by the CKD-EPI formula or, if < 120 ml/min/1.73m2, 
then >80% of eGFR at entry. 
 Prednisone dose tapered to 10 mg/day, or as specified in section 
5.5.2. 
6. Proportion of participants with complete response at week 48. 
7. Proportion of participants with an overall response (complete or 
partial response) at week 48. 
8. Proportion of participants with complete response at week 96 
(cumulative complete response). 
9. Proportion of participants with sustained complete response at week 
96 (representing “clinical tolerance”). Sustained complete response 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 8 of 38 
is defined as a complete response measured at 48 and 96 weeks. 
10. Proportion of participants with an overall response (complete or 
partial response) at week 96. 
11. Proportion of participants with treatment failure at or before week 
24, 48, and 96, as defined by withdrawal from the protocol due to 
worsening nephritis, infection, or study medication toxicity.  
12. Frequency of non-renal flares at or before week 24, 48, and 96, 
defined by the British Isles Lupus Assessment Group (BILAG) 
criteria. 
13. Anti-dsDNA antibodies and C3, C4 levels at week 24, 48, and 96 
14. Frequency of the following specific AEs: 
 Any event leading to death. 
 Grade 2 or greater leukopenia or thrombocytopenia. 
 Premature ovarian failure.  
 Malignancy. 
 Venous thromboembolic event (deep venous thrombosis or 
pulmonary embolism). 
 Disease- or study medication-related event leading to 
hospitalization. 
 Infusion reactions (within 24 hours of infusion) that result in the 
cessation of further infusions (including cytokine-release allergic 
reaction). 
Inclusion Criteria 
1. Diagnosis of Systemic Lupus Erythematosus (SLE) by American 
College of Rheumatology (ACR) criteria or Systemic Lupus 
International Collaborating Clinics (SLICC) criteria. 
2. Positive antinuclear antibody (ANA) or positive anti-ds DNA test 
results at visit -1 or any time within 14 days before visit -1. 
3. Age 18 years or older. 
4. Active proliferative lupus nephritis, as defined by either of the 
following: 
a. Kidney biopsy documentation within the last 3 months of 
ISN/RPS proliferative nephritis:  Class III, Class IV, or Class V 
in combination with Class III or IV. 
b. Kidney biopsy documentation within the last 18 months of 
ISN/RPS proliferative nephritis:  Class III, Class IV, or Class V 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 9 of 38 
in combination with Class III or IV, associated with at least one 
of the following:  
i. Active urinary sediment as defined by any one of 
the following:  
a. >4 RBC/hpf in the absence of menses and 
infection; 
b. >5 WBC/hpf in the absence of infection; or  
c. cellular casts limited to RBC or WBC casts. 
ii. UPCR ≥3 based on a 24-hour collection at visit -1 
or any time within 14 days before visit -1. 
iii. Confirmed increase in UPCR compared to a prior 
UPCR determination within 3 months of study 
entry. An increase in proteinuria will be considered 
to be confirmed if present on 2 consecutive 
assessments, or if increase led to a change in 
treatment. Increase in UPCR is defined as: 
a. UPCR to >1 if prior UPCR was ≤0.2; 
b. UPCR >2 if prior UPCR was ≤1 but >0.2; 
c. UPCR >double the prior UPCR if prior 
UPCR was >1. 
5. UPCR >1 based on a 24-hour collection at visit -1 or any time 
within 14 days before visit -1. 
6. Ability to provide informed consent. 
Exclusion Criteria 
1. 
New onset lupus nephritis, defined as lupus nephritis for which the 
participant has not yet been treated with either mycophenolate 
mofetil or cyclophosphamide. 
2. 
Neutropenia (absolute neutrophil count <1500/mm3). 
3. Thrombocytopenia (platelets <50,000/mm3). 
4. Moderately severe anemia (Hgb <8 mg/dL). 
5. Positive QuantiFERON – TB Gold test results. PPD tuberculin test 
may be substituted for QuantiFERON – TB Gold test. 
6. Pulmonary fibrotic changes on chest radiograph consistent with prior 
healed tuberculosis. 
7. Active bacterial, viral, fungal, or opportunistic infections. 
8. Evidence of infection with human immunodeficiency virus (HIV), 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 10 of 38 
hepatitis B (as assessed by HBsAg and anti-HBc) or hepatitis C. 
9. Hospitalization for treatment of infections, or parenteral (IV or IM) 
antibacterials, antivirals, anti-fungals, or anti-parasitic agents within 
the past 60 days. 
10. Chronic infection that is currently being treated with suppressive 
antibiotic or antiviral therapy, including but not limited to 
tuberculosis, pneumocystis, cytomegalovirus, herpes simplex virus, 
herpes zoster, and atypical mycobacteria. 
11. History of significant infection or recurrent infection that, in the 
investigator’s opinion, places the participant at risk by participating 
in this study. 
12. Receipt of a live-attenuated vaccine within 3 months of study 
enrollment. 
13. End-stage renal disease (eGFR <20 mL/min/1.73m2) 
14. Concomitant malignancies or a history of malignancy, with the 
exception of adequately treated basal and squamous cell carcinoma 
of the skin, or carcinoma in situ of the cervix. 
15. History of transplantation.  
16. History of primary immunodeficiency. 
17. Pregnancy. 
18. Breastfeeding. 
19. Unwillingness to use an FDA-approved form of birth control 
(including but not limited to a diaphragm, an intrauterine device, 
progesterone implants or injections, oral contraceptives, the double-
barrier method, or a condom). 
20. Use of cyclophosphamide within the past 6 months. 
21. Use of anti-TNF medication, other biologic medications, or non-
biologic experimental therapeutic agents within the past 90 days, or 
5 half-lives prior to screening, whichever is greater. 
22. Intravenous immunoglobulin (IVIG), plasmapheresis, or 
leukopheresis within the past 90 days. 
23. Use of an investigational biologic agent within the past 6 months. 
24. Prior treatment with rituximab. 
25. Treatment with other biologic B cell therapy within the past 12 
months. 
26. Liver function test (aspartate aminotransferase [AST], alanine 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 11 of 38 
aminotransferase [ALT], or alkaline phosphatase) results that are ≥2 
times the upper limit of normal.  
27. Severe, progressive, or uncontrolled renal, hepatic, hematological, 
gastrointestinal, pulmonary, cardiac, or neurological disease, either 
related or unrelated to SLE, with the exception of active lupus 
nephritis (or, in the investigator’s opinion, any other concomitant 
medical condition that places the participant at risk by participating 
in this study). 
28. Comorbidities requiring corticosteroid therapy, including those 
which have required three or more courses of systemic 
corticosteroids within the previous 12 months. 
29. Current substance abuse or history of substance abuse within the past 
year. 
30. History of severe allergic or anaphylactic reactions to chimeric or 
fully human monoclonal antibodies.  
31. History of anaphylactic reaction to parenteral administration of 
contrast agents. 
32. Lack of peripheral venous access. 
33. History of severe depression or severe psychiatric condition. 
34. History of suicidal thoughts within the past 2 months or suicidal 
behavior within the past 6 months, or a significant suicide risk in the 
investigator’s opinion. 
35. Inability to comply with study and follow-up procedures. 
 


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2. INTRODUCTION 
This statistical analysis plan (SAP) only includes analyses related to the clinical 
endpoints outlined in the protocol.  Mechanistic analyses will be performed at the 
Immune Tolerance Network (ITN), and a separate analysis plan will be created to detail 
the planned analyses.  Relevant clinical data from the study will be submitted to the ITN 
Biomarker and Discovery Research (BDR) to augment the mechanistic analyses. 


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3. GENERAL ANALYSIS AND REPORTING CONVENTIONS 
The following analyses and reporting conventions will be used: 
 Randomized treatment groups: 
o Rituximab/Cyclophosphamide (RC) treatment arm refers to the subjects 
who are randomized to be maintained on prednisone from week 4 through 
week 96. 
o Rituximab/Cyclophosphamide/Belimumab (RCB) treatment arm refers to 
the subjects who are randomized to receive IV belimumab at weeks 4, 6, 8 
and then every 4 weeks through week 48 in addition to the prednisone 
maintenance.  After week 48, subjects in the RCB treatment arm are 
maintained on prednisone through week 96. 
 Categorical variables will be summarized using counts (n) and percentages (%) 
and will be presented in the form “n (%).”  Percentages will be rounded to one 
decimal place. 
 Numeric variables will be summarized using n, mean, standard deviation (SD), 
median, minimum (min), maximum (max).  The min/max will be reported at the 
same level of significant digits as original data.  The mean and median will be 
reported at one more significant digit than the precision of the data, and SD will 
be reported at two more significant digits than the precision of the data. 
 The median will be reported as the average of the two middle numbers if the 
dataset contains an even number of observations. 
 Test statistics including t and z test statistics will be reported to two decimal 
places.  
 P-values will be reported to three decimal places if greater than or equal to 0.001.  
If less than 0.001, the value will be reported as “<0.001.”  A p-value can be 
reported as “1.000” only if it is exactly 1.000 without rounding.  A p-value can be 
reported as “0.000” only if it is exactly 0.000 without rounding. 
If departures from these general conventions are present in the specific evaluations 
section of this SAP, then those conventions will take precedence over these general 
conventions.  
 


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4. ANALYSIS SAMPLES 
Modified intent to treat sample (MITT) will be defined as all randomized participants 
who receive study regimen, as defined below: 
 Receive 1 dose of Solumedrol 
 Receive 1 dose of rituximab 
 Receive 1 dose of cyclophosphamide (CTX) 
 Receive 1 dose of belimumab if in the RCB Group 
Any randomized subject who fails to meet any objectively measured entry criterion 
assessed prior to randomization will be excluded per the guidelines described for the “full 
analysis set” in ICH E9 Section V.5.2.1. 
There is one MITT analysis population, and it will be used to provide summary statistics 
and compare the treatment groups at each of the protocol time points (i.e. weeks 24, 48 
and 96). 
Per protocol samples (PP) will be defined as follows: 
PP24: Treated participants in the Modified ITT sample who receive study regimen 
through week 24 and meet the following criteria: 
 Receive 2 doses each of Solumedrol, rituximab, and CTX 
 Receive at least 80% of belimumab infusions if in the RCB Group 
This analysis population will be used to provide summary statistics and compare the 
treatment groups for the PP analysis at week 24. 
PP48: Treated participants in the PP24 sample who receive study regimen through week 
48 and meet the following criteria: 
 Receive at least 80% of belimumab infusions if in the RCB Group 
This analysis population may be different than the PP24 analysis population and will be 
used to provide summary statistics and compare the treatment groups for the PP analysis 
at week 48. 
PP96: Treated participants in the PP48 sample who receive study regimen through week 
96.  
This analysis population may be different than the PP24 and PP48 analysis populations 
and will be used to provide summary statistics and compare the treatment groups for the 
PP analysis at week 96. 
The Study Management Team will review deviations from the protocol in a blinded 
listing including, for example, violations of entry criteria, departures from assigned 
treatment regimen, or administration of study procedures outside the specified visit 
windows. The panel may exclude subjects with serious protocol deviations from the Per 
protocol samples.  
 


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Safety sample (SS) will be defined as all participants who receive at least one dose of 
study treatment. 
 


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5. STUDY SUBJECTS 
5.1 Disposition of Subjects 
The disposition of all enrolled subjects will be summarized in tables and listed. 
The numbers and percentages of subjects enrolled, randomized, in each analysis sample, 
and completing the treatment regimen, as well as reasons for early termination from the 
study will be presented by treatment group and overall.   For subjects discontinuing study 
treatment early, the reasons for discontinuing study treatment early will also be presented.  
A CONSORT diagram will be prepared to graphically display the disposition changes by 
treatment group throughout the phases of the study.  Disposition of all enrolled subjects 
will be listed by treatment group and subject. 
5.2 Demographic and Other Baseline Characteristics 
Summary descriptive statistics for baseline and demographic characteristics will be 
reported by treatment group and overall for the MITT sample.  Characteristics to be 
summarized include: 
 Demographics 
o Age  
o Race 
o Ethnicity 
o Sex 
o Body weight 
 Duration of lupus nephritis (i.e time from onset of lupus nephritis to screening 
visit) 
 Proportion of subjects with >1 year duration of lupus nephritis 
 Lupus nephritis class according to International Society of Nephrology/Renal 
Pathology Society (ISN/RPS) classification at screening 
 Presence of active non-renal lupus (i.e. classification of A, B or C in any non-
renal body system in BILAG 2004)  
 Baseline laboratory assessments 
o Urine protein to creatinine ratio (UPCR) from a 24-hour collection 
o Serum albumin 
o Serum creatinine 
o eGFR 
o B cell counts 
o IgG levels 
o Proportion of subjects with UPCR > 3 from a 24-hour collection 
o Proportion of subjects with IgG < 450 mg/dL 
o Proportion of subjects with C3 hypocomplementemia (see section 7.3.6) 
o Proportion of subjects with C4 hypocomplementemia (see section 7.3.6) 
o Proportion of subjects with positive anti-dsDNA (see section 7.3.7) 
Demographic and baseline characteristic data for all enrolled subjects will also be 
presented in a data listing by treatment group and subject. 


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6. STUDY OPERATIONS 
6.1 
Protocol Deviations 
The number of major protocol deviations, the number of each type of deviation, the 
number of site level deviations and the number of consented subjects with at least one 
deviation will be summarized over all sites. 
Protocol deviations will be sorted by site and subject, and listed with information such as 
type of deviation, date of occurrence, details of the deviation, steps taken to address the 
deviation, who identified the deviation, and whether the deviation met IRB reporting 
requirements. 
6.2 
Treatment Adherence 
Treatment adherence will be summarized for the MITT sample by treatment group and 
overall for rituximab, CTX and Solumedrol doses received during infusions administered 
prior to randomization.  Treatment adherence will also be summarized for the MITT 
sample in the RCB treatment arm for belimumab infusions received from week 4 through 
week 48.  The total number of infusions received by each subject will be calculated along 
with the percent of the expected infusions and total dose received for each study 
medication.  Prednisone dose taken by subjects at major time points will be summarized 
by treatment group at week 12 for the MITT sample, at week 24 for the MITT and PP24 
samples, at week 48 for the MITT and week 48 samples, and at week 96 for the MITT 
and PP96 samples.  The proportion of subjects who are taking 10mg/day or less of 
prednisone will be summarized by treatment group at week 12 for the MITT sample, at 
week 24 for the MITT and PP24 samples, at week 48 for the MITT and week 48 samples, 
and at week 96 for the MITT and PP96 samples.  Study drug administration data will be 
listed by treatment group and subject. 
6.2.1 Rituximab/Cyclophosphamide/Solumedrol 
Subjects will receive infusions by site personnel of Solumedrol 100mg, rituximab 
1000mg, and CTX 750mg intravenously (IV) at week 0 and week 2.   
The date and time of infusion, dose administered and information on missed infusions or 
dose reductions will be recorded by site staff at the time of infusion. 
6.2.2 Prednisone 
All enrolled subjects will self-administer oral doses of prednisone 40 mg/day for the first 
2 weeks, starting at week 0. Prednisone will then be tapered until study week 12 to a dose 
of 10 mg/day. This dose will be continued until week 48.  Between week 48 and week 96, 
prednisone may be further tapered. However, the rate of taper should not be greater than 
1 mg every month, and the dose should not be tapered below 5 mg/day. 
The start date, end date, dose administered and information on dose changes will be 
recorded by site staff in the dosing log. 
6.2.3 Belimumab 
Subjects randomized to the RCB treatment arm will receive infusions by site personnel of 
belimumab 10mg/kg at weeks 4, 6, 8, and then every 4 weeks through week 48. 


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The date and time of infusion, dose administered and information on missed infusions or 
dose reductions will be recorded by site staff at the time of infusion. 
 


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7. ENDPOINT EVALUATION 
7.1 
Overview of Efficacy Analysis Methods 
7.1.1 Multicenter Studies 
Study subjects were recruited from 14 study sites.  Study data will be analyzed as a 
whole. Because randomization was not stratified by clinical site, it will not be included as 
a covariate in the analyses. 
7.1.2 Assessment Time Windows 
Visit 0 (week 0) must occur within 21 days of visit –1 (screening visit). All other 
scheduled study visits should occur within the time limits specified below: 
Visits 1 (week 2) through visit 4 (week 8): ±2 days 
Visit 5 (week 12) through visit 14 (week 48): ±7 days 
Visit 15 (week 60) through visit 18 (week 96): ±14 days  
Randomized subjects who discontinue from the study treatment regimen, as described in 
section 5.6 of the protocol, will be asked to complete the early discontinuation visit (visit 
18) assessments.  Early discontinuation subjects will be asked to return for a follow-up 
assessment 30 days after the early discontinuation visit.  The subject will then be asked to 
complete the visits at week 24, 36, 48, 72, and 96, if these visits have not already 
occurred, for safety follow up. 
Data collected outside of the assessment time windows will not be excluded from the 
analyses. 
Unscheduled visits may also be performed throughout the study to document any new 
symptoms. The results captured in any unscheduled visit will not be included in summary 
displays by visit, but will be displayed in any subject level plots over time and in listings. 
Early discontinuation visits are recorded in the database as an unscheduled visit but will 
be handled differently than other unscheduled visits. Early discontinuation visit 
evaluations will be applied to the closest scheduled missed visit for summary displays but 
will be labeled as an early discontinuation visit in listings.  
7.1.3 Summary of Primary and Secondary Efficacy Analysis Methods 
Table 7-2 
Table of Endpoints and Analysis Methods 
Endpoint 
Time Points 
Analysis Samples 
Analysis Methods 
Primary Endpoint Analysis 
Proportion of subjects who 
experience at least one Grade 3 or 
higher infectious adverse event 
Week 48 
MITT, PP48 
 95% confidence intervals by 
treatment group using 
Clopper-Pearson (exact) 
method for binomial 
proportions 
 Logistic regression model 
on treatment group 


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Secondary Endpoints Analysis 
Proportion of subjects who 
experience at least one Grade 3 or 
higher infectious adverse event 
Weeks 24, 
96 
MITT, PP24, 
PP96 
Same as primary endpoint 
Proportion of subjects who 
experience at least one occurrence 
of Grade 4 hypogammaglobulinemia 
Weeks 24, 
48, 96 
MITT, PP24, 
PP48, PP96 
Same as primary endpoint 
Proportion of subjects with B cell 
reconstitution 
Weeks 24, 
48, 96 
MITT, PP24, 
PP48, PP96 
Same as primary endpoint 
Proportion of subjects who achieve 
a complete response 
Weeks 24, 
48, 96 
MITT, PP24, 
PP48, PP96 
Same as primary endpoint 
Proportion of subjects who achieve 
an overall response 
Weeks 24, 
48, 96 
MITT, PP24, 
PP48, PP96 
Same as primary endpoint 
Proportion of subjects who achieve 
a sustained complete response 
Week 96 
MITT, PP96 
Same as primary endpoint 
Proportion of subjects who 
experience treatment failure 
Weeks 24 
MITT 
Same as primary endpoint 
Week 48 
MITT, PP24 
Same as primary endpoint 
Week 96 
MITT, PP48 
Same as primary endpoint 
Proportion of subjects who have a 
negative anti-dsDNA result 
Weeks 24, 
48, 96 
MITT, PP24, 
PP48, PP96 
Same as primary endpoint 
Proportion of subjects who are 
hypocomplementemic 
Weeks 24, 
48, 96 
MITT, PP24, 
PP48, PP96 
Same as primary endpoint 
Frequency of non-renal flares 
Weeks 24, 
48, 96 
MITT, PP24, 
PP48, PP96 
 Pearson’s chi-square test by 
treatment group (or Fisher’s 
exact test by treatment group 
for small sample sizes) 
 
7.2 Primary Endpoint 
7.2.1 Computation of the Primary Endpoint 
The primary endpoint is the proportion of subjects who experience at least one Grade 3 or 
higher treatment-emergent infectious adverse event (G3IAE) at or prior to week 48.   
All adverse events (AEs) will be classified by system organ class and preferred term, 
according to the Medical Dictionary for Regulatory Activities [MedDRA] version 17.0.  
The severity of AEs will be classified using the National Cancer Institute’s (NCI’s) 
Common Toxicity Criteria for Adverse Events (CTCAE) version 4.03.  Each AE is 
entered on the electronic case report form (eCRF) once at the highest severity. AEs will 


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be collected from screening through study termination. Treatment-emergent AEs will be 
identified as those with an onset date on or after the first dose of study medication as well 
as those with onset before first dose but that continued and worsened in severity after first 
dose.  If the start of the AE in relation to the start of study medication cannot be 
established (e.g., the start date for the AE is missing), then the AE will be considered 
treatment-emergent.   
The study team will review the MedDRA body systems and preferred terms of all Grade 
3 or higher adverse events to determine if they are infectious adverse events.   
7.2.2 Primary Analysis of the Primary Endpoint 
The primary analysis for the primary endpoint will be performed on the MITT sample 
and is designed to provide point estimates and confidence intervals for the proportion of 
subjects in each treatment arm who experience at least one Grade 3 or higher treatment-
emergent infectious adverse event (G3IAE) at or prior to week 48. 
The 95% confidence interval bounds for the proportion estimates in each treatment group 
will be calculated using the Clopper-Pearson (exact) method for binomial proportions. 
7.2.3 Secondary Analyses of the Primary Endpoint 
The primary analysis method described above will be repeated using the PP48 sample, if 
different from the MITT sample. 
Additional analyses will be performed to compare the proportions of subjects between the 
two treatment arms by a logistic regression model with an indicator of whether the 
subject experienced at least one G3IAE as the dependent variable and treatment group as 
the independent variable.  The logistic regression analysis will be performed on the MITT 
and PP48 samples. 
The confidence intervals and logistic regression analyses will be repeated on the 
proportion of subjects who experience at least one post-randomization G3IAE at or prior 
to week 48.  Post-randomization AEs are defined as those occurring on or after the 
subject’s week 4 visit.  The analyses on the proportions of subjects who experience at 
least one post-randomization G3IAE at or prior to week 48 will be performed on the 
MITT and PP48 samples.  
7.3 Secondary Endpoints and Analyses 
The secondary analyses will support the primary analysis by providing a deeper 
understanding of events. P-values for all inferential analyses will be presented as a 
description of strength of evidence of relationships rather than tests of hypotheses. As 
such, no corrections for multiplicity are planned.   
Listings will be prepared for all efficacy assessments with the subjects in the MITT 
sample. All efficacy listings will be sorted in order of treatment group, subject identifier, 
and time of assessment (e.g., visit, time, and/or event). 
7.3.1 Grade 3 or Higher Infectious Adverse Events 
In addition to the primary and secondary analyses for the primary endpoint, the following 
analyses on G3IAEs are planned: 


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 The proportion of subjects who experienced at least one G3IAE at or prior to 
week 24 will be analyzed using a logistic regression model similar to the one used 
in the primary endpoint analysis.  The 95% confidence interval bounds for the 
proportion estimates in each treatment group will also be calculated using the 
Clopper-Pearson (exact) method.  The week 24 analysis will be performed on the 
MITT and PP24 samples.  The analyses for week 24 will also be repeated for 
week 96 using the MITT and PP96 samples. 
 The proportion of subjects who experienced at least one post-randomization 
G3IAE at or prior to week 24 will be analyzed using a logistic regression model 
similar to the one used in the primary endpoint analysis.  The 95% confidence 
interval bounds for the proportion estimates in each treatment group will also be 
calculated using the Clopper-Pearson (exact) method.  The week 24 analysis will 
be performed on the MITT and PP24 samples.  The analyses for week 24 will also 
be repeated for week 96 using the MITT and PP96 samples. 
7.3.2 Hypogammaglobulinemia 
Hypogammaglobulinemia will be assessed throughout the subject’s study participation.  
Blood samples will be collected from subjects at every visit to assess IgG levels.  An 
adverse event of Grade 4 hypogammaglobulinemia will be reported by the site if a 
subject has an IgG test result < 300 mg/dL that is associated with a G3IAE.  The 
following analyses are planned:   
 The proportion of subjects who experienced at least one event of Grade 4 
hypogammaglobulinemia at or prior to week 24 will be analyzed using a logistic 
regression model similar to the one used in the primary endpoint analysis.  The 
95% confidence interval bounds for the proportion estimates in each treatment 
group will also be calculated using the Clopper-Pearson (exact) method.  The 
week 24 analysis will be performed on the MITT and PP24 samples.  The 
analyses for week 24 will be repeated for week 48 using the MITT and PP48 
samples, and at week 96 using the MITT and PP96 samples. 
 IgG level at week 24 will be analyzed using an analysis of covariance model 
(ANCOVA) with the IgG level as the dependent variable, urine protein-to-
creatinine ratio (UPCR) based on a 24-hour collection at week 24 as the 
independent variable and treatment group as a covariate.  The week 24 analysis 
will be performed on the MITT and PP24 samples.  The analyses for week 24 will 
be repeated for week 48 using the MITT and PP48 samples, and at week 96 using 
the MITT and PP96 samples.  
 IgG level at week 24 will be plotted against the 24-hour UPCR at week 24 by 
treatment group for the MITT and PP24 samples.  The figures for week 24 will be 
repeated for week 48 using the MITT and PP48 samples, and at week 96 using the 
MITT and PP96 samples. 
 


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7.3.3 B cells 
Blood samples will be collected from subjects at weeks 0, 12, 24, 36, 48, 60, 72, 84 and 
96 to assess B cell levels.  B cell reconstitution is defined as a B cell count that is greater 
than or equal to the subject’s baseline B cell count, or the lower limit of normal for the 
laboratory test, whichever is lower.  The following analyses are planned: 
 The proportion of subjects who achieved B cell reconstitution at week 24 will be 
analyzed using a logistic regression model similar to the one used in the primary 
endpoint analysis.  The 95% confidence interval bounds for the proportion 
estimates in each treatment group will also be calculated using the Clopper-
Pearson (exact) method.  The week 24 analysis will be performed on the MITT 
and PP24 samples.  The analyses for week 24 will be repeated for week 48 using 
the MITT and PP48 samples, and at week 96 using the MITT and PP96 samples. 
 B cell count at week 24 will be analyzed using an analysis of covariance model 
(ANCOVA) with the B cell count as the dependent variable, IgG level at week 24 
as the independent variable and treatment group as a covariate.  The week 24 
analysis will be performed on the MITT and PP24 samples.  The analyses for 
week 24 will be repeated for week 48 using the MITT and PP48 samples, and at 
week 96 using the MITT and PP96 samples.  
 B cell count at week 24 will be plotted against the IgG level at week 24 by 
treatment group for the MITT and PP24 samples.  The figures for week 24 will be 
repeated for week 48 using the MITT and PP48 samples, and at week 96 using the 
MITT and PP96 samples. 
  
 
7.3.4 Response to Treatment 
Response to treatment will be assessed at screening (visit -1) and weeks 12, 24, 36, 48 
and 96.   
Complete response is defined as meeting all of the following criteria: 
 Urine protein-to-creatinine ratio (UPCR) < 0.5, based on a 24-hour collection 
 Estimated glomerular filtration rate (eGFR) ≥120 ml/min/1.73m2 calculated by 
the CKD-EPI formula  (Levey, et al., 2009) or, if <120 ml/min/1.73m2, then 
>80% of eGFR at screening. 
 Prednisone dose tapered to 10 mg/day, or as specified in section 5.5.2 of the 
protocol 
Overall response is defined as meeting all of the following criteria: 
 > 50% improvement in the UPCR from screening, based on a 24-hour collection 
 Estimated glomerular filtration rate (eGFR) ≥120 ml/min/1.73m2 calculated by 
the CKD-EPI formula  (Levey, et al., 2009) or, if <120 ml/min/1.73m2, then 
>80% of eGFR at screening. 


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 Prednisone dose tapered to 10 mg/day, or as specified in section 5.5.2 of the 
protocol 
Sustained complete response is defined as achieving complete response at both week 48 
and week 96 
Partial response is defined as meeting the criteria for overall response, but not meeting 
the criteria for complete response. 
Non-response is defined as not meeting the overall response criteria. 
The following analyses are planned: 
 The proportion of subjects who achieved complete response at week 24 will be 
analyzed using a logistic regression model similar to the one used in the primary 
endpoint analysis.  The 95% confidence interval bounds for the proportion 
estimates in each treatment group will also be calculated using the Clopper-
Pearson (exact) method.  The week 24 analysis will be performed on the MITT 
and PP24 samples.  The analyses for week 24 will be repeated for week 48 using 
the MITT and PP48 samples, and at week 96 using the MITT and PP96 samples. 
 The proportion of subjects who achieved overall response at week 24 will be 
analyzed using a logistic regression model similar to the one used in the primary 
endpoint analysis.  The 95% confidence interval bounds for the proportion 
estimates in each treatment group will also be calculated using the Clopper-
Pearson (exact) method.  The week 24 analysis will be performed on the MITT 
and PP24 samples.  The analyses for week 24 will be repeated for week 48 using 
the MITT and PP48 samples, and at week 96 using the MITT and PP96 samples. 
 
 The proportion of subjects who achieved sustained complete response at week 96 
will be analyzed using a logistic regression model similar to the one used in the 
primary endpoint analysis.  The 95% confidence interval bounds for the 
proportion estimates in each treatment group will also be calculated using the 
Clopper-Pearson (exact) method.  The week 96 analysis will be performed on the 
MITT and PP96 samples.  
 The numbers and percentages of subjects who achieved complete response and of 
subjects who achieved an overall response at week 24 will be presented by race 
and treatment group on the MITT and PP24 samples.  The analyses for week 24 
will be repeated for week 48 using the MITT and PP48 samples, and at week 96 
using the MITT and PP96 samples. 
 The numbers and percentages of subjects who achieved complete response , 
partial response and non-response at week 24 will be analyzed using a Fisher’s 
exact test by treatment group on the MITT and PP24 samples.  The analyses for 
week 24 will be repeated for week 48 using the MITT and PP48 samples, and at 
week 96 using the MITT and PP96 samples. 
 


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7.3.5 Treatment Failure 
Subjects may be discontinued from the protocol treatment regimen at any point during 
the study if any of the criteria for treatment discontinuation specified in section 5.6 of the 
protocol are met.   
Treatment failure is defined as discontinuation from the protocol treatment regimen due 
to worsening nephritis, infection or study medication toxicity.  The Study Management 
Team will review treatment discontinuation reasons in a blinded listing to determine 
which treatment discontinuation reasons are indicative of renal treatment failure or non-
renal treatment failure.   
The following analyses are planned: 
 The proportion of subjects who met the criteria for treatment failure at or prior to 
week 24 will be analyzed using a logistic regression model similar to the one used 
in the primary endpoint analysis.  The 95% confidence interval bounds for the 
proportion estimates in each treatment group will also be calculated using the 
Clopper-Pearson (exact) method.  The week 24 analysis will be performed on the 
MITT sample.  The analyses for week 24 will be repeated for week 48 using the 
MITT sample, and at week 96 using the MITT and PP96 samples. 
 The proportion of subjects who met the criteria for renal treatment failure at or 
prior to week 24 will be analyzed using a logistic regression model similar to the 
one used in the primary endpoint analysis.  The 95% confidence interval bounds 
for the proportion estimates in each treatment group will also be calculated using 
the Clopper-Pearson (exact) method.  The week 24 analysis will be performed on 
the MITT sample.  The analyses for week 24 will be repeated for week 48 using 
the MITT sample, and at week 96 using the MITT and PP96 samples. 
 The proportion of subjects who met the criteria for non-renal treatment failure at 
or prior to week 24 will be analyzed using a logistic regression model similar to 
the one used in the primary endpoint analysis.  The 95% confidence interval 
bounds for the proportion estimates in each treatment group will also be 
calculated using the Clopper-Pearson (exact) method.  The week 24 analysis will 
be performed on the MITT sample.  The analyses for week 24 will be repeated for 
week 48 using the MITT sample, and at week 96 using the MITT and PP96 
samples. 
 
7.3.6 Hypocomplementemia 
Blood samples will be collected from subjects at weeks 0, 4 and every visit from week 8 
through 96 to assess levels of C3 and C4.  A subject will be classified as having 
hypocomplementemia for C3 if the C3 level is lower than the lower limit of normal for 
the laboratory test.  A subject will be classified as having hypocomplementemia for C4 if 
the C4 level is lower than the lower limit of normal for the laboratory test.  The following 
analyses are planned: 
 The proportion of subjects who are hypocomplementemic for C3 at week 24 will 
be analyzed using a logistic regression model similar to the one used in the 


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primary endpoint analysis.  The 95% confidence interval bounds for the 
proportion estimates in each treatment group will also be calculated using the 
Clopper-Pearson (exact) method.  The week 24 analysis will be performed on the 
MITT and PP24 samples.  The analyses for week 24 will be repeated for week 48 
using the MITT and PP48 samples, and at week 96 using the MITT and PP96 
samples. 
 The proportion of subjects who are hypocomplementemic for C4 at week 24 will 
be analyzed using a logistic regression model similar to the one used in the 
primary endpoint analysis.  The 95% confidence interval bounds for the 
proportion estimates in each treatment group will also be calculated using the 
Clopper-Pearson (exact) method.  The week 24 analysis will be performed on the 
MITT and PP24 samples.  The analyses for week 24 will be repeated for week 48 
using the MITT and PP48 samples, and at week 96 using the MITT and PP96 
samples. 
 The proportion of subjects who are not hypocomplementemic for C3 at week 24, 
out of subjects who were hypocomplementemic for C3 at baseline, will be 
analyzed using a logistic regression model similar to the one used in the primary 
endpoint analysis.  The 95% confidence interval bounds for the proportion 
estimates in each treatment group will also be calculated using the Clopper-
Pearson (exact) method.  The week 24 analysis will be performed on the MITT 
and PP24 samples.  The analyses for week 24 will be repeated for week 48 using 
the MITT and PP48 samples, and at week 96 using the MITT and PP96 samples. 
 The proportion of subjects who are not hypocomplementemic for C4 at week 24, 
out of subjects who were hypocomplementemic for C4 at baseline, will be 
analyzed using a logistic regression model similar to the one used in the primary 
endpoint analysis.  The 95% confidence interval bounds for the proportion 
estimates in each treatment group will also be calculated using the Clopper-
Pearson (exact) method.  The week 24 analysis will be performed on the MITT 
and PP24 samples.  The analyses for week 24 will be repeated for week 48 using 
the MITT and PP48 samples, and at week 96 using the MITT and PP96 samples. 
 The proportion of subjects who are not hypocomplementemic for C3 and C4 at 
week 24, out of subjects who were hypocomplementemic for C3 or C4 at 
baseline, will be analyzed using a logistic regression model similar to the one 
used in the primary endpoint analysis.  The 95% confidence interval bounds for 
the proportion estimates in each treatment group will also be calculated using the 
Clopper-Pearson (exact) method.  The week 24 analysis will be performed on the 
MITT and PP24 samples.  The analyses for week 24 will be repeated for week 48 
using the MITT and PP48 samples, and at week 96 using the MITT and PP96 
samples. 
7.3.7 Anti-dsDNA 
Blood samples will be collected from subjects at weeks 0, 4 and every visit from week 8 
through 96 to assess levels of anti-dsDNA.  A subject will be classified as having 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 27 of 38 
negative anti-dsDNA if the test result is within normal range.  The following analyses are 
planned: 
 The proportion of subjects who have a negative anti-dsDNA result at week 24 
will be analyzed using a logistic regression model similar to the one used in the 
primary endpoint analysis.  The 95% confidence interval bounds for the 
proportion estimates in each treatment group will also be calculated using the 
Clopper-Pearson (exact) method.  The week 24 analysis will be performed on the 
MITT and PP24 samples.  The analyses for week 24 will be repeated for week 48 
using the MITT and PP48 samples, and at week 96 using the MITT and PP96 
samples. 
 The proportion of subjects who have a negative anti-dsDNA result at week 24, out 
of subjects who had a positive anti-dsDNA result at baseline, will be analyzed 
using a logistic regression model similar to the one used in the primary endpoint 
analysis.  The 95% confidence interval bounds for the proportion estimates in 
each treatment group will also be calculated using the Clopper-Pearson (exact) 
method.  The week 24 analysis will be performed on the MITT and PP24 samples.  
The analyses for week 24 will be repeated for week 48 using the MITT and PP48 
samples, and at week 96 using the MITT and PP96 samples. 
7.3.8 Non-renal Flares/BILAG 
British Isles Lupus Assessment Group (BILAG) assessments will be evaluated at weeks 
0, 4 and every visit from week 8 through 96.  A non-renal flare is defined as any new “A” 
finding in a non-renal organ system according to the BILAG 2004 guidelines  (Isenberg, 
et al., 2005) that occurs after week 0.  The BILAG “A” finding represents a significant 
increase in, or new manifestation of, lupus disease activity.  The following analyses are 
planned: 
 The frequency of non-renal flares at or prior to week 24 will be analyzed using a 
Pearson’s chi-square test by treatment group.  If the number of non-renal flares at 
or prior to week 24 is small, Fisher’s exact test will be used in place of the 
Pearson’s chi-square test.  The week 24 analysis will be performed on the MITT 
and PP24 samples.  The analyses for week 24 will be repeated for week 48 using 
the MITT and PP48 samples, and at week 96 using the MITT and PP96 samples. 
7.3.9 Exploratory analyses 
Additional exploratory analyses are planned to assess renal status. 
  
1. UPCR < 0.8, based on a 24-hour collection 
The following analyses are planned: 
 The proportion of subjects who achieved UPCR <0.8 at week 48 will be analyzed 
using a logistic regression model similar to the one used in the primary endpoint 
analysis.  The 95% confidence interval bounds for the proportion estimates in 
each treatment group will also be calculated using the Clopper-Pearson (exact) 
method.  The week 48 analysis will be performed on the MITT and PP48 samples.   


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 28 of 38 
2. Percent change in UPCR from screening, based on a 24-hour collection 
The following analyses are planned: 
 The percent change in UPCR from screening, based on a 24-hour collection will 
be summarized at week 24 for the MITT and PP24 samples, at week 48 for the 
MITT and PP48 samples, and at week 96 for the MITT and PP96 samples.   
 
 
 
 
 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 29 of 38 
8. SAFETY EVALUATION 
8.1 Overview of Safety Analysis Methods 
All safety analyses will be carried out using the safety sample defined in Section 4 unless 
otherwise noted.  Missing safety information will not be imputed.  These analyses will 
not be stratified by site.   
Listings will be prepared for all safety assessments with the subjects in the safety sample. 
All safety listings will be sorted in order of treatment group, subject identifier, and time 
of assessment (e.g., visit, time, and/or event). 
8.2 Adverse Events 
All AEs will be classified by system organ class and preferred term, according to the 
Medical Dictionary for Regulatory Activities (MedDRA) version 17.0.  The severity of 
AEs will be classified using the National Cancer Institute’s (NCI’s) Common Toxicity 
Criteria for Adverse Events (CTCAE) version 4.03.  Each AE is entered on the electronic 
case report form (eCRF) once at the highest severity. AEs will be collected from 
screening through study termination. Treatment-emergent AEs will be identified as those 
with an onset date on or after the first dose of study medication as well as those with 
onset before first dose but that continued and worsened in severity after first dose.  If the 
start of the AE in relation to the start of study medication cannot be established (e.g., the 
start date for the AE is missing), then the AE will be considered treatment-emergent.  All 
data tabulations will be of only treatment-emergent events while non-treatment-emergent 
AEs will be included in the listings.  
An overall summary table will present the number of events and the number and 
percentage of subjects having at least one event in the following categories by treatment 
group and overall for treatment-emergent AEs through the end of treatment.  End of 
treatment for AE summaries is defined as 30 days after the date the subject discontinues 
the study treatment regimen. : 
 AEs 
 AEs indicated as serious 
 AEs that lead to study drug discontinuation 
 AEs that were reported as being related to a study drug 
 AEs reported by severity 
An additional overall summary table will present post-randomization AEs for the above 
categories through the end of treatment. 
An additional overall summary table will present post-treatment AEs for the above 
categories.   Post-treatment AEs are defined as AEs with an initiation date after the end of 
treatment. 
Any treatment-emergent AEs that are classified in the following categories will be 
considered AEs of interest: 
 Any event leading to death (Grade 5) 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 30 of 38 
 Grade 2 or greater leukopenia or thrombocytopenia 
 Premature ovarian failure 
 Malignancy 
 Venous thromboembolic event (deep venous thrombosis or pulmonary embolism) 
 Disease- or study medication-related event leading to hospitalization 
 Infusion reactions (within 24 hours of infusion) that result in the cessation of 
further infusions (including cytokine-release allergic reaction) 
For AEs of interest, the number of events and the number and percentage of subjects 
having at least one event at or prior to week 24 for each category will be summarized by 
treatment group and overall.  Additional summary tables of AEs of interest will also be 
presented for events at or prior to week 48, and for events at or prior to week 96. 
In addition, AEs classified by MedDRA system organ class and preferred term will be 
summarized by treatment group and overall for each of the following: 
 All AEs 
 AEs by severity 
 AEs by relationship to study drug 
Separate data listings will be provided for treatment-related AEs and AEs leading to 
study drug discontinuation. 
8.3 Deaths and Serious Adverse Events  
Serious adverse events (SAEs) will be listed by treatment group and subject. If any 
subjects die, a listing will be created and will include the primary cause of death and time 
to death. 
8.4 Pregnancies 
Pregnancies that occurred in enrolled subjects during study participation will be listed by 
treatment group and subject.  The listing will include date of last menstrual period, 
expected date of delivery, and date and type of pregnancy outcome. 
8.5 Clinical Laboratory Evaluation 
Clinical laboratory measurements include serum chemistry, hematology, anti-dsDNA, 
ANA, complements, B cells, anticardiolipin antibodies, quantitative serum 
immunoglobulins, anti-ENA, 24-hour urine chemistry, spot urine chemistry, and 
urinalysis.  Results will be converted to standardized units where possible.   
The following analyses are planned: 
 Laboratory data will be plotted by treatment group for the Safety sample to show 
patterns over time.  Summary statistics including 25th percentile, median, and 75th 
percentile will be plotted for each visit by treatment group.  Lines connecting 
individual subject results from subjects with grade 2 or higher values will be 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 31 of 38 
overlaid on each figure. For lab results that are not gradable, results from subjects 
with values outside of 2 *upper limit of normal or 0.5*lower limit of normal will 
be overlaid. Tests with qualitative results (such as “present” or “positive”) will 
not be plotted.    
 Laboratory data will be plotted by treatment group for the MITT sample to show 
patterns over time.  Summary statistics including 25th percentile, median, and 75th 
percentile will be plotted for each visit by treatment group.  Lines connecting 
individual subject results from subjects with grade 2 or higher values will be 
overlaid on each figure. For lab results that are not gradable, results from subjects 
with values outside of 2 *upper limit of normal or 0.5*lower limit of normal will 
be overlaid. Tests with qualitative results (such as “present” or “positive”) will 
not be plotted.  Data presented in the figures will be censored after the subject has 
been discontinued from study treatment regimen. 
 Change in laboratory results from baseline at each laboratory collection visit will 
be summarized by treatment group and overall for the Safety and MITT samples. 
8.6 Vital Signs, Physical Findings, and Other Observations Related to 
Safety 
8.6.1 Vital Signs 
Vital sign results will be plotted by treatment group to show patterns over time. Summary 
statistics including 25th percentile, median, and 75th percentile will be plotted for each 
visit. Lines connecting individual subject results from subjects with grade 2 or higher 
values will be overlaid on each figure. Vital signs collected during infusions will be 
presented in a separate listing by treatment group, subject and time point. 
8.6.2 Physical Examinations 
Physical examination results of normal, abnormal, and not done will be summarized as 
frequencies and percentages by body system and visit by treatment group and overall.  
Body systems classified as abnormal in the physical exams will be listed.  


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 32 of 38 
9. OTHER ANALYSES 
9.1 Use of Medications 
Medications will be coded according to the World Health Organization (WHO) Drug 
Dictionary (version V2014.01). The number and percentage of subjects receiving prior 
and concomitant medications will be presented overall and by medication class.  When 
reporting the number of subjects receiving the medication, a subject will only be counted 
once if they ever received the medication within the medication class.  Percentages will 
be based on the number of subjects in the safety sample.  Concomitant medications will 
be presented in a data listing and prohibited medications will be flagged. Medications that 
were started prior to week 0 will be denoted with an asterisk. 
9.2 Medical History 
Body systems classified as abnormal in the medical history eCRF will be listed by 
treatment group, subject and body system.   
 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 33 of 38 
10. INTERIM ANALYSES AND DATA MONITORING 
The progress of the study will be monitored by the Autoimmune Data and Safety 
Monitoring Board (DSMB).  The Autoimmune DSMB will be chartered to review safety 
data and to make recommendations regarding continuation, termination, or modification 
of the study.  The DSMB will formally review the safety data at least yearly.  The 
discontinuation of study treatment will also be periodically reported to the DSMB.  
In addition, safety data will be reviewed by the DSMB when an event occurs that is of 
sufficient concern to the National Institute of Allergy and Infectious Diseases (NIAID) 
medical monitor or protocol chair to warrant review, or when an event occurs that could 
contribute to a predefined stopping rule specified in the protocol.  


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 34 of 38 
11. CHANGES TO THE ANALYSES PLANNED IN THE PROTOCOL 
11.1 Analysis populations 
The definition for Per protocol 96 sample (PP96) was modified from the definition in 
protocol version 2.0.  The definition of PP96 in the protocol is: 
PP96: Treated participants in the PP48 sample who continue in the study beyond 48 
weeks. 
The definition for the PP96 sample was revised so that it includes subjects who complete 
the full study on the study treatment regimen, instead of subjects who continue on the 
study treatment regimen beyond week 48.  The revised definition for PP96 sample in this 
Statistical Analysis Plan is: 
PP96: Treated participants in the PP48 sample who receive study regimen through week 
96. 


Immune Tolerance Network 
 
Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 35 of 38 
12. REFERENCES 
Isenberg, D. A., Rahman, A., Allen, E., Farewell, V., Akil, M., Bruce, I. N., et al. (2005). 
BILAG 2004. Development and initial validation of an updated version of the 
British Isles Lupus Assessment Group's disease activity index for patients with 
systemic lupus erythematosus. Rheumatology (Oxford, England), 902-6. 
Levey, A. S., Stevens, L. A., Schmid, C. H., Zhang, Y. L., Castro, A. F., Feldman, H. I., 
et al. (2009). A new equation to estimate glomerular filtration rate. Annals of 
internal medicine, 604-12. 
 
 
 
 
 


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Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 36 of 38 
13. APPENDICES 
13.1 Study Flow Chart 
 
Participants (age > 18 years) with active lupus nephritis
Week 0 and Week 2:
 
Solumedrol (100 mg) IV
 
Rituximab (1000 mg) IV
 
Cyclophosphamide (750 mg) IV
 
Prednisone (40 mg/day; taper to 10 mg/day by week 12)
Randomization
Week 4
RC Group
 
Prednisone taper to 10 mg/day by week 12
 
Continue prednisone 10 mg/day to week 96
RCB Group
 
Belimumab (10 mg/kg IV) at weeks 4, 6, 8, 
and every 4 weeks to week 48
 
Prednisone taper to 10 mg/day by week 12
 
Continue prednisone 10 mg/day to week 96 
 
 
 
 
 
 


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Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 37 of 38 
13.2 Schedule of Events 
Study Week 
 
0 
2 
4 
6 
8 
12 
16 
20 
24 
28 
32 
36 
40 
44 
48 
60 
72 
84 
96 
 
U1 
Visit Number 
-1 
0 
1 
2 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
13 
14 
15 
16 
17 
18 
U 
General Assessments 
 
Informed consent 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Randomization 
 
 
 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Medical history 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Lupus history 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Adverse events 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Concomitant 
medications 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Comprehensive 
physical 
examination 
x 
 
 
 
 
 
 
 
 
x 
 
 
 
 
 
x 
 
 
 
x 
 
Limited physical 
examination 
 
x 
x 
x 
x 
x 
x 
x 
x 
 
x 
x 
x 
x 
x 
 
x 
x 
x 
 
x 
Vital signs 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Study Drug Administration 
 
Diphenhydramine 
 
x 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Acetaminophen 
 
x 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Solumedrol 
 
x 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Rituximab  
 
x 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Cyclophosphamide  
 
x 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Belimumab2 
 
 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
 
 
 
 
 
Prednisone3 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
 
Clinical Laboratory Assessments 
 
Hematology 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Serum creatinine 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Serum chemistry 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Serum albumin 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Serum urea 
nitrogen 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Serum pregnancy 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Spot urine 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
24-hour urine 
x 
 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
 
 
 
x 
x 
Urinalysis  
x 
x 
 
x 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
STAT urine 
pregnancy 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
 
x 
 
ANA 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
x 
 
 
 
x 
 
HIV 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Hepatitis B  
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Hepatitis C 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Chest x-ray 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                 
1 U= unscheduled visit 
2 Belimumab administered only to the RCB group as outlined in section 3.1 
3 Taken daily. First dose will be administered the day following Visit 0. Methylprednisolone may be 
substituted for prednisone in equivalent doses, at the discretion of the investigator. 


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Statistical Analysis Plan 
Protocol No. ITN055AI CALIBRATE 
 
07 May 2018 
Version:  1.0 
 
Page 38 of 38 
Study Week 
 
0 
2 
4 
6 
8 
12 
16 
20 
24 
28 
32 
36 
40 
44 
48 
60 
72 
84 
96 
 
U1 
Visit Number 
-1 
0 
1 
2 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
13 
14 
15 
16 
17 
18 
U 
Anti-dsDNA 
x 
x 
 
x 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
 
x 
C3, C4 
 
x 
 
x 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
CD19 
 
x 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
x 
x 
x 
x 
 
Anticardiolipin Ab 
(IgA, IgG, and 
IgM) 
 
x 
 
 
 
 
 
 
 
x 
 
 
 
 
 
x 
 
 
 
x 
 
Quantitative serum 
immunoglobulins 
(IgA, IgG, and 
IgM) 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
 
 
 
x 
Anti-ENA (anti-Sm 
and anti-RNP) 
 
x 
 
 
 
 
 
 
 
x 
 
 
 
 
 
x 
 
 
 
x 
 
QuantiFERON - 
TB Gold test4 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Lupus Assessments 
 
BILAG-2004 
 
x 
 
x 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
SELENA-SLEDAI 
 
x 
 
x 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
SLICC 
 
x 
 
 
 
 
 
 
 
x 
 
 
 
 
 
x 
 
x 
 
x 
 
Clinical Pathology Assessment 
 
Kidney biopsy5 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Mechanistic Laboratory Assessments6 
 
Whole blood 
autoreactive B cell 
frequency 
 
x 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
x 
x 
x 
x 
 
Whole blood flow 
cytometry panel 
staining 
 
x 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
x 
x 
x 
x 
 
Whole blood gene 
expression 
profiling 
 
x 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
x 
x 
x 
x 
 
Serum secreted 
cytokines 
 
x 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
x 
x 
x 
x 
 
Genotyping 
 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Antibody to John 
Cunningham virus 
 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Urine studies 
 
x 
 
 
 
 
x 
 
 
x 
 
 
x 
 
 
x 
x 
x 
x 
x 
 
 
 
                                                 
4 PPD tuberculin test may be substituted for QuantiFERON – TB Gold test. 
5 If clinically indicated. 
6 Perform only when Hgb ≥ 8 g/dL at previous visit.