Conditions: HIV Kidney Transplant Liver Transplant
Allocation: NA | Intervention model: SINGLE_GROUP
Enrollment: 10
Healthy volunteers: no

Brief summary:
Zortress (everolimus), the 40-O-(2-hydroxyethyl)-derivative of rapamycin, is an mTOR inhibitor approved for rejection prophylaxis in kidney transplant recipients. mTOR inhibition may favorably impact the HIV viral reservoir, and we hypothesize that adding everolimus to the transplant immunosuppressive regimen of HIV positive transplant recipients will decrease HIV persistence in CD4+ lymphocytes.

Detailed description:
Open-label, single arm study that will enroll antiretroviral-treated HIV-infected adults who are doing well post-liver or post-kidney transplant who are eligible and willing to add everolimus to their immunosuppressive regimen (with a target trough level between 3-8 ng/ml). Calcineurin inhibitors will be decreased to obtain a 50% reduction in trough levels with the addition of everolimus. Subjects will be maintained on that regimen for 6 months.

Biologic specimens for intensive immunology and virology studies will be obtained before, during and after exposure to everolimus. Samples will be analyzed at screening, baseline (prior to addition of everolimus), and at weeks 8 and 26 (while on everolimus), and week 52 (6 months post everolimus discontinuation).

Arms:
arm 1: None

Interventions: intervention 1: everolimus
Intervention descriptions: intervention 1: None

Protocol document:
Prot_SAP_000.pdf: 
Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
Page 1 of 33 
 
University of California, San Francisco 
 
Clinical Research Protocol 
IMPACT OF EVEROLIMUS ON HIV PERSISTENCE POST KIDNEY (AND 
KIDNEY/PANCREAS) OR LIVER TRANSPLANT 
VERSION 3.0 
Protocol Number: 
HIVTR-EVE 
Version Date: 
3/11/2016 
Investigational Product: 
Zortress (everolimus) 
Development Phase: 
exploratory 
Sponsor: 
Peter Stock, MD, PhD 
505 Parnassus Ave, Suite M-884 
San Francisco, CA 94143-0780 
Funding Organization: 
amfAR 
Principal Investigator: 
Name: Peter Stock, MD, PhD 
Telephone: 415-353-8617 
 
Fax: 415-353-8974 
 
 
E-mail: Peter.Stock@ucsf.edu 
 
 
Approval: 
 
 
 
PI or Sponsor Signature (Name and Title)  
 
Date 
This confidential information about an investigational product is provided for the exclusive use of 
investigators of this product and is subject to recall at any time.  The information in this document 
may not be disclosed unless federal or state law or regulations require such disclosure.  Subject to the 
foregoing, this information may be disclosed only to those persons involved in the study who have a 
need to know, with the obligation not to further disseminate this information.   


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
Page 2 of 33 
 
TABLE OF CONTENTS 
 
1 
BACKGROUND 
9 
1.1 
Overview of Clinical Studies ............................................................................................. 9 
2 
STUDY RATIONALE 
9 
2.1 
Risk / Benefit Assessment .................................................................................................. 11 
3 
STUDY OBJECTIVES 
11 
3.1 
Primary Objective .............................................................................................................. 11 
3.2 
Secondary Objectives ......................................................................................................... 11 
4 
STUDY DESIGN 
11 
4.1 
Study Overview .................................................................................................................. 11 
5 
CRITERIA FOR EVALUATION 
12 
5.1 
Primary Efficacy Endpoint ................................................................................................. 12 
5.2 
Secondary Efficacy Endpoints ........................................................................................... 12 
5.3 
Safety Evaluations .............................................................................................................. 12 
6 
SUBJECT SELECTION 
12 
6.1 
Study Population ................................................................................................................ 12 
6.2 
Inclusion Criteria ................................................................................................................ 12 
6.3 
Exclusion Criteria .............................................................................................................. 13 
7 
CONCURRENT MEDICATIONS 
13 
7.1 
Allowed Medications and Treatments................................................................................ 13 
8 
STUDY TREATMENTS 
14 
8.1 
Formulation of Test and Control Products ......................................................................... 14 
8.2 
Supply of Study Drug at the Site ........................................................................................ 14 
8.3 
Supply of Study Drug at the Site ........................................................................................ 15 
8.4 
Study Drug Accountability ................................................................................................ 15 
8.5 
Measures of Treatment Compliance .................................................................................. 15 
9 
STUDY PROCEDURES AND GUIDELINES 
15 
9.1 
Clinical Assessments .......................................................................................................... 15 
9.2 
Clinical Laboratory Measurements .................................................................................... 16 
9.3 
Research Laboratory Measurements for Mechanistic Studies ........................................... 17 
10 EVALUATIONS BY VISIT 
18 
10.1 Visit 1 (Screening) ............................................................................................................. 18 
10.2 Visit 2 (Baseline/Day 0) ..................................................................................................... 18 
10.3 Visit 3 (Week 1) ................................................................................................................. 18 
10.4 Visit 4 (Week 2) ................................................................................................................. 19 
10.5 Visit 5 (Week 3) ................................................................................................................. 19 
10.6 Visit 6 (Week 4) ................................................................................................................. 19 
10.7 Visit 7 (Week 8 ±7 days) ................................................................................................... 19 
10.8 Visit 8 (Week 12) ............................................................................................................... 19 
10.9 Visit 9 (Week 16) ............................................................................................................... 20 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
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10.10 Visit 10 (Week 20) ............................................................................................................. 20 
10.11 Visit 11 (Week 26 ±7 days) ............................................................................................... 20 
10.12 Visit 12 (Week 52 ±7 days) ............................................................................................... 20 
10.13 Early Withdrawal Visit ...................................................................................................... 20 
11 ADVERSE EXPERIENCE REPORTING AND DOCUMENTATION 
21 
11.1 Adverse Events .................................................................................................................. 21 
11.2 Serious Adverse Experiences (SAE) .................................................................................. 22 
12 DISCONTINUATION AND REPLACEMENT OF SUBJECTS 
23 
12.1 Early Discontinuation of Study Drug ................................................................................. 23 
12.3 Withdrawal of Subjects from the Study ............................................................................. 23 
12.4 Replacement of Subjects .................................................................................................... 24 
13 PROTOCOL VIOLATIONS 
24 
14 STATISTICAL METHODS AND CONSIDERATIONS 
24 
14.1 Data Sets Analyzed ............................................................................................................ 24 
14.2 Analysis of Primary Endpoint ............................................................................................ 24 
14.3 Analysis of Secondary Endpoints ...................................................................................... 25 
15 DATA COLLECTION, RETENTION AND MONITORING 
25 
15.1 Data Collection Instruments ............................................................................................... 25 
15.2 Data Management Procedures ............................................................................................ 25 
15.3 Data Quality Control and Reporting .................................................................................. 25 
15.4 Archival of Data ................................................................................................................. 25 
15.5 Availability and Retention of Investigational Records ...................................................... 26 
15.6 Monitoring ......................................................................................................................... 26 
15.7 Subject Confidentiality....................................................................................................... 26 
16 ADMINISTRATIVE, ETHICAL, REGULATORY CONSIDERATIONS 
26 
16.1 Protocol Amendments ........................................................................................................ 27 
16.2 Institutional Review Boards and Independent Ethics Committees .................................... 27 
16.3 Informed Consent Form ..................................................................................................... 27 
16.4 Publications ........................................................................................................................ 28 
16.5 Investigator Responsibilities .............................................................................................. 28 
 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
Page 4 of 33 
 
LIST OF ABBREVIATIONS 
 
AE 
adverse event 
ART 
Antiretroviral therapy 
BUN 
blood urea nitrogen 
CFR 
Code of Federal Regulations 
CRF 
case report form 
DMC 
Data Monitoring Committee 
DSMB 
Data Safety Monitoring Board 
FDA 
Food and Drug Administration 
GCP 
Good Clinical Practice 
HIPAA 
HIV 
Health Insurance Portability and Accountability Act of 1996 
Human Immunodeficiency Virus 
ICF 
informed consent form 
ICH 
International Conference on Harmonisation 
IEC 
Independent Ethics Committee 
IRB 
Institutional Review Board 
PI 
Principal Investigator 
SAE 
serious adverse experience 
SAP 
Statistical Analysis Plan 
TCR 
T-Cell Receptor 
TILDA 
Tat/Rev Induced Limiting Dilution Assay 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
Page 5 of 33 
 
PROTOCOL SYNOPSIS 
TITLE 
Impact of everolimus on HIV persistence post kidney (and 
kidney/pancreas) or liver transplant 
SPONSOR 
University of California, San Francisco 
FUNDING 
ORGANIZATION 
American Foundation for AIDS Research (amfAR) 
STUDY DRUG 
Zortress (everolimus) 
NUMBER OF SITES 
1 
RATIONALE 
We hypothesize that the addition of an mTOR inhibitor (everolimus) 
to the immunosuppressive regimens of HIV infected transplant 
recipients will decrease HIV persistence in CD4+ lymphoctyes.  
STUDY DESIGN 
This is an open-label, single arm, exploratory study 
PRIMARY 
OBJECTIVE 
To determine the effect of everolimus on HIV DNA and RNA in 
CD4+ T cells in HIV infected patients on stable antiretroviral 
regimens. 
SECONDARY 
OBJECTIVES 
1. To determine the effect of everolimus on plasma HIV-1 RNA 
when added to a stable antiretroviral regimen. 
2. To determine the safety and tolerability of everolimus at standard 
immunosuppressive doses in HIV-infected transplant recipients 
who are on stable antiretroviral drugs and immunosuppressive 
regimens.  
NUMBER OF 
SUBJECTS 
10 
SUBJECT 
SELECTION 
CRITERIA 
Inclusion Criteria: 
1. Solid organ (kidney, kidney/pancreas, or liver) transplant 
recipient 
2. Male or female ≥ 18 years of age. 
3. Documentation of  HIV-1 infection diagnosis as evidenced by 
any licensed ELISA and confirmation by Western Blot, or 
documented history of detectable HIV-1 RNA 
4. HIV-1 plasma RNA <50 copies/ml for at least 2 years with at 
least one measurement per year and most recent viral load within 
16 weeks of enrollment and study drug initiation. Episodes of a 
single HIV plasma RNA 50 - 500 copies/ml will not exclude 
participation if the subsequent HIV plasma RNA was <50 
copies/ml. 
5. CD4+ T cell count greater than 200 cell/µl within 16 weeks of 
enrollment and study drug initiation. 
6. Receiving combination antiretroviral therapy (at least 3 agents) 
7. Written informed consent  obtained from subject or subject’s 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
Page 6 of 33 
 
legal representative and ability for subject to comply with the 
requirements of the study. 
 
Exclusion Criteria: 
1. Pregnant, breastfeeding, or unwilling to practice birth control 
during participation in the study. 
2. Presence of a condition or abnormality that in the opinion of the 
Investigator would compromise the safety of the patient or the 
quality of the data. 
3. Patients who are intending to modify antiretroviral therapy in the 
next 6 months for any reason. 
4. Serious illness requiring hospitalization or parenteral antibiotics 
within preceding 3 months. 
5. A screening hemoglobin below 11.5 g/dL. 
6. A screening TSH consistent with hypothyroidism. 
7. Significant renal disease (eGFR < 60 ml/min) or acute nephritis 
8. Clinically active hepatitis as evidenced by clinical jaundice or 
Grade 2 or higher liver function test abnormalities. 
9. Hepatic cirrhosis or decompensated chronic liver disease.  
10. Concurrent treatment with immunomodulatory drugs, such an 
interferon-alpha, or exposure to any immunomodulatory drug in 
past 16 weeks (outside of standard immunosuppression). 
TEST PRODUCT, 
DOSE, AND ROUTE 
OF 
ADMINISTRATION 
Everolimus will be added to subject’s immunosuppressive regimen at 
.5 mg – 1.5 mg oral twice a day. Dose will depend on a target trough 
level between 3-8 ng/ml).  
Calcineurin inhibitors will be decreased to obtain a 50% reduction in 
trough levels with the addition of everolimus. Subjects will be 
maintained on that regimen for 6 months.  
DURATION OF 
SUBJECT 
PARTICIPATION 
AND DURATION OF 
STUDY 
Subjects will be on study for up to 53 weeks 
Screening:  up to 7 days 
Treatment:  182 days (6 months) 
Follow-up:  182 days (6 months) 
The total duration of the study is expected to be 2 years.  12 months 
for subject recruitment and 12 for final subject follow-up. 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
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CONCOMMITANT 
MEDICATIONS 
 
Allowed: Standard therapy for HIV-1 infection and for post renal or 
liver transplant management are allowed except for treatments noted 
in the exclusion criteria described above and as noted in the prohibited 
medications section below.   
Prohibited: The following medications are prohibited during the study 
and administration will be considered a protocol violation. 
• Immunomodulatory drugs outside of standard 
immunosuppression. 
PRIMARY VIROLOGIC 
ENDPOINT 
The primary virologic endpoint of the study will be change from 
baseline in frequency of CD4+ T cell-associated HIV-1 DNA copy 
number. 
SECONDARY 
ENDPOINTS 
Secondary endpoints will include cell-associated total HIV RNA, 
plasma RNA, and changes in inducible msRNA, (TILDA) at 
treatment completion.  
SAFETY 
EVALUATIONS 
BUN, Creatinine levels will be monitored weekly for one month and 
then monthly  to detect rejection and/or nephrotoxicity.  AST , ALT 
and ALP will also be monitored weekly in liver transplant recipients. 
Tacrolimus and everolimus drug levels (12 hour trough levels) will be 
monitored weekly for one month, then monthly 
STATISTICS 
Primary Analysis Plan 
The primary virologic endpoint of the study will be change from 
baseline in frequency of CD4+ T cell-associated HIV-1 DNA copy 
number . Secondary endpoints will include cell-associated total HIV 
RNA, plasma RNA, and changes in inducible msRNA, (TILDA) at 
treatment completion  
 
Based on a design with ten patients and a null hypotheses that there is 
no change in the HIV DNA over time, we estimate that the study will 
have approximately 80% power to detect a 0.5 log (3.2 fold) 
difference in HIV DNA levels between baseline and 6-month post-
treatment time point (at the 0.05 significance level using a paired t-
test). We also estimate the study has 80% power to detect 0.7 log (5.0 
fold) and 0.4 log (2.5 fold) differences between pre-treatment and 
post-treatment in cell-associated RNA and inducible msRNA 
(TILDA), respectively.  These estimates are based on the assumption 
that HIV DNA, cell-associated RNA and inducible msRNA are log 
normally distributed and that the standard deviation of the difference 
in pre- and post-dose levels is 0.5 log10, 0.7 log10, and 0.4 log10, 
respectively (derived from previous work). We expect to see trends in 
decreasing cell-associated DNA and RNA by week 26 of everolimus 
treatment based on our retrospective analysis. The durability of this 
potential effect will be evaluated 6 months after everolimus 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
Page 8 of 33 
 
discontinuation. 
 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
Page 9 of 33 
 
1 
BACKGROUND 
Zortress (everolimus), the 40-O-(2-hydroxyethyl)-derivative of rapamycin, is an mTOR inhibitor 
approved for rejection prophylaxis in kidney transplant recipients.   
1.1 
Overview of Clinical Studies 
There are three clinical trials in HIV negative kidney transplant recipients which study the safety 
and efficacy of concomitant use of everolimus and tacrolimus. These three trials include the 
US09 trial (n=92) [1], the ASSET study (n=224) [2], and the EVEROTAC study (n=35) [3]. 
These three trials suggest that the use of concentration-controlled everolimus allow substantial 
minimization of TAC exposure to achieve good renal function without compromising efficacy or 
safety in de novo renal transplant recipients. 
In a separate study in HIV positive kidney recipients, the impact of immunosuppressant therapy 
on peripheral blood measures of HIV persistence on HIV persistence was explored. Stored 
plasma and peripheral blood mononubear cells prior to transplantation and at weeks 12, 26, 52, 
and 104 post-transplant were obtained from 91 transplant recipients. In a multivariate model, a 
higher baseline CD4 T cell counts (p=.001) and sirolimus use (p=.04) were associated with lower 
post-transplant HIV DNA levels. Kidney function was not compromised in the patients on 
sirolimus, and was associated with a significant increase in GFR over time. [4] 
2 
STUDY RATIONALE 
HIV-1 is a retrovirus that integrates into the host genome, primarily in memory CD4+ T cells 
that can harbor latent, replication-competent HIV-1 DNA for years [5-7]. This latent HIV-1 
reservoir is thought to be established during acute infection [8-10], although precisely when, 
where, and how the reservoir is seeded remains to be determined. The reservoir has a remarkably 
long half-life and is resistant to antiretroviral therapy (ART), resulting in lifelong infection and 
viral rebound in the vast majority of HIV-1-infected individuals when ART is discontinued [10, 
11]. Major research efforts are currently underway to understand the biology of the viral 
reservoir, the mechanism of viral latency, and the potential of various therapeutic approaches to 
target the reservoir.  
 
The HIV reservoir is maintained during ART  by (1) the long half-life of infected memory T 
cells, (2) homeostatic proliferation of these cells[12, 13] and perhaps (3) low levels of cell-to-cell 
virus transfer (“cryptic replication”).[14] In the absence of therapy, the frequency of activated T 
cells is associated with the level of viremia. During long-term suppressive ART, a similar albeit 
less consistent association exists, with the frequency of activated CD4+ T cells expressing HLA-
DR, CCR5, and PD-1 correlated with the frequency of cells containing HIV-1 RNA or DNA.[15, 
16] The mechanism for this association is not known. Theoretically, an inflammatory immune 
environment may contribute to the persistence of the viral reservoir by a number of 
mechanisms.[17] T cell activation promotes cell-to-cell virus transfer as activated cells are both 
more likely to produce virus and more likely to become infected. TCR engagement by cognate 
antigen or cytokines (e.g., IL-7) stimulates CD4+ T cell proliferation and the expansion of the 
infected cell population.[13] Indeeed, HIV may commandeer the pathways by which cell 
proliferation is controlled, leading to preferential expansion of infected cells.[18, 19] A chronic 
inflammatory environment would also be expected to prevent the generation of optimal HIV-1-


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
Page 10 of 33 
 
specific immune responses. Chronic inflammation stimulates potent and sustained 
immunoregulatory responses, including expansion of T regulatory cells and the up-regulation of 
PD-1 and other negative regulators on effector cells.[12, 20, 21]  
 
There is intense interest in “shock and kill” strategies in which intracellular pathways that 
regulate DNA transcription are manipulated (the “shock”), leading to the production of virus and 
hopefully the death of the infected cell (the “kill”). The most effective way to stimulate HIV 
production from the latent reservoir is to activate CD4+ T cells. Theoretically, any activating 
intervention could lead to proliferation and expansion of the infected cell population. 
Combination approaches toward a cure might require addition of immune-modifying agents that 
prevent non-specific T cell proliferation and activation. 
mTOR inhibition and  the reservoir during ART:  T cell activation and proliferation are 
controlled by a number of signalling pathways, including those involving the mammalian target 
of rapamycin (mTOR), signal transducer and activator of transcription 5a (STAT5a) and 
forkhead box O3a (FOXO3a).[22] Specific inhibitors of these pathways might therefore reduce 
the size of the latent viral reservoir. For example, sirolimus (rapamycin) is a naturally occurring 
macrolide that inhibits mTOR, and as a consequence it blocks cell cycle progression from G1 to 
S phase in activated T cells and reduces CCR5 expression.[23] Dendritic cells exposed to mTOR 
inhibitors in vitro failed to make interferon-alpha when exposed to deactivated HIV.[24] mTOR 
inhibitors also block the negative effect HIV has on autophagy, which might result in a less 
favorable environment for HIV replication.[25] Finally, mTOR inhibitors enhance CD8+ T cell 
memory formation and improve vaccine responsiveness in murine and non-human primate 
models, suggesting it might in humans enhance effector response to HIV and other 
pathogens.[26] 
 
In order to define the potential role of immunosuppressive drugs on reservoir during effective 
antiretroviral therapy, we explored the impact of immunosuppressant therapy on peripheral blood 
measures of HIV persistence following kidney transplantation. A higher baseline HIV DNA 
(p<.0001) was significantly associated with higher HIV DNA levels post-transplant, while higher 
CD4+ T cell count (p=0.001), sirolimus use (p=0.04) and a longer duration of follow-up 
(p=0.06) were associated with lower post-transplant HIV DNA levels.[4] Although lacking a 
control group in this retrospective analysis, the apparent decrease in HIV DNA levels over time 
post-transplant suggest that mTOR inhibitors may impact HIV persistence during antiretroviral 
therapy.  
 
Like sirolimus, everolimus inhibits mTOR, although it inhibits both mTORC1 and mTORC2 
(sirolimus only inhibits mTORC1). Everolimus is being using with increasing frequency in 
immunosuppressive regimens in transplant recipients as obtaining therapeutic drug levels is 
facilitated by more favorable pharmacokinetics as compared to sirolimus. In this prospective 
study, we will initiate everolimus in a transplant population and perform a comprehensive 
assessment of the CD4 T-cell reservoir. Multiple measurements of the reservoir will be 
measured, including: 1) quantitative measurements of CD4+ T cell-associated HIV-1 DNA 
(total, integrated and 2-LTR circle DNA);  2) HIV-1 total cellular RNA quantification providing 
a snapshot of HIV-1 “transcriptional activity” of the target infected cells; and 3) A cellular HIV 
RNA induction assay, the Tat/Rev Induced Limiting Dilution Assay (TILDA) to measure 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
Page 11 of 33 
 
changes in transcriptionally latent, but inducible HIV. Blood plasma RNA will be monitored 
using a commercial real-time PCR assay modified for single copy detection.[27] 
 
We hypothesize that the addition of an mTOR inhibitor (everolimus) to the immunosuppressive 
regimens of HIV infected transplant recipients will decrease HIV persistence in CD4+ 
lymphoctyes.  
2.1 
Risk / Benefit Assessment 
The risk of minimizing tacrolimus (dose reduction 50%) and adding everolimus is principally 
related to the risk of rejection and potential nephrotoxicity related to drug-drug interactions. In 
three large trials [1-3] in HIV negative patients, the use of concentration-controlled everolimus 
allowed substantial minimization of TAC exposure to achieve better renal function without 
compromising efficacy or safety in de novo renal transplants. Similarly, the use of another TOR 
inhibitor (sirolimus) in 91 HIV positive kidney transplant recipients was actually associated with 
an increase in eGFR over time and a reduction in HIV DNA levels. [4] 
To mitigate against the potential adverse impact of drug-drug interactions between the anti-
retroviral agents (most notably the protease inhibitors) and immunosuppressive agents (most 
notably the calcineurin inhibitors and TOR inhibitors), trough levels will be monitored weekly 
during the first month of the study. Dose adjustments will be made based on previous 
pharmacokinetic studies in the HIV infected kidney transplant recipients. [28-30] 
3 
STUDY OBJECTIVES 
3.1 
Primary Objective 
To determine the effect of everolimus on HIV DNA and RNA in CD4+ T cells in HIV infected 
patients on stable antiretroviral regimens. 
3.2 
Secondary Objectives 
1. To determine the effect of everolimus on plasma HIV-1 RNA when added to a stable 
antiretroviral regimen. 
2. To determine the safety and tolerability of everolimus at standard immunosuppressive 
doses in HIV-infected transplant recipients who are on stable antiretroviral drugs and 
immunosuppressive regimens.  
4 
STUDY DESIGN 
4.1 
Study Overview 
We will perform an open-label, single arm, exploratory study in which antiretroviral-treated 
post-solid organ transplant adults will add everolimus to their immunosuppressive regimen. We 
will enroll antiretroviral treated HIV-infected adults who are doing well post-liver, post-kidney 
or post kidney/pancreas transplant at UCSF who are eligible and willing to add everolimus to 
their immunosuppressive regimen (with a target trough level between 3-8 ng/ml). Calcineurin 
inhibitors will be decreased to obtain a 50% reduction in trough levels with the addition of 
everolimus. Subjects will be maintained on that regimen for 6 months. Novartis will provide 
study drug.  


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
Page 12 of 33 
 
 
Biologic specimens for intensive immunology and virology studies will be obtained before, 
during and after exposure to everolimus. Samples will be analyzed at screening, baseline (prior 
to addition of everolimus), and at weeks 8 and 26 (while on everolimus), and week 52 (6 months 
post everolimus discontinuation). 
 
5 
CRITERIA FOR EVALUATION 
5.1 
Primary Efficacy Endpoint 
The primary virologic endpoint of the study will be change from baseline in frequency of CD4+ 
T cell-associated HIV-1 DNA copy number. 
5.2 
Secondary Efficacy Endpoints 
Secondary endpoints will include cell-associated total HIV RNA, plasma RNA, and changes in 
inducible msRNA, (TILDA) at treatment completion  
5.3 
Safety Evaluations 
 
• BUN, Creatinine levels will be monitored weekly for one month and then monthly  to 
detect rejection and/or nephrotoxicity.  AST , ALT and ALP will also be monitored 
weekly in liver transplant recipients. 
• Tacrolimus and everolimus drug levels (12 hour trough levels) will be monitored 
weekly for one month, then monthly  
6 
SUBJECT SELECTION 
6.1 
Study Population 
We will study solid organ (kidney, kidney/pancreas, or liver) transplant recipient who are doing 
well on ART and who meet the criteria for everolimus therapy. We will exclude individuals on 
mTOR inhibitors or related drugs. We will exclude individuals who intend to modify ART or 
who have significant kidney, liver and/or thyroid dysfunction. 
6.2 
Inclusion Criteria 
1. Solid organ (kidney, kidney/pancreas, or liver) transplant recipient who is at least 6 months 
post transplant.  
2. Male or female ≥ 18 years of age. 
3. Documentation of  HIV-1 infection diagnosis as evidenced by any licensed ELISA and 
confirmation by Western Blot, or documented history of detectable HIV-1 RNA) 
4. HIV-1 plasma RNA <50 copies/ml for at least 2 years with at least one measurement per 
year and most recent viral load within 16 weeks of enrollment and study drug initiation. 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
Page 13 of 33 
 
Episodes of a single HIV plasma RNA 50 - 500 copies/ml will not exclude participation if 
the subsequent HIV plasma RNA was <50 copies/ml. 
5. CD4+ T cell count greater than 200 cell/µl within 16 weeks of enrollment and study drug 
initiation. 
6. Receiving combination antiretroviral therapy (at least 3 agents) 
7. Written informed consent  obtained from subject or subject’s legal representative and ability 
for subject to comply with the requirements of the study. 
6.3 
Exclusion Criteria 
1. Pregnant, breastfeeding, or unwilling to practice birth control during participation in the 
study. 
2. Presence of a condition or abnormality that in the opinion of the Investigator would 
compromise the safety of the patient or the quality of the data. 
3. Patients who are intending to modify antiretroviral therapy in the next 6 months for any 
reason. 
4. Serious illness requiring hospitalization or parenteral antibiotics within preceding 3 months. 
5. A screening hemoglobin below 11.5 g/dL. 
6. A screening TSH consistent with hypothyroidism. 
7. Significant renal disease (eGFR < 45 ml/min for kidney or kidney/pancreas transplant 
recipients or eGFR < 60 ml/min for liver transplant recipients) or acute nephritis 
8. Clinically active hepatitis as evidenced by clinical jaundice or Grade 2 or higher liver 
function test abnormalities. 
9. Hepatic cirrhosis or decompensated chronic liver disease.  
10. Concurrent treatment with immunomodulatory drugs, such an interferon-alpha, or exposure 
to any immunomodulatory drug in past 16 weeks (outside of standard immunosuppression). 
7 
CONCURRENT MEDICATIONS 
All subjects should be maintained on the same medications throughout the entire study period, as 
medically feasible, with no introduction of new chronic therapies. 
7.1 
Allowed Medications and Treatments 
Standard therapy for HIV-1 infection and for post renal or liver transplant management are 
allowed except for treatments noted in the exclusion criteria described above and as noted in the 
prohibited medications section below.   
Prohibited Medications and Treatments 
The following medications are prohibited during the study and administration will be considered 
a protocol violation. 
• Immunomodulatory drugs such as interferon-alpha (outside of standard 
immunosuppression) 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
Page 14 of 33 
 
8 
STUDY TREATMENTS 
8.1 
Formulation of Test and Control Products 
Study drug: Zortress (everolimus) manufactured by Novartis. 
8.1.1 
Formulation of Test Product 
Formulation of Zortress (everolimus)  
 
Zortress (everolimus) 
Active Ingredient 
everolimus 
Other ingredient 
butylated hydroxytoluene, 
magnesium stearate, lactose 
monohydrate, hypromellose, 
crospovidone and lactose anhydrous 
8.1.2 
Formulation of Control Product 
No control product. 
8.1.3 
Packaging and Labeling 
Zortress (everolimus) will be packaged and labeled by Novartis.  As mentioned previously the 
study will not be blinded and no placebo is being used. 
Study drug is supplied in cartons containing 32 single use tablets (0.25 mg per tablet).  The 
tablets will be packaged in sets of 4 enclosed within a laminated foil pouch.  Eight pouches will 
be contained in each carton (1 extra pouch containing 4 tablets in the event of breakage).  
Each carton (kit) of study drug will be labeled with the required FDA warning statement, the 
protocol number, a treatment number, the name of the sponsors, and directions for patient use 
and storage.  
8.2 
Supply of Study Drug at the Site 
Novartis will ship Study Drug to the UCSF investigational pharmacy.  The initial study drug 
shipment will be shipped after study activation (i.e., all required regulatory documentation has 
been completed and the contract is signed). Subsequent study drug shipments will be made after 
site request for resupply. 
8.2.1 
Dosage/Dosage Regimen 
Everolimus will be added to subjects immunosuppressive regimen at .5 mg – 1.5 mg oral twice a 
day. Dose will depend on a target trough level between 3-8 ng/ml). Calcineurin inhibitors will be 
decreased to obtain a 50% reduction in trough levels with the addition of everolimus. Subjects 
will be maintained on that regimen for 6 months.  
The study drug will be dispensed to the subject by the investigator, and will be taken at home 
twice daily. 


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8.3 
Supply of Study Drug at the Site 
Study drug will be supplied to the UCSF investigational pharmacy by Novartis at study 
initiation.  Study drugs must be received by a designated person at UCSF, handled and stored 
safely and properly, and kept in a secured location to which only the investigator and designated 
assistants have access. Upon receipt, all study drugs should be stored according to the 
instructions specified on the drug labels. Clinical supplies are to be dispensed only in accordance 
with the protocol. 
8.4 
Study Drug Accountability 
An accurate and current accounting of the dispensing and return of study drug for each subject 
will be maintained on an ongoing basis by a member of the study site staff.  The number of study 
drug dispensed and returned by the subject will be recorded on the Investigational Drug 
Accountability Record.  At the conclusion of the study, and as appropriated during the course of 
the study, the investigator will return all unused study drug, packaging, drug labels, and a copy 
of the completed Drug Accountability Record to the Novartis address provided in the 
investigator folder.  
8.5 
Measures of Treatment Compliance 
Subjects will be asked to keep a patient diary noting the day and date they take their study drug 
(or noting variances to the required daily dose) and any adverse events. They will be asked to 
bring their patient diary to each study visit along with all used and unused study drug containers. 
9 
STUDY PROCEDURES AND GUIDELINES 
A Schedule of Events representing the required testing procedures to be performed for the 
duration of the study is diagrammed in Appendix 1. 
Prior to conducting any study-related activities, written informed consent and the Health 
Insurance Portability and Accountability Act (HIPAA) authorization must be signed and dated 
by the subject.   
9.1 
Clinical Assessments 
9.1.1 
Immunosuppression and ARV Medication Logs 
All ARV and Immunosuppression medications from Visit 1 – 5 will be recorded in the source 
documentation for each study subject. Any changes in drug, dose or frequency through Visit 
5will be documented. 
9.1.2 
Concomitant Medications 
All concomitant medication and concurrent therapies will be documented at Visits 1 – 5.  
However, only document concomitant medications that subject is on at the study visit. Dose, 
route, and unit frequency will be captured. 
9.1.3 
Subject Diary 
All subjects will be asked to keep a written Subject Diary to record any deviations in prescribed 
medications (i.e. missed doses, etc). The subject will also record any adverse events. The Subject 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
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Diary will be initiated at Visit 2, and will be reviewed by someone on the study team at Visits 2 
– 5. 
9.1.4 Medical History and Demographics  
Demographic information (date of birth, gender, race) as well as relevant medical history, 
including history of current disease, other pertinent respiratory history, and information 
regarding underlying diseases will be recorded at Visit 1. 
9.1.5 
Physical Examination 
A complete physical examination will be performed by either the investigator or a sub-
investigator who is a physician at Visit 1.  Qualified staff (MD, NP, RN, and PA) may complete 
an abbreviated physical exam at visits 11.   
9.1.6 
Adverse Events 
Information regarding occurrence of adverse events will be documented throughout the study. 
Duration (start and stop dates), severity/grade, outcome, treatment and relation to study drug will 
be recorded on the case report form (CRF). 
9.2 
Clinical Laboratory Measurements 
9.2.1 
Pregnancy Test 
A urine pregnancy test will be obtained from female subjects who are of childbearing age prior 
to their participation in the study, prior to initiation of study drug on Visit 2. 
9.2.2 
Safety Labs 
Blood will be obtained for the following safety labs at the specified  Visits 1 – 12 as outlined in 
the schedule of events. Kidney/pancreas transplant recipients are followed the same as kidney 
only transplant recipients:  
• 
Complete blood count (hemoglobin, hematocrit, red blood cell count, white blood cell count, 
white blood cell differential, and platelet count) 
• 
Creatinine 
• 
BUN 
• 
Sodium 
• 
Potassium 
• 
Glucose 
• 
Calcium (kidney subjects) 
• 
CO2 (kidney subjects) 
• 
Magnesium (kidney subjects) 
• 
Phosphorous (kidney subjects) 
• 
T Bili (liver subjects) 
• 
SGOT/AST (liver subjects) 
• 
SGOT/ALT (liver subjects) 
• 
Alkaline phosphatase (liver subjects) 
• 
Tacrolimus and  everolimus trough levels 


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9.2.3 
HIV RNA (standard) and CD4+/CD8+ T cell counts 
HIV RNA (standard) and CD4+/CD8+ T cell counts will be recorded at Visits 1 – 5. However, 
since insurance only covers these 4 times a year, the research team will contact the subject’s 
primary provider to obtain standard of care labs, which can be used for the closest target visit 
date. 
9.3 
Research Laboratory Measurements for Mechanistic Studies 
All Research Laboratory Measurements  outlined in this section will require 10 x 10cc EDTA 
tubes of blood from each designated  study visit. 
9.3.1 
HIV-1 RNA: Single copy assay 
Measured at Baseline, Screening and at weeks 8, 26, and 52 
9.3.2 
Cell associated HIV RNA and DNA in CD4+ T-cells (blood) 
Measured at Baseline, Screening and at weeks 8, 26, and 52. There is no well-accepted gold-
standard for measuring the size of the replication-competent reservoir. Given the proposed 
mechanism of action for everolimus and our preliminary data with sirolimus we will use a 
quantitative measurement of HIV DNA in isolated CD4+ T cells as our primary outcome 
measure. We will also quantify HIV RNA within these cells. Peripheral blood CD4 T cells will 
be enriched by negative selection using antibody-coupled magnetic beads (Stem Cell 
Technologies) prior to simultaneous RNA and DNA isolation using cell-sparing protocols 
(AllPrep, Qiagen). Total DNA, integrated proviral and unintegrated 2-LTR circle species will be 
measured using calibrated quantitation standards following published qPCR procedures that have 
been validated for single copy detection.[31, 32]  While 2-LTR circles are often undetectable in 
long-term ART-suppressed subjects, a transient increase has been seen with drug intensification 
studies3 and warrants further investigation with immunosuppressive agents. Also, the levels of 
total (integrated plus unintegrated) and integrated DNA are typically equivalent in suppressed 
patients. However independent measurements of each species are expected to fully capture 
potential dynamics in each component of the DNA reservoir. Finally, cell-associated RNA 
measurements, coupled with DNA measurements (RNA:DNA ratio) will be used to assess the 
transcriptional activity of the HIV reservoir.[33]  
9.3.3 
TILDA 
Measured at Screening and week 26. Dr. Nicholas Chomont and his group at the Vaccine & 
Gene Therapy Institute of Florida have developed a novel assay that measures the frequency of 
cells harboring inducible HIV, serving as a cost effective proxy for expensive and time 
consuming in vitro viral outgrowth assays requiring large amounts of patient blood. By 
combining ultrasensitive detection of multiply-spliced (ms) nascent tat/rev RNAs after CD4 T 
cell stimulation and limiting dilution, this method measures the frequency of cells harboring 
transcriptionally silent – but nonetheless inducible - viruses. While unspliced HIV RNAs are 
frequently detected in latently infected cells in the absence of viral production, HIV msRNAs 
reflect de novo viral production.[32, 34] To our knowledge, TILDA is the only method that 
measures the frequency of latently infected cells harboring inducible virus that can be performed 
with less than a million CD4+ T cells. Dr. Chomont has kindly shared the procedures pre-
publication and will advise on the technical and analytical aspects of the assay. 


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10 EVALUATIONS BY VISIT 
10.1 Visit 1 (Screening) 
1. 
Review the study with the subject (subject’s legal representative) and obtain written 
informed consent and HIPAA authorization. 
2. 
Assign the subject a unique screening number. 
3. 
Record demographic data, medical history, including a history of HIV and kidney or liver 
transplant. 
4. 
Perform a complete physical examination. 
5. 
Perform and record vital signs. 
6. 
Record ARV, Immunosuppression, and concomitant medication regimens. 
7. 
Collect blood for safety labs. 
8. 
Collect historical HIV RNA and CD4+/CD8+ T cell counts from subject or subject’s 
primary care provider 
9. 
Collect blood for Mechanistic Studies 
10. 
Schedule subject for Visit 2 if eligible. 
10.2 Visit 2 (Baseline/Day 0) 
1. 
Record ARV, Immunosuppression, and concomitant medication regimens. 
2. 
Perform Pregnancy Test (urine) 
3. 
Initiated Subject Diary 
4. 
Collect blood for safety labs. 
5. 
Collect historical HIV RNA and CD4+/CD8+ T cell counts from subject or subject’s 
primary care provider 
6. 
Collect blood for Mechanistic Studies 
7. 
Initiate study drug 
8. 
Schedule subject for Visit 3 
 
NOTE: Visit 1 and 2 can occur on the same day if subject has been pre-screened. 
10.3 Visit 3 (Week 1) 
1. Record ARV, Immunosuppression, and concomitant medication regimens. 
2. Record any Adverse Experiences and/or Review subject diary for adverse experiences and 
dosing compliance. 
3. Collect blood for safety labs. 
4. Schedule subject for Visit 4 


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10.4 Visit 4 (Week 2) 
1. Record ARV, Immunosuppression, and concomitant medication regimens. 
2. Record any Adverse Experiences and/or Review subject diary for adverse experiences and 
dosing compliance. 
3. Collect blood for safety labs. 
4. Schedule subject for Visit 5 
10.5 Visit 5 (Week 3) 
1. Record ARV, Immunosuppression, and concomitant medication regimens. 
2. Record any Adverse Experiences and/or Review subject diary for adverse experiences and 
dosing compliance. 
3. Collect blood for safety labs. 
4. Schedule subject for Visit 6 
10.6 Visit 6 (Week 4) 
1. 
Record ARV, Immunosuppression, and concomitant medication regimens 
2. 
Record any Adverse Experiences and/or Review subject diary for adverse experiences and 
dosing compliance. 
3. 
Collect blood for safety labs. 
4. 
Schedule subject for Visit 7 
10.7 Visit 7 (Week 8 ±7 days) 
5. 
Record ARV, Immunosuppression, and concomitant medication regimens 
6. 
Record any Adverse Experiences and/or Review subject diary for adverse experiences and 
dosing compliance. 
7. 
Collect blood for safety labs. 
8. 
Collect historical HIV RNA and CD4+/CD8+ T cell counts from subject or subject’s 
primary care provider 
9. 
Collect blood for Mechanistic Studies 
10. 
Schedule subject for Visit 8 
10.8 Visit 8 (Week 12) 
1. Record ARV, Immunosuppression, and concomitant medication regimens 
2. Record any Adverse Experiences and/or Review subject diary for adverse experiences and 
dosing compliance. 
3. Collect blood for safety labs. 
4. Schedule subject for Visit 9 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
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10.9 Visit 9 (Week 16) 
1. Record ARV, Immunosuppression, and concomitant medication regimens 
2. Record any Adverse Experiences and/or Review subject diary for adverse experiences and 
dosing compliance. 
3. Collect blood for safety labs. 
4. Schedule subject for Visit 10 
10.10 Visit 10 (Week 20) 
1. Record ARV, Immunosuppression, and concomitant medication regimens 
2. Record any Adverse Experiences and/or Review subject diary for adverse experiences and 
dosing compliance. 
3. Collect blood for safety labs. 
4. Schedule subject for Visit 11 
10.11 Visit 11 (Week 26 ±7 days) 
1. Stop study drug 
2. Record ARV, Immunosuppression, and concomitant medication regimens 
3. Record any Adverse Experiences and/or Review subject diary for adverse experiences and 
dosing compliance. 
4. Perform abbreviated physical examination. 
5. Collect blood for safety labs. 
6. Collect historical HIV RNA and CD4+/CD8+ T cell counts from subject or subject’s primary 
care provider 
7. Collect blood for Mechanistic Studies 
8. Schedule subject for Visit 12 
10.12 Visit 12 (Week 52 ±7 days) 
1. Record ARV, Immunosuppression, and concomitant medication regimens 
2. Record any Adverse Experiences and/or Review subject diary for adverse experiences and 
dosing compliance. 
3. Collect blood for safety labs. 
4. Collect historical HIV RNA and CD4+/CD8+ T cell counts from subject or subject’s primary 
care provider 
5. Collect blood for Mechanistic Studies 
10.13 Early Withdrawal Visit 
1. Record ARV, Immunosuppression, and concomitant medication regimens 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
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2. Record any Adverse Experiences and/or Review subject diary for adverse experiences and 
dosing compliance. 
3. Collect blood for safety labs. 
4. Collect blood for Mechanistic Studies 
 
11 ADVERSE EXPERIENCE REPORTING AND DOCUMENTATION 
11.1 Adverse Events 
An adverse event (AE) is any untoward medical occurrence in a clinical investigation of a patient 
administered a pharmaceutical product and that does not necessarily have a causal relationship 
with the treatment.  An AE is therefore any unfavorable and unintended sign (including an 
abnormal laboratory finding), symptom or disease temporally associated with the administration 
of an investigational product, whether or not related to that investigational product.  An 
unexpected AE is one of a type not identified in nature, severity, or frequency in the current 
Investigator’s Brochure or of greater severity or frequency than expected based on the 
information in the Investigator’s Brochure. 
The Investigator will probe, via discussion with the subject, for the occurrence of AEs during 
each subject visit and record the information in the site’s source documents.  Adverse events will 
be recorded in the patient CRF.  Adverse events will be described by duration (start and stop 
dates and times), severity, outcome, treatment and relation to study drug, or if unrelated, the 
cause. 
AE Severity 
The National Cancer Institute’s Common Terminology Criteria for Adverse Events (CTCAE) 
Version 3.0 should be used to assess and grade AE severity, including laboratory abnormalities 
judged to be clinically significant. The modified criteria can be found in the study manual.  If the 
experience is not covered in the modified criteria, the guidelines shown in Table 1 below should 
be used to grade severity.  It should be pointed out that the term “severe” is a measure of 
intensity and that a severe AE is not necessarily serious. 
Table 1.  AE Severity Grading 
Severity (Toxicity Grade) 
Description 
Mild (1) 
Transient or mild discomfort; no limitation in activity; no medical 
intervention or therapy required. The subject may be aware of the sign 
or symptom but tolerates it reasonably well. 
Moderate (2) 
Mild to moderate limitation in activity, no or minimal medical 
intervention/therapy required. 
Severe (3) 
Marked limitation in activity, medical intervention/therapy required, 
hospitalizations possible. 
Life-threatening (4) 
The subject is at risk of death due to the adverse experience as it 
occurred. This does not refer to an experience that hypothetically 
might have caused death if it were more severe. 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
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AE Relationship to Study Drug 
The relationship of an AE to the study drug should be assessed using the following the guidelines 
in Table 2. 
Table 2.  AE Relationship to Study Drug 
Relationship 
to Drug 
Comment 
Definitely 
Previously known toxicity of agent; or an event that follows a reasonable temporal 
sequence from administration of the drug; that follows a known or expected response 
pattern to the suspected drug; that is confirmed by stopping or reducing the dosage of 
the drug; and that is not explained by any other reasonable hypothesis. 
Probably 
An event that follows a reasonable temporal sequence from administration of the 
drug; that follows a known or expected response pattern to the suspected drug; that is 
confirmed by stopping or reducing the dosage of the drug; and that is unlikely to be 
explained by the known characteristics of the subject’s clinical state or by other 
interventions. 
Possibly 
An event that follows a reasonable temporal sequence from administration of the 
drug; that follows a known or expected response pattern to that suspected drug; but 
that could readily have been produced by a number of other factors. 
Unrelated 
An event that can be determined with certainty to have no relationship to the study 
drug. 
11.2 Serious Adverse Experiences (SAE) 
An SAE is defined as any AE occurring at any dose that results in any of the following 
outcomes: 
• 
death 
• 
a life-threatening adverse experience 
• 
inpatient hospitalization or prolongation of existing hospitalization 
• 
a persistent or significant disability/incapacity 
• 
a congenital anomaly/birth defect  
Other important medical events may also be considered an SAE when, based on appropriate 
medical judgment, they jeopardize the subject or require intervention to prevent one of the 
outcomes listed.  
 
11.2.1 Serious Adverse Experience Reporting 
Investigator or Study Coordinadtor will document all SAEs that occur (whether or not related to 
study drug) per UCSF CHR Guidelines.  The collection period for all SAEs will begin after 
informed consent is obtained and end after procedures for the final study visit have been 
completed. 


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In accordance with the standard operating procedures and policies of the local Institutional 
Review Board (IRB)/Independent Ethics Committee (IEC), the site investigator will report SAEs 
to the IRB/IEC.   
   
12 DISCONTINUATION AND REPLACEMENT OF SUBJECTS 
12.1 Early Discontinuation of Study Drug  
A subject may be discontinued from study treatment at any time if the subject, the investigator, 
or the Sponsor feels that it is not in the subject’s best interest to continue.  The following is a list 
of possible reasons for study treatment discontinuation: 
• Subject withdrawal of consent (or assent) 
• Subject is not compliant with study procedures 
• Adverse event that in the opinion of the investigator would be in the best interest of the 
subject to discontinue study treatment 
• Protocol violation requiring discontinuation of study treatment 
• Lost to follow-up 
• Sponsor request for early termination of study 
• Positive pregnancy test (females) 
If a subject is withdrawn from treatment due to an adverse event, the subject will be followed 
and treated by the Investigator until the abnormal parameter or symptom has resolved or 
stabilized.   
All subjects who discontinue study treatment should come in for an early discontinuation visit as 
soon as possible and then should be encouraged to complete all remaining scheduled visits and 
procedures. 
All subjects are free to withdraw from participation at any time, for any reason, specified or 
unspecified, and without prejudice. 
Reasonable attempts will be made by the investigator to provide a reason for subject 
withdrawals.  The reason for the subject’s withdrawal from the study will be specified in the 
subject’s source documents Refer to section 10.13 for early termination procedures. 
12.3 
Withdrawal of Subjects from the Study 
A subject may be withdrawn from the study at any time if the subject, the investigator, or the 
Sponsor feels that it is not in the subject’s best interest to continue.   
All subjects are free to withdraw from participation at any time, for any reason, specified or 
unspecified, and without prejudice. 
Reasonable attempts will be made by the investigator to provide a reason for subject 
withdrawals.  The reason for the subject’s withdrawal from the study will be specified in the 
subject’s source documents.  As noted above, subjects who discontinue study treatment early 
(i.e., they withdraw prior to Visit 4) should have an early discontinuation visit. Refer to Section 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
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10.13 for early termination procedures.  Subjects who withdraw after Visit 4 but prior to Visit 5 
should be encouraged to come in for a final visit (and the procedures to be followed would 
include those for their next scheduled visit).   
12.4 
Replacement of Subjects 
Subjects who withdraw from the study treatment will be replaced.   
Subjects who withdraw from the study will be replaced.   
 
13 PROTOCOL VIOLATIONS 
A protocol violation occurs when the subject or investigator fails to adhere to significant protocol 
requirements affecting the inclusion, exclusion, subject safety and primary endpoint criteria.  
Protocol violations for this study include, but are not limited to, the following: 
• Failure to meet inclusion/exclusion criteria 
• Use of a prohibited concomitant medication 
• Failure to comply with Good Clinical Practice (GCP) guidelines will also result in a 
protocol violation. The Principal Investigator will determine if a protocol violation will 
result in withdrawal of a subject. 
When a protocol violation occurs, it will be discussed with the investigator and a Protocol 
Violation Form detailing the violation will be generated. This form will be signed by a Sponsor 
representative and the Investigator. A copy of the form will be filed in the site’s regulatory 
binder and in the Sponsor’s files. 
14 STATISTICAL METHODS AND CONSIDERATIONS 
Prior to the analysis of the final study data, a detailed Statistical Analysis Plan (SAP) will be 
written describing all analyses that will be performed.  The SAP will contain any modifications 
to the analysis plan described below.   
14.1 Data Sets Analyzed 
All eligible patients who receive at least one dose of the study drug (the Safety Population) will 
be included in the safety and efficacy analysis. 
14.2 Analysis of Primary Endpoint 
The primary virologic endpoint of the study will be change from baseline in frequency of CD4+ 
T cell-associated HIV-1 DNA copy number. Based on a design with ten patients and a null 
hypotheses that there is no change in the HIV DNA over time, we estimate that the study will 
have approximately 80% power to detect a 0.5 log (3.2 fold) difference in HIV DNA levels 
between baseline and 6-month post-treatment time point (at the 0.05 significance level using a 
paired t-test).  


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
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14.3 Analysis of Secondary Endpoints 
Secondary virologic endpoints will include cell-associated total HIV RNA, plasma RNA, and 
changes in inducible msRNA, (TILDA) at treatment completion We estimate the study has 80% 
power to detect 0.7 log (5.0 fold) and 0.4 log (2.5 fold) differences between pre-treatment and 
post-treatment in cell-associated RNA and inducible msRNA (TILDA), respectively.  These 
estimates are based on the assumption that HIV DNA, cell-associated RNA and inducible 
msRNA are log normally distributed and that the standard deviation of the difference in pre- and 
post-dose levels is 0.5 log10, 0.7 log10, and 0.4 log10, respectively (derived from previous 
work). We expect to see trends in decreasing cell-associated DNA and RNA by week 26 of 
everolimus treatment based on our retrospective analysis. The durability of this potential effect 
will be evaluated 6 months after everolimus discontinuation. 
15 DATA COLLECTION, RETENTION AND MONITORING 
15.1 Data Collection Instruments 
The Investigator will prepare and maintain adequate and accurate source documents designed to 
record all observations and other pertinent data for each subject treated with the study drug.   
Study personnel will enter data from source documents corresponding to a subject’s visit into the 
protocol-specific paper CRF when the information corresponding to that visit is available.  
Subjects will not be identified by name in the study database or on any study documents to be 
collected by the Sponsor (or designee), but will be identified by a subject number. 
For paper CRFs:  If a correction is made on a CRF, the study staff member will line through the 
incorrect data, write in the correct data and initial and date the change. 
The Investigator is responsible for all information collected on subjects enrolled in this study.  
All data collected during the course of this study must be reviewed and verified for completeness 
and accuracy by the Investigator.   
15.2 Data Management Procedures 
The data will be entered into a validated database.  The Data Management group will be 
responsible for data processing, in accordance with procedural documentation.  Database lock 
will occur once quality assurance procedures have been completed. 
All procedures for the handling and analysis of data will be conducted using good computing 
practices meeting FDA guidelines for the handling and analysis of data for clinical trials. 
15.3 Data Quality Control and Reporting 
After data have been entered into the study database, a system of computerized data validation 
checks will be implemented and applied to the database on a regular basis. The study database 
will be updated in accordance with the resolved queries.  All changes to the study database will 
be documented. 
15.4 Archival of Data 
The database is safeguarded against unauthorized access by established security procedures; 
appropriate backup copies of the database and related software files will be maintained.  


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Databases are backed up by the database administrator in conjunction with any updates or 
changes to the database.   
At critical junctures of the protocol (e.g., production of interim reports and final reports), data for 
analysis is locked and cleaned per established procedures. 
15.5 Availability and Retention of Investigational Records 
The Investigator must make study data accessible to the monitor, other authorized 
representatives of the Sponsor (or designee), IRB/IEC, and Regulatory Agency (e.g., FDA) 
inspectors upon request.  A file for each subject must be maintained that includes the signed 
Informed Consent, HIPAA Authorization and Assent Form and copies of all source 
documentation related to that subject.  The Investigator must ensure the reliability and 
availability of source documents from which the information on the CRF was derived. 
All study documents (patient files, signed informed consent forms, copies of CRFs, Study File 
Notebook, etc.) must be kept secured for a period of two years following marketing of the 
investigational product or for two years after centers have been notified that the IND has been 
discontinued.  There may be other circumstances for which the Sponsor is required to maintain 
study records and, therefore, the Sponsor should be contacted prior to removing study records for 
any reason. 
15.6 Monitoring 
Monitoring visits will be conducted by representatives of the Sponsor according to the U.S. CFR 
Title 21 Parts 50, 56, and 312 and ICH Guidelines for GCP (E6).    By signing this protocol, the 
Investigator grants permission to the Sponsor (or designee), and appropriate regulatory 
authorities to conduct on-site monitoring and/or auditing of all appropriate study documentation. 
15.7 Subject Confidentiality 
In order to maintain subject confidentiality, only a subject number will identify all study subjects 
on CRFs and other documentation submitted to the Sponsor.  Additional subject confidentiality 
issues (if applicable) are covered in the Clinical Study Agreement. 
16 ADMINISTRATIVE, ETHICAL, REGULATORY CONSIDERATIONS 
The study will be conducted according to the Declaration of Helsinki, Protection of Human 
Volunteers (21 CFR 50), Institutional Review Boards (21 CFR 56), and Obligations of Clinical 
Investigators (21 CFR 312). 
To maintain confidentiality, all laboratory specimens, evaluation forms, reports and other records 
will be identified by a coded number and initials only.  All study records will be kept in a locked 
file cabinet and code sheets linking a patient’s name to a patient identification number will be 
stored separately in another locked file cabinet.  Clinical information will not be released without 
written permission of the subject, except as necessary for monitoring by the FDA.  The 
Investigator must also comply with all applicable privacy regulations (e.g., Health Insurance 
Portability and Accountability Act of 1996, EU Data Protection Directive 95/46/EC). 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
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16.1 Protocol Amendments 
Any amendment to the protocol will be written by Principal Investigator.  Protocol amendments 
cannot be implemented without prior written IRB/IEC approval except as necessary to eliminate 
immediate safety hazards to patients.  A protocol amendment intended to eliminate an apparent 
immediate hazard to patients may be implemented immediately, provided the IRBs are notified 
within five working days. 
16.2 Institutional Review Boards and Independent Ethics Committees 
The protocol and consent form will be reviewed and approved by the IRB/IEC of each 
participating center prior to study initiation.  Serious adverse experiences regardless of causality 
will be reported to the IRB/IEC in accordance with the standard operating procedures and 
policies of the IRB/IEC, and the Investigator will keep the IRB/IEC informed as to the progress 
of the study.  The Investigator will obtain assurance of IRB/IEC compliance with regulations. 
Any documents that the IRB/IEC may need to fulfill its responsibilities (such as protocol, 
protocol amendments, Investigator’s Brochure, consent forms, information concerning patient 
recruitment, payment or compensation procedures, or other pertinent information) will be 
submitted to the IRB/IEC.  The IRB/IECs written unconditional approval of the study protocol 
and the informed consent form will be in the possession of the Investigator before the study is 
initiated.  This approval must refer to the study by exact protocol title and number and should 
identify the documents reviewed and the date of review. 
Protocol and/or informed consent modifications or changes may not be initiated without prior 
written IRB/IEC approval except when necessary to eliminate immediate hazards to the patients 
or when the change(s) involves only logistical or administrative aspects of the study.  Such 
modifications will be submitted to the IRB/IEC and written verification that the modification 
was submitted and subsequently approved should be obtained.   
The IRB/IEC must be informed of revisions to other documents originally submitted for review; 
serious and/or unexpected adverse experiences occurring during the study in accordance with the 
standard operating procedures and policies of the IRB; new information that may affect 
adversely the safety of the patients of the conduct of the study; an annual update and/or request 
for re-approval; and when the study has been completed. 
16.3 Informed Consent Form  
Informed consent will be obtained in accordance with the Declaration of Helsinki, ICH GCP, US 
Code of Federal Regulations for Protection of Human Subjects (21 CFR 50.25[a,b], CFR 50.27, 
and CFR Part 56, Subpart A), the Health Insurance Portability and Accountability Act (HIPAA, 
if applicable), and local regulations. 
The Investigator will prepare the informed consent form, assent and HIPAA authorization and 
provide the documents to the Sponsor or designee for approval prior to submission to the 
IRB/IEC.  The consent form generated by the Investigator must be acceptable to the Sponsor and 
be approved by the IRB/IEC.  The written consent document will embody the elements of 
informed consent as described in the International Conference on Harmonisation and will also 
comply with local regulations. The Investigator will send an IRB/IEC-approved copy of the 
Informed Consent Form to the Sponsor (or designee) for the study file. 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
Version Date: 3/11/2016 
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A properly executed, written, informed consent will be obtained from each subject prior to 
entering the subject into the trial.  Information should be given in both oral and written form and 
subjects must be given ample opportunity to inquire about details of the study.  If appropriate 
and required by the local IRB/IEC, assent from the subject will also be obtained.  If a subject is 
unable to sign the informed consent form (ICF) and the HIPAA authorization, a legal 
representative may sign for the subject.   A copy of the signed consent form will be given to the 
subject and the original will be maintained with the subject’s records. 
16.4 Publications  
The preparation and submittal for publication of manuscripts containing the study results shall be 
in accordance with a process determined by mutual written agreement among the study Sponsor 
and participating institutions.  The publication or presentation of any study results shall comply 
with all applicable privacy laws, including, but not limited to, the Health Insurance Portability 
and Accountability Act of 1996.  
16.5 Investigator Responsibilities 
By signing the Agreement of Investigator form, the Investigator agrees to: 
1. Conduct the study in accordance with the protocol and only make changes after notifying 
the Sponsor (or designee), except when to protect the safety, rights or welfare of subjects. 
2. Personally conduct or supervise the study (or investigation). 
3. Ensure that the requirements relating to obtaining informed consent and IRB review and 
approval meet federal guidelines, as stated in § 21 CFR, parts 50 and 56. 
4. Report to the Sponsor or designee any AEs that occur in the course of the study, in 
accordance with §21 CFR 312.64. 
5. Ensure that all associates, colleagues and employees assisting in the conduct of the study are 
informed about their obligations in meeting the above commitments. 
6. Maintain adequate and accurate records in accordance with §21 CFR 312.62 and to make 
those records available for inspection with the Sponsor (or designee). 
7. Ensure that an IRB that complies with the requirements of §21 CFR part 56 will be 
responsible for initial and continuing review and approval of the clinical study. 
8. Promptly report to the IRB and the Sponsor (or designee) all changes in the research activity 
and all unanticipated problems involving risks to subjects or others (to include amendments 
and IND safety reports). 
9. Seek IRB approval before any changes are made in the research study, except when 
necessary to eliminate hazards to the patients/subjects. 
10. Comply with all other requirements regarding the obligations of clinical investigators and all 
other pertinent requirements listed in § 21 CFR part 312. 
 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
 
 
Version Date: 3/11/2016 
Page 29 of 33 
 
APPENDIX 1.  SCHEDULE OF STUDY VISITS 
 
 
ON STUDY DRUG 
 
 
VISIT 1 
Screening1 
VISIT 2 
BASELINE1 
VISIT 3 
WEEK 1 
VISIT 4 
WEEK  2 
VISIT 5 
WEEK 3 
VISIT 6 
WEEK 4 
VISIT 7 
WEEK 8 
VISIT 8 
WEEK 12 
VISIT 9 
WEEK 16 
VISIT 10 
WEEK 20 
VISIT 11 
WEEK 26 
VISIT 12 
WEEK 52 
Informed Consent 
X 
 
 
 
 
 
 
 
 
 
 
 
Record Medical History/Demographics 
X 
 
 
 
 
 
 
 
 
 
 
 
Complete Physical Exam 
X 
 
 
 
 
 
 
 
 
 
 
 
Abbreviated Physical Exam 
 
 
 
 
 
 
 
 
 
 
X 
 
Pregnancy Test (Urine)  
 
X 
 
 
 
 
 
 
 
 
 
 
Record CD4+/CD8+ T cell counts (as 
standard of care from primary provider) 
X 
X 
 
 
 
 
X 
 
 
 
X 
X 
Record HIV RNA: Standard assay (as 
standard of care from primary provider) 
X 
X 
 
 
 
 
X 
 
 
 
X 
X 
Start Study Drug 
 
X 
 
 
 
 
 
 
 
 
 
 
Initiate Subject Diary and Review 
(medication deviations and adverse 
events) 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Medication Review/Recording 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Evaluate for Adverse Events 
 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Stop Study Drug 
 
 
 
 
 
 
 
 
 
 
X 
 
Safety Labs2 
 
 
 
 
 
 
 
 
 
 
 
 
Record Complete Blood Count  
(Kidney, Liver) 
X 
X 
 
 
 
X 
X 
X 
X 
X 
X 
X 
Record Creatinine  (Kidney, Liver) 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Record BUN (Kidney, Liver) 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Record Sodium (Kidney, Liver) 
X 
X 
 
 
 
X 
X 
X 
X 
X 
X 
X 
Record Potassium  (Kidney, Liver) 
X 
X 
 
 
 
X 
X 
X 
X 
X 
X 
X 
Record Glucose  (Kidney, Liver) 
X 
X 
 
 
 
X 
X 
X 
X 
X 
X 
X 
Record Calcium (Kidney) 
X 
X 
 
 
 
X 
X 
X 
X 
X 
X 
X 


Protocol  HIVTR-EVE                                                                                       Peter Stock, MD, PhD 
 
 
 
Version Date: 3/11/2016 
Page 30 of 33 
 
 
 
ON STUDY DRUG 
 
 
VISIT 1 
Screening1 
VISIT 2 
BASELINE1 
VISIT 3 
WEEK 1 
VISIT 4 
WEEK  2 
VISIT 5 
WEEK 3 
VISIT 6 
WEEK 4 
VISIT 7 
WEEK 8 
VISIT 8 
WEEK 12 
VISIT 9 
WEEK 16 
VISIT 10 
WEEK 20 
VISIT 11 
WEEK 26 
VISIT 12 
WEEK 52 
Record CO2 (Kidney) 
X 
X 
 
 
 
X 
X 
X 
X 
X 
X 
X 
Record Magnesium (Kidney) 
X 
X 
 
 
 
X 
X 
X 
X 
X 
X 
X 
Record Phosphorous (Kidney) 
X 
X 
 
 
 
X 
X 
X 
X 
X 
X 
X 
Record Total Bilirubin (Liver) 
X 
X 
 
 
 
X 
X 
X 
X 
X 
X 
X 
Record SGOT/AST (Liver) 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Record SGOT/ALT (Liver) 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Record Alkaline Phosphatase (ALP) 
(Liver) 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Tacrolimus and Everolimus 12 hour 
trough levels  (Kidney, Liver) 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
MECHANISTIC STUDIES 
 
 
 
 
 
 
 
 
 
 
 
 
HIV RNA: Single copy assay 
X 
X 
 
 
 
 
X 
 
 
 
X 
X 
Cell associated HIV RNA and DNA in 
CD4+ T-cells (blood) 
X 
X 
 
 
 
 
X 
 
 
 
X 
X 
TILDA 
 
X 
 
 
 
 
 
 
 
 
X 
 
1 Visit 1 and Visit 2 can occur on the same day if the subject has been prescreened. In these cases, all events indicated for visit 1 and for visit 2 should be performed, but only once. 
2All safety labs are recorded from standard of care results for post kidney or liver transplant recipients except for the week 1, 2 and 3 safety labs post study drug initiation which 
will be performed for this protocol  
3Everolimus levels will be performed for this study at all indicated study visits. Tacrolimus levels will be recorded from standard of care results, except for the weeks 1, 2 and 3 
levels which will be performed for this protocol.  
 


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1. 
Chan, L., et al., Multicenter, randomized study of the use of everolimus with 
tacrolimus after renal transplantation demonstrates its effectiveness. 
Transplantation, 2008. 85(6): p. 821-6. 
2. 
Langer, R.M., et al., Everolimus plus early tacrolimus minimization: a phase III, 
randomized, open-label, multicentre trial in renal transplantation. Transpl Int, 
2012. 25(5): p. 592-602. 
3. 
Pascual, J., et al., Interaction between everolimus and tacrolimus in renal 
transplant recipients: a pharmacokinetic controlled trial. Transplantation, 2010. 
89(8): p. 994-1000. 
4. 
Stock, P.G., et al., Reduction of HIV persistence following transplantation in HIV-
infected kidney transplant recipients. Am J Transplant, 2014. 14(5): p. 1136-41. 
5. 
Finzi, D., et al., Identification of a reservoir for HIV-1 in patients on highly active 
antiretroviral therapy. Science, 1997. 278(5341): p. 1295-300. 
6. 
Persaud, D., et al., Latency in human immunodeficiency virus type 1 infection: no 
easy answers. J Virol, 2003. 77(3): p. 1659-65. 
7. 
Chun, T.W., et al., Presence of an inducible HIV-1 latent reservoir during highly 
active antiretroviral therapy. Proc Natl Acad Sci U S A, 1997. 94(24): p. 13193-7. 
8. 
Chun, T.W., et al., Early establishment of a pool of latently infected, resting 
CD4(+) T cells during primary HIV-1 infection. Proceedings of the National 
Academy of Sciences of the United States of America, 1998. 95(15): p. 8869-73. 
9. 
Chun, T.W., et al., Quantification of latent tissue reservoirs and total body viral 
load in HIV-1 infection. Nature, 1997. 387(6629): p. 183-8. 
10. 
Chun, T.W., et al., Re-emergence of HIV after stopping therapy. Nature, 1999. 
401(6756): p. 874-5. 
11. 
Finzi, D., et al., Latent infection of CD4+ T cells provides a mechanism for lifelong 
persistence of HIV-1, even in patients on effective combination therapy. Nat Med, 
1999. 5(5): p. 512-7. 
12. 
Chomont, N., et al., HIV reservoir size and persistence are driven by T cell survival 
and homeostatic proliferation. Nat Med, 2009. 15(8): p. 893-900. 
13. 
Vandergeeten, C., et al., Interleukin-7 promotes HIV persistence during 
antiretroviral therapy. Blood, 2013. 121(21): p. 4321-9. 
14. 
Buzon, M.J., et al., HIV-1 replication and immune dynamics are affected by 
raltegravir intensification of HAART-suppressed subjects. Nat Med, 2010. 16(4): p. 
460-5. 
15. 
Hatano, H., et al., Cell-Based Measures of Viral Persistence Are Associated With 
Immune Activation and Programmed Cell Death Protein 1 (PD-1)-Expressing 
CD4+ T cells. The Journal of infectious diseases, 2012. 
16. 
Murray, J.M., et al., HIV DNA subspecies persist in both activated and resting 
memory CD4+ T cells during antiretroviral therapy. Journal of virology, 2014. 
88(6): p. 3516-26. 


Protocol Number 
Confidential 
 
 
Version Date: 3/20/2015  
Page 32 of 33 
Protocol Template © CFFT TDN   Effective: 12 SEP 2007 
17. 
Klatt, N.R., et al., Immune activation and HIV persistence: implications for curative 
approaches to HIV infection. Immunological reviews, 2013. 254(1): p. 326-42. 
18. 
Maldarelli, F., et al., HIV latency. Specific HIV integration sites are linked to clonal 
expansion and persistence of infected cells. Science, 2014. 345(6193): p. 179-83. 
19. 
Wagner, T.A., et al., HIV latency. Proliferation of cells with HIV integrated into 
cancer genes contributes to persistent infection. Science, 2014. 345(6196): p. 570-
3. 
20. 
Chevalier, M.F. and L. Weiss, The split personality of regulatory T cells in HIV 
infection. Blood, 2013. 121(1): p. 29-37. 
21. 
Chevalier, M.F., et al., The Th17/Treg ratio, IL-1RA and sCD14 levels in primary 
HIV infection predict the T-cell activation set point in the absence of systemic 
microbial translocation. PLoS Pathog, 2013. 9(6): p. e1003453. 
22. 
Riou, C., et al., Convergence of TCR and cytokine signaling leads to FOXO3a 
phosphorylation and drives the survival of CD4+ central memory T cells. J Exp 
Med, 2007. 204(1): p. 79-91. 
23. 
Heredia, A., et al., Rapamycin causes down-regulation of CCR5 and accumulation 
of anti-HIV beta-chemokines: an approach to suppress R5 strains of HIV-1. Proc 
Natl Acad Sci U S A, 2003. 100(18): p. 10411-6. 
24. 
Zhou, D., K.H. Kang, and S.A. Spector, Production of interferon alpha by human 
immunodeficiency virus type 1 in human plasmacytoid dendritic cells is dependent 
on induction of autophagy. The Journal of infectious diseases, 2012. 205(8): p. 
1258-67. 
25. 
Zhou, D. and S.A. Spector, Human immunodeficiency virus type-1 infection inhibits 
autophagy. AIDS, 2008. 22(6): p. 695-9. 
26. 
Araki, K., et al., mTOR regulates memory CD8 T-cell differentiation. Nature, 2009. 
460(7251): p. 108-12. 
27. 
Yukl, S.A., et al., Modification of the Abbott RealTime assay for detection of HIV-1 
plasma RNA viral loads less than one copy per milliliter. J Virol Methods, 2011. 
175(2): p. 261-5. 
28. 
Frassetto, L., et al., Changes in clearance, volume and bioavailability of 
immunosuppressants when given with HAART in HIV-1 infected liver and kidney 
transplant recipients. Biopharm Drug Dispos, 2013. 34(8): p. 442-51. 
29. 
Frassetto, L.A., et al., Immunosuppressant pharmacokinetics and dosing 
modifications in HIV-1 infected liver and kidney transplant recipients. Am J 
Transplant, 2007. 7(12): p. 2816-20. 
30. 
Frassetto LA, C.W., Kansal N, Levi M, Carlson L, Roland ME, Stock PG, Benet 
LZ. Immunosuppressant adjustments of doses and dosing intervals in HIV-infected 
kidney and liver transplant patients. in TransplantAsia 2004. 2004. Singapore. 
31. 
Vandergeeten, C., et al., Cross-clade ultrasensitive PCR-based assays to measure 
HIV persistence in large-cohort studies. J Virol, 2014. 88(21): p. 12385-96. 
32. 
Lewin, S.R., et al., Use of real-time PCR and molecular beacons to detect virus 
replication in human immunodeficiency virus type 1-infected individuals on 
prolonged effective antiretroviral therapy. J Virol, 1999. 73(7): p. 6099-103. 


Protocol Number 
Confidential 
 
 
Version Date: 3/20/2015  
Page 33 of 33 
Protocol Template © CFFT TDN   Effective: 12 SEP 2007 
33. 
Yukl, S.A., et al., The distribution of HIV DNA and RNA in cell subsets differs in 
gut and blood of HIV-positive patients on ART: implications for viral persistence. J 
Infect Dis, 2013. 208(8): p. 1212-20. 
34. 
Pasternak, A.O., et al., Cellular levels of HIV unspliced RNA from patients on 
combination antiretroviral therapy with undetectable plasma viremia predict the 
therapy outcome. PloS one, 2009. 4(12): p. e8490.