untitled h1
8.4.4 events of special interest

Selected non-serious and serious adverse events are also known as Events of Clinical Interest (ECI) and must be recorded as such on the Adverse Event case report form and reported within 24 hours to Merck Global Safety (See Section 8.1.2). Events of clinical interest for this trial include: 1. An overdose of Merck product, (as defined in Section 8.1.1.1 - Definition of an Overdose) that is not associated with clinical symptoms or abnormal laboratory results. 2. An elevated AST or ALT lab value that is greater than or equal to 3X the upper limit of normal and an elevated total bilirubin lab value that is greater than or equal to 2X the upper limit of normal and, at the same time, an alkaline phosphatase lab value that is less than 2X the upper limit of normal, as determined by way of protocol-specified laboratory testing or unscheduled laboratory testing.  
3. In the event a subject develops any of the following AEs, a detailed narrative of the event should be reported as an ECI within 24 hours to Merck Global Safety (See Section 8.1.2)
a. Grade ≥ 3 diarrhea b. Grade ≥ 3 colitis c. Grade ≥ 2 pneumonitis d. Grade ≥ 3 hypo- or hyperthyroidism A separate guidance document has been provided entitled "event of Clinical Interest and ImmuneRelated Adverse Event Guidance Document." This document provides guidance regarding identification, evaluation and management of ECIs and irAEs. Additional ECIs are identified in this guidance document and also need to be reported within 24 hours to Merck Global Safety.  
Subjects should be assessed for possible ECIs prior to each dose. Lab results should be evaluated and subjects should be asked for signs and symptoms suggestive of an immune-related event. Subjects who develop an ECI thought to be immune-related should have additional testing to rule out other etiologic causes. If lab results or symptoms indicate a possible immune-related ECI, then additional testing should be performed to rule out other etiologic causes. If no other cause is found, then it is assumed to be immune-related.  
ECIs that occur in any subject from the date of first dose through 90 days following cessation of treatment, or the initiation of a new anticancer therapy, whichever is earlier, whether or not related to the Merck's product, must be reported within 24 hours to Merck Global Safety (See Section 8.1.2).
untitled h1
8.4.4.2 janssen special reporting situations

Safety events of interest for a Janssen medicinal product that require expediting reporting and/or safety evaluation include, but are not limited to:
- Drug exposure during pregnancy (maternal and paternal)
- Overdose of a Janssen medicinal product - Exposure to a Janssen medicinal product from breastfeeding - Suspected abuse/misuse of a Janssen medicinal product
- Inadvertent or accidental exposure to a Janssen medicinal product
- Any failure of expected pharmacological action (i.e., lack of effect) of a Janssen medicinal product
- Medication error involving a Janssen medicinal product (with or without patient exposure to the Janssen medicinal product, e.g., name confusion)
- Suspected transmission of any infectious agent via administration of a medicinal product
- Unexpected therapeutic or clinical benefit from use of a Janssen medicinal product These safety events may not meet the definition of an adverse event; however, from Janssen Scientific Affairs, LLC perspective, they are treated in the same manner as adverse events. Special situations should be recorded on the Adverse Event page of the CRF.
untitled h1
8.5 study halting rules

Safety assessments will consist of monitoring and recording all adverse events and serious adverse events, the regular monitoring of hematology and blood chemistry parameters and regular physical examinations. Adverse events will be evaluated continuously throughout the study. Safety and tolerability will be assessed according to the NIH/NCI Common Terminology Criteria for Adverse Events version 5.0 (CTCAE v5.0) that is available at: http://evs.nci.nih.gov/ftp1/CTCAE/About.html The Protocol Monitoring Committee (PMC) at Moffitt monitors its assigned ongoing research protocols for: adverse event reporting, data and safety monitoring, and internal audit findings. The PMC, upon review of any agenda item, may approve the study for continuation, require revisions, suspend or close a protocol. Investigators of studies which are designated to be reviewed by the PMC for data and safety monitoring, shall provide a statistical report of the study's progress and summary of adverse events and deviations based on the phase of the study and the associated risk of the study or more often if applicable. The PI will be notified for recommendations or notifications after the PMC review in regards of continuation or stopping the clinical trial Serious Adverse Events: Serious Adverse Events (SAEs) from this protocol will be reported concurrently to the IRB and the study sponsor within 24 hours of staff awareness of the event. The Protocol Monitoring Committee (PMC) will review these SAEs in accordance with their policy. The data and safety plan will define dose limiting toxicities, rules for escalation of dose, and criteria for stopping the trial according to rules set forth by this protocol. This trial will be continuously monitored by the PI and the research team. A final safety and monitoring report will be submitted to the PMC. This protocol will be subject to periodic internal audits based on risk or as recommended by the PMC.
untitled h1
9 clinical monitoring

Data will be captured in OnCore, Moffitt's electronic Clinical Trials Database. For each participant enrolled, the electronic CRF must be completed by the assigned data manager or other authorized study staff. Any paper forms should be typed or filled out indelible ink and must be legible. Errors should be crossed out but not obliterated, the correction inserted, and the change initialed and dated by the investigator or his/her authorized delegate. This also applies to records for those patients who fail to complete the study. If a patient stops dosing or terminates from the study, the dates and reasons must be noted on the CRF. If a patient terminates from the study because of a DLT, thorough efforts should be made to clearly document the outcome. Regulatory documents and case reports forms will be monitored internally according to the Moffitt Cancer Center monitoring policies. Monitoring will be performed regularly by the MCC Clinical Monitoring Core for accuracy, completeness, and source verification on data entry, validation of appropriate consent process, reporting on SAEs, and adherence of the protocol, GCP guidelines and applicable regulatory requirements.
untitled h1
10 statistical considerations 10.1 statistical

Enrolled patients will be evaluable for response assessment if receiving at least 4 weeks into ibrutinib therapy and at least 2 cycles of pembrolizumab. It will be used for efficacy and safety analysis. The primary endpoint of this trial is the complete response (CR) with the hypothesis of obtaining CR in 30% of patients and the secondary end point is the overall response rate (ORR, the immune response to the vaccine measured as T cell subset alterations, B-cell immune response potency to the vaccine and the cytokine patterns in treated patients. Exact binomial 95% confidence intervals for the true ORR will be calculated.
untitled h1
10.2 description of statistical methods

The Simon's minmax two-stage design will be used to test the null hypothesis that complete response (CR) ≤
10% versus the alternative that CR ≥ 30% with 90% power and a type I error rate of 10%. This will result in an expected sample size of 20.37 and a probability of early termination of 0.52. After testing the drug combination on 16 patients in the first stage, the trial will be terminated if 1 or fewer respond. If the trial goes on to the second stage, a total of 25 patients will be studied. If the total number responding is less than or equal to 4, the drug combination will be rejected. Statistical analyses will be descriptive in nature. Patients' demographics, AEs and serious AEs, disease status, and CR will summarized by descriptive statistics.  
Clinical response rates will be calculated with 95% CIs.  
10.2.2 ANALYSIS OF THE SECONDARY ENDPOINT(S)
1. Change in T cell exhaustion and/or inhibition following treatment 2. Change in serum immunoglobulin levels following treatment 3. Progression free survival (PFS) and association with immune biomarkers To determine if T cell exhaustion or inhibition have change due to treatment with the combination therapy at baseline immune testing to immune testing following completion of pembrolizumab and ibruntinib treatments
(week 52) using paired t-tests with the null hypothesis being that there is no change in immune measurements following treatment (i.e., :  = 0). If the assumptions of normality do not hold upon assessment, we will instead use nonparametric t-tests (i.e., Wilcoxon Sign Rank Test). Similar tests will be used to determine if changes in serum immunoglobulin levels also resulted following treatment. Tests will be one-sided as based on biology expect the change in immune response to be in one direction following treatment. Tests will be considered statistically significant if the p-value is less than 0.05. Assuming the study go on to stage II and enroll 25 patients, we will be able to detect a modest effect size of 0.60. To determine the association of progression free survival (PFS) with immune biomarkers (T cell exhaustion and/or inhibition, serum immunoglobulin levels), Cox proportional hazards models will be fit with assumption of proportional hazards
(PH) assumption check via Schoenfeld residuals. If the PH assumption does not hold, we will rely on use of non-parametric methods (Kaplan-Meier curve with log-rank tests) where the biomarkers will be dichotomized for analysis based on an optimal cut-point determination based on an outcome-oriented approach outlined by Contral and O'Quigley (Contal C, O'Quigley J. An application of changepoint methods in studying the effect of age on survival in breast cancer. Computational Statistics & Data Analysis. 1999;30:253-70.). A Cox regression of the log hazard ratio on the continuous biomarker (assuming a standard deviation of 1 and an anticipated event rate of 0.50) will have 80% power at a 0.05 significance level to detect a regression coefficient equal to 0.79 (i.e., hazard ratio of 2.20).
untitled h1
10.2.3safety review

Evaluation is based on strict stopping criteria for unacceptable toxicities. Specifically, in the 1st stage, we continuously evaluate toxicity for the 1st 16 patients (e.g., patients in first stage of Phase II study). Toxicity will be also evaluated at end of the 2nd stage for the total 25 patients. We consider 20% as the maximum allowable unacceptable toxicity rate (failure to engraft included) with a 0.05 probability of stopping early. Sequential boundaries will be used to monitor dose-limiting toxicity rate as outlined by Ivanova et al. [59]. The accrual will be halted if excessive numbers of dose-limiting toxicities are seen, that is, if the number of dose-limiting toxicities is equal to or exceeds bn out of n patients (see table below).
untitled h1
number of patients n 1

Biological samples for each of the 25 patients enrolled in the trial will be collected at 4 time-points. As the correlative experiments are not the primary focus of the study and are more exploratory in nature, no sample size / power calculations were completed. Summary statistics will be used to summarize the quantitative measures (e.g., cytokine levels, expression levels) for the patients at the 4 time-points with two-sample t-test use to determine if quantitative measurements differ between patients that response and patients that do not response at each time point. When assessing changes in quantitative measurements between time-points (e.g., pre and post treatment measurements) paired t-tests will be used. Longitudinal analysis with linear mixed models will also be used to look for statistical differences between the responders and non-responders using quantitative measurements at all 4 time-points. Correlation between quantitative measurements will be assessed with Spearman correlation.
untitled h1
11 source documents and access

The PI and other appropriate study staff are responsible for maintaining appropriate medical and research records for this trial, in compliance with ICH E6 and regulatory and institutional requirements for the protection of confidentiality of participants. Representatives of Merck, Janssen, and federal regulatory agencies may examine records for the purpose of quality assurance reviews, evaluation of the study safety, progress of the trial, and data validity. Source documentation in both electronic and paper form shall be retained for at least two years after the final closure of the trial. These include hospital records, clinical research subject charts (with paper AE
logs), research laboratory notes, electronic CRFs, and pharmacy dispensing records.
untitled h1
12 quality assurance and quality

Quality control procedures will be implemented beginning with the OnCore data entry system and data QC checks that will be run on the database will be generated. Any missing data or data anomalies will be communicated to the staff for clarification/resolution.  
Following written SOPs, the Moffitt internal monitors will verify that the clinical trial is conducted and data are generated, documented (recorded), and reported in compliance with the protocol, GCP, and the applicable regulatory requirements (e.g., good laboratory practices (GLP), good manufacturing practices (GMP)).  
The investigational site will provide direct access to source data/documents, and reports for the purpose of monitoring and auditing, and inspection by local and regulatory authorities.  
All staff will be trained by the PI through a site initiation presentation, power point training for training on the initial protocol for those staff unable to attend the initiation presentation, and ongoing self-study as protocol amendments are approved. Training will be documented on a signature log that will be filed in the electronic regulatory binder.  
13 ETHICS/PROTECTION OF HUMAN SUBJECTS
untitled h1
13.1 ethical standard

The investigator will ensure that this study is conducted in full conformity with Regulations for the Protection of Human Subjects of Research codified in 45 CFR Part 46, 21 CFR Part 50, 21 CFR Part 56, and/or the ICH E6.
untitled h1
13.2 institutional review board

The protocol, informed consent form(s), recruitment materials, and all participant materials will be submitted to the IRB for review and approval. Approval of both the protocol and the consent form must be obtained before any participant is enrolled. Any amendment to the protocol will require review and approval by the IRB before the changes are implemented to the study. All changes to the consent form will be IRB approved; a determination will be made regarding whether previously consented participants need to be re-consented.
untitled h1
participants

Consent forms describing in detail the study agent, study procedures, and risks will be given to the participant and written documentation of informed consent will be required prior to starting intervention/administering study product.  
Other documents to be submitted for review:
- Oral study drug Patient Compliance Diary
untitled h1
13.3.2 consent procedures and documentation

Informed consent is a process that is initiated prior to the individual's agreeing to participate in the study and continues throughout the individual's study participation. Extensive discussion of risks and possible benefits of participation will be provided to the participants and their families. Consent forms will be IRBapproved and the participant will be asked to read and review the document. The investigator will explain the research study to the participant and answer any questions that may arise. All participants will receive a verbal explanation in terms suited to their comprehension of the purposes, procedures, and potential risks of the study and of their rights as research participants. Participants will have the opportunity to carefully review the written consent form and ask questions prior to signing.  
The participants should have the opportunity to discuss the study with their surrogates or think about it prior to agreeing to participate. The participant will sign the informed consent document prior to any procedures being done specifically for the study. The participants may withdraw consent at any time throughout the course of the trial. A copy of the informed consent document will be given to the participants for their records. The rights and welfare of the participants will be protected by emphasizing to them that the quality of their medical care will not be adversely affected if they decline to participate in this study.
untitled h1
13.4 participant and data confidentiality

Participant confidentiality is strictly held in trust by the participating investigators, their staff, and the Moffitt Cancer Center Protocol Template - v3.2 2018-08-10 51 sponsor and their agents. This confidentiality is extended to cover testing of biological samples and genetic tests in addition to the clinical information relating to participants. Therefore, the study protocol, documentation, data, and all other information generated will be held in strict confidence. No information concerning the study or the data will be released to any unauthorized third party without prior written approval of the sponsor. The Moffitt study monitor, other authorized representatives of Moffitt, representatives of the IRB or pharmaceutical companies supplying study products may inspect all documents and records required to be maintained by the investigator, including but not limited to, medical records (office, clinic, or hospital) and pharmacy records for the participants in this study. The clinical study site will permit access to such records. The study participant's contact information will be securely stored at each clinical site for internal use during the study. At the end of the study, all records will continue to be kept in a secure location for as long a period as dictated by local IRB and Institutional regulations.  
Study participant research data, which is for purposes of statistical analysis and scientific reporting, will be transmitted to and stored at Moffitt. This will not include the participants' contact or identifying information. Rather, individual participants and their research data will be identified by a unique study identification number. The study data entry and study management systems used by clinical sites and by Moffitt research staff will be secured and password protected. At the end of the study, all study databases will be de-identified and archived at the Moffitt.
untitled h1
13.5 future use of stored

Data collected for this study will be analyzed and stored at Moffitt Cancer Center. After the study is completed, the de-identified, archived data will be stored at Moffitt Cancer Center, under the supervision of Eva Sahakian, PhD, for use by other researchers including those outside of the study. Software tracking programs include FileMaker Pro and Excel.  
With the participant's approval and as approved by local IRBs, de-identified biological samples will be stored at Dr. Sahakian's lab at Moffitt Cancer Center. These samples could be used for research into the causes of CLL, its complications, and other conditions for which individuals with CLL are at increased risk, and to improve treatment. After completion of the study, samples to be stored will be identified by using only the subject initials and date of collection. During the conduct of the study, an individual participant can choose to withdraw consent to have biological specimens stored for future research. However, withdrawal of consent with regard to biosample storage will not be possible after the study is completed. When the study is completed, access to study data and/or samples will be provided through Eva Sahakian, PhD or her successor.
untitled h1
14 data handling and record

Data collection is the responsibility of the clinical trial staff at the site under the supervision of the site PI. The PI is responsible for ensuring the accuracy, completeness, legibility, and timeliness of the data reported.  
Protocol <\#>
All source documents should be completed in a neat, legible manner to ensure accurate interpretation of data. Black ink is required to ensure clarity of reproduced copies. When making changes or corrections, cross out the original entry with a single line, and initial and date the change. All paper source documents will be scanned into the electronic medical record of each subject for storage. DO NOT
ERASE, OVERWRITE, OR USE CORRECTION FLUID OR TAPE ON THE ORIGINAL.  
Copies of the electronic CRF (eCRF) will be provided for use as source documents and maintained for recording data for each participant enrolled in the study. Data reported in the eCRF derived from source documents should be consistent with the source documents or the discrepancies should be explained and captured in a progress note and maintained in the participant's official electronic study record.  
Clinical data (including AEs, concomitant medications, and expected adverse reactions data) and clinical laboratory data will be entered into OnCore, a 21 CFR Part 11-compliant data capture system provided by Moffitt. The data system includes password protection and internal quality checks, such as automatic range checks, to identify data that appear inconsistent, incomplete, or inaccurate. Clinical data will be entered directly from the source documents.
untitled h1
14.2 study records retention

Study documents should be retained for a minimum of 2 years after the last approval of a marketing application in an ICH region and until there are no pending or contemplated marketing applications in an ICH region or until at least 2 years have elapsed since the formal discontinuation of clinical development of the drug combination studied in this protocol. No records will be destroyed without the written consent of the sponsor, if applicable.
untitled h1
14.3 protocol deviations

A protocol deviation is any noncompliance with the clinical trial protocol, GCP, or MOP requirements.  
The noncompliance may be either on the part of the participant, the investigator, or the study site staff. As a result of deviations, corrective actions are to be developed by the site and implemented promptly.  
These practices are consistent with ICH E6:
- 4.5 Compliance with Protocol, sections 4.5.1, 4.5.2, and 4.5.3
- 5.1 Quality Assurance and Quality Control, section 5.1.1
- 5.20 Noncompliance, sections 5.20.1, and 5.20.2.  
It is the responsibility of the site to use continuous vigilance to identify and report deviations as defined by the Moffitt Clinical Trials Office standard. All deviations must be addressed in study source documents. Protocol deviations must be sent to the local IRB per their guidelines. The site PI/study staff is responsible for knowing and adhering to their IRB requirements.
untitled h1
14.4 publication and data sharing

The International Committee of Medical Journal Editors (ICMJE) member journals have adopted a clinical trials registration policy as a condition for publication. The ICMJE defines a clinical trial as any research project that prospectively assigns human subjects to intervention or concurrent comparison or control groups to study the cause-and-effect relationship between a medical intervention and a health outcome.  
Medical interventions include drugs, surgical procedures, devices, behavioral treatments, process-of-care changes, and the like. Health outcomes include any biomedical or health-related measures obtained in Moffitt Cancer Center Protocol Template - v3.2 2018-08-10 53 Protocol <\#>
patients or participants, including pharmacokinetic measures and adverse events. The ICMJE policy, and the Section 801 of the Food and Drug Administration Amendments Act of 2007, requires that all clinical trials be registered in a public trials registry such as ClinicalTrials.gov, which is sponsored by the National Library of Medicine.  
The PI will provide to the Protocol Information Specialist at Moffitt Cancer Center, details as requested for registering and reporting results for this clinical trial on ClinicalTrials.gov. At the conclusion of the trial, the PI will make study results available to the research community and the public-at-large. Authorship in publications will be determined by the PI depending on participation, enrollment, and significant contribution during trial process and manuscript elaboration.
untitled h1
16 conflict of interest policy

The independence of this study from any actual or perceived influence, such as by the pharmaceutical industry, is critical. Therefore any actual conflict of interest of persons who have a role in the design, conduct, analysis, publication, or any aspect of this trial will be disclosed and managed. Furthermore, persons who have a perceived conflict of interest will be required to have such conflicts managed in a way that is appropriate to their participation in the trial. The study leadership and the Moffitt Cancer Center have established policies and procedures for all study group members to disclose all conflicts of interest and will establish a mechanism for the management of all reported dualities of interest.
untitled h1
17 literature references

1. Jemal, A., et al., *Cancer statistics, 2007.* CA Cancer J Clin, 2007. 57(1): p. 43-66.  
2. Molica, S., *Sex differences in incidence and outcome of chronic lymphocytic leukemia patients.* Leuk Lymphoma, 2006. 47(8): p. 1477-80.  
3. Morton, L.M., et al., Lymphoma *incidence patterns by WHO subtype in the United States, 1992-2001.*
Blood, 2006. 107(1): p. 265-76.  
4. Watson, L., P. Wyld, and D. Catovsky, Disease burden of chronic lymphocytic leukaemia within the European Union. Eur J Haematol, 2008. 81(4): p. 253-8.  
5. Mauro, F.R., et al., Clinical characteristics and outcome of young chronic lymphocytic leukemia patients: a single institution study of 204 cases. Blood, 1999. 94(2): p. 448-54.  
6. Chiorazzi, N., K.R. Rai, and M. Ferrarini, *Chronic lymphocytic leukemia.* N Engl J Med, 2005. 352(8): p.  
804-15.  
7. Kikushige, Y., et al., Self-renewing hematopoietic stem cell is the primary target in pathogenesis of human chronic lymphocytic leukemia. Cancer Cell, 2011. 20(2): p. 246-59.  
8. Calin, G.A., et al., Frequent deletions and down-regulation of micro- *RNA genes miR15 and miR16 at* 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A, 2002. 99(24): p. 15524-9.  
9. Zenz, T., et al., *From pathogenesis to treatment of chronic lymphocytic leukaemia.* Nat Rev Cancer, 2010. 10(1): p. 37-50.  
10. Quesada, V., et al., *Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene* Moffitt Cancer Center Protocol Template - v3.2 2018-08-10 54 in chronic lymphocytic leukemia. Nat Genet, 2012. 44(1): p. 47-52.  
11. Hallek, M., et al., *Addition of rituximab to fludarabine and cyclophosphamide in patients with chronic* lymphocytic leukaemia: a randomised, open-label, phase 3 trial. Lancet, 2010. 376(9747): p. 1164-74.  
12. Zenz, T., et al., TP53 mutation profile in chronic lymphocytic leukemia: evidence for a disease specific profile from a comprehensive analysis of 268 mutations. Leukemia, 2010. 24(12): p. 2072-9.  
13. Puente, X.S., et al., *Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic* leukaemia. Nature, 2011. 475(7354): p. 101-5.  
14. Hallek, M., et al., Guidelines for the diagnosis and treatment of chronic lymphocytic leukemia: a report from the International Workshop on Chronic Lymphocytic Leukemia updating the National Cancer Institute-Working Group 1996 guidelines. Blood, 2008. 111(12): p. 5446-56.  
15. Disis, M.L., *Immune regulation of cancer.* J Clin Oncol, 2010. 28(29): p. 4531-8.  
16. Dong, H., et al., Tumor-associated B7-H1 promotes T-cell apoptosis: a potential mechanism of immune evasion. Nat Med, 2002. 8(8): p. 793-800.  
17. Sharpe, A.H. and G.J. Freeman, *The B7-CD28 superfamily.* Nat Rev Immunol, 2002. 2(2): p. 116-26.  
18. Brown, J.A., et al., Blockade of programmed death-1 ligands on dendritic cells enhances T cell activation and cytokine production. J Immunol, 2003. 170(3): p. 1257-66.  
19. Francisco, L.M., P.T. Sage, and A.H. Sharpe, *The PD-1 pathway in tolerance and autoimmunity.*
Immunol Rev, 2010. 236: p. 219-42.  
20. Hamblin, A.D. and T.J. Hamblin, *The immunodeficiency of chronic lymphocytic leukaemia.* Br Med Bull, 2008. 87: p. 49-62.  
21. Thompson, R.H., et al., PD-1 is expressed by tumor-infiltrating immune cells and is associated with poor outcome for patients with renal cell carcinoma. Clin Cancer Res, 2007. 13(6): p. 1757-61.  
22. Talmadge, J.E., M. Donkor, and E. Scholar, *Inflammatory cell infiltration of tumors: Jekyll or Hyde.*
Cancer Metastasis Rev, 2007. 26(3-4): p. 373-400.  
23. Usubutun, A., et al., *Prognostic factors in renal cell carcinoma.* J Exp Clin Cancer Res, 1998. 17(1): p.  
77-81.  
24. Al-Shibli, K.I., et al., *Prognostic effect of epithelial and stromal lymphocyte infiltration in non-small cell* lung cancer. Clin Cancer Res, 2008. 14(16): p. 5220-7.  
25. Wolchok, J.D., et al., Guidelines for the evaluation of immune therapy activity in solid tumors:
immune-related response criteria. Clin Cancer Res, 2009. 15(23): p. 7412-20.  
26. Lyford-Pike, S., et al., *Evidence for a role of the PD-1:PD-L1 pathway in immune resistance of HPVassociated head and neck squamous cell carcinoma.* Cancer Res, 2013. 73(6): p. 1733-41.  
27. Deschoolmeester, V., et al., Tumor infiltrating lymphocytes: an intriguing player in the survival of colorectal cancer patients. BMC Immunol, 2010. 11: p. 19.  
28. Shaffer, A.L., A. Rosenwald, and L.M. Staudt, *Lymphoid malignancies: the dark side of B-cell* differentiation. Nat Rev Immunol, 2002. 2(12): p. 920-32.  
29. Bishop, G.A., et al., *Antigen-specific B-lymphocyte activation.* Crit Rev Immunol, 2003. 23(3): p. 14997.  
30. Byrd, J.C., et al., *Targeting BTK with ibrutinib in relapsed chronic lymphocytic leukemia.* N Engl J Med, 2013. 369(1): p. 32-42.  
31. Treon, S.P., et al., *Ibrutinib in previously treated Waldenstrom's macroglobulinemia.* N Engl J Med, 2015. 372(15): p. 1430-40.  
32. de Claro, R.A., et al., FDA Approval: Ibrutinib for Patients with Previously Treated Mantle Cell Lymphoma and Previously Treated Chronic Lymphocytic Leukemia. Clin Cancer Res, 2015. 21(16): p.  
3586-90.  
33. Wang, M.L., et al., *Targeting BTK with ibrutinib in relapsed or refractory mantle-cell lymphoma.* N Engl J Med, 2013. 369(6): p. 507-16.  
34. Dubovsky, J.A., et al., Ibrutinib is an irreversible molecular inhibitor of ITK driving a Th1-selective pressure in T lymphocytes. Blood, 2013. 122(15): p. 2539-49.  
35. Mizoguchi, H., et al., *Alterations in signal transduction molecules in T lymphocytes from tumorbearing mice.* Science, 1992. 258(5089): p. 1795-8.  
Moffitt Cancer Center Protocol Template - v3.2 2018-08-10 55 36. Spranger, S., et al., Up-regulation of PD-L1, IDO, and T(regs) in the melanoma tumor microenvironment is driven by CD8(+) T cells. Sci Transl Med, 2013. 5(200): p. 200ra116.  
37. Drake, C.G., E. Jaffee, and D.M. Pardoll, *Mechanisms of immune evasion by tumors.* Adv Immunol, 2006. 90: p. 51-81.  
38. Topalian, S.L., C.G. Drake, and D.M. Pardoll, Targeting the PD-1/B7-H1(PD-L1) pathway to activate anti-tumor immunity. Curr Opin Immunol, 2012. 24(2): p. 207-12.  
39. Rabinovich, G.A., D. Gabrilovich, and E.M. Sotomayor, Immunosuppressive strategies that are mediated by tumor cells. Annu Rev Immunol, 2007. 25: p. 267-96.  
40. Chen, D.S., B.A. Irving, and F.S. Hodi, *Molecular pathways: next-generation immunotherapy--*
inhibiting programmed death-ligand 1 and programmed death-1. Clin Cancer Res, 2012. 18(24): p.  
6580-7.  
41. Chen, D.S. and I. Mellman, *Oncology meets immunology: the cancer-immunity cycle.* Immunity, 2013.  
39(1): p. 1-10.  
42. Coulie, P.G., et al., *Tumour antigens recognized by T lymphocytes: at the core of cancer* immunotherapy. Nat Rev Cancer, 2014. 14(2): p. 135-46.  
43. Hegde, P.S., V. Karanikas, and S. Evers, The Where, the When, and the How of Immune Monitoring for Cancer Immunotherapies in the Era of Checkpoint Inhibition. Clin Cancer Res, 2016. 22(8): p. 1865-74.  
44. Slaney, C.Y., M.H. Kershaw, and P.K. Darcy, *Trafficking of T cells into tumors.* Cancer Res, 2014.  
74(24): p. 7168-74.  
45. Lennerz, V., et al., *The response of autologous T cells to a human melanoma is dominated by mutated* neoantigens. Proc Natl Acad Sci U S A, 2005. 102(44): p. 16013-8.  
46. Gabrilovich, D.I., I.F. Ciernik, and D.P. Carbone, Dendritic cells in antitumor immune responses. I.  
Defective antigen presentation in tumor-bearing hosts. Cell Immunol, 1996. 170(1): p. 101-10.  
47. Brahmer, J.R., et al., *Safety and activity of anti-PD-L1 antibody in patients with advanced cancer.* N
Engl J Med, 2012. 366(26): p. 2455-65.  
48. Joyce, J.A. and D.T. Fearon, T cell *exclusion, immune privilege, and the tumor microenvironment.*
Science, 2015. 348(6230): p. 74-80.  
49. Taube, J.M., et al., Colocalization of inflammatory response with B7-h1 expression in human melanocytic lesions supports an adaptive resistance mechanism of immune escape. Sci Transl Med, 2012. 4(127): p. 127ra37.  
50. Ribas, A., et al. Association of response to programmed death receptor 1 (PD-1) blockade with pembrolizumab (MK-3475) with an interferon-inflammatory immune gene signature. in ASCO Annual Meeting Proceedings. 2015.  
51. Kim, J.M. and D.S. Chen, *Immune escape to PD-L1/PD-1 blockade: seven steps to success (or failure).*
Ann Oncol, 2016.  
52. Gururajan, M., C.D. Jennings, and S. Bondada, Cutting edge: constitutive B cell receptor signaling is critical for basal growth of B lymphoma. J Immunol, 2006. 176(10): p. 5715-9.  
53. Kuppers, R., *Mechanisms of B-cell lymphoma pathogenesis.* Nat Rev Cancer, 2005. 5(4): p. 251-62.  
54. Meeker, T., et al., *Emergence of idiotype variants during treatment of B-cell lymphoma with antiidiotype antibodies.* N Engl J Med, 1985. 312(26): p. 1658-65.  
55. Satterthwaite, A.B. and O.N. Witte, The role of Bruton's tyrosine kinase in B-cell development and function: a genetic perspective. Immunol Rev, 2000. 175: p. 120-7.  
56. Honigberg, L.A., et al., *The Bruton tyrosine kinase inhibitor PCI-32765 blocks B-cell activation and is* efficacious in models of autoimmune disease and B-cell malignancy. Proc Natl Acad Sci U S A, 2010.  
107(29): p. 13075-80.  
57. Herman, S.E., et al., Bruton tyrosine kinase represents a promising therapeutic target for treatment of chronic lymphocytic leukemia and is effectively targeted by PCI-32765. Blood, 2011. 117(23): p. 628796.  
58. Dighiero, G., et al., Chlorambucil in indolent chronic lymphocytic leukemia. French Cooperative Group on Chronic Lymphocytic Leukemia. N Engl J Med, 1998. 338(21): p. 1506-14.  
59. Shanafelt, T.D., et al., Prospective evaluation of clonal evolution during long-term follow-up of Moffitt Cancer Center Protocol Template - v3.2 2018-08-10 56 patients with untreated early-stage chronic lymphocytic leukemia. J Clin Oncol, 2006. 24(28): p. 463441.  
60. Cymbalista, F., et al., Early Versus Deferred Treatment With Combined Fludarabine, Cyclophosphamide and Rituximab (FCR) Improves Event-Free Survival In Patients With High-Risk Binet Stage A Chronic Lymphocytic Leukemia - First Results Of a Randomized German-French Cooperative Phase III Trial. Blood, 2013. 122(21): p. 524-524.  
61. An international prognostic index for patients with chronic lymphocytic leukaemia (CLL-IPI): a metaanalysis of individual patient data. The Lancet Oncology. 17(6): p. 779-790.  
62. Awan, F.T., et al., A Phase 2 Trial of Early Intervention with Ibrutinib in Patients with Asymptomatic, High-Risk CLL. Blood, 2017. 130(Suppl 1): p. 1748-1748.  
63. Sagiv-Barfi, I., et al., Ibrutinib enhances the antitumor immune response induced by intratumoral injection of a TLR9 ligand in mouse lymphoma. Blood, 2015. 125(13): p. 2079-86.  
64. Younes, A., et al., Safety and Efficacy of the Combination of Ibrutinib and Nivolumab in Patients with Relapsed Non-Hodgkin Lymphoma or Chronic Lymphocytic Leukemia. Blood, 2017. 130(Suppl 1): p.  
833-833.  
65. Jain, N., et al., Nivolumab Combined with Ibrutinib for CLL and Richter Transformation: A Phase II
Trial. Blood, 2016. 128(22): p. 59-59.  
66. Cassidy, E.L., E. Baird, and J.I. Sheikh, Recruitment and retention of elderly patients in clinical trials:
issues and strategies. Am J Geriatr Psychiatry, 2001. 9(2): p. 136-40.  
67. Ivanova, A., B.F. Qaqish, and M.J. Schell, *Continuous toxicity monitoring in phase II trials in oncology.*
Biometrics, 2005. 61(2): p. 540-5.
untitled h1
appendix appendix a

iwCLL Criteria to Initiate Treatment of CLL (Reference \#14)
c. Evidence of progressive marrow failure manifested as worsening anemia and/or thrombocytopenia (Rai stages III or IV)
d. Massive or progressive or symptomatic splenomegaly. e. Massive lymphadenopathy (at least 10 cm in the longest diameter) or progressive or symptomatic lymphadenopathy f. Progressive lymphocytosis with an increase of more than 50% over a 2 month period or lymphocyte doubling time (LDT) of less than 6 months. LDT can also be obtained as liner regression at 2 weeks intervals over an observation period of 2 to 3 months.  
g. Autoimmune anemia or thrombocytopenia that is poorly responsive to corticosteroids or other standard therapy h. Constitutional symptoms defines as: unintentional weight loss of 10% or more within the previous 6 months, significant fatigue (i.e, ECOG PS 2 or worse, inability to work or perform usual activities), fever higher than 100.5 oF (38.0 oC for 2 or more weeks without evidence of infection, night sweats.  
| Grade                                                                                                                                                                                                                                                                      | Description                                                                                                                                                                       |
|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 0                                                                                                                                                                                                                                                                          | Normal activity. Fully active, able to carry on all pre-disease performance  without restriction. Symptoms, but ambulatory. Restricted in physically strenuous activity, but      |
| 1                                                                                                                                                                                                                                                                          | ambulatory and able to carry out work of a light or sedentary nature (e.g.,  light housework, office work). In bed <50% of the time. Ambulatory and capable of all self-care, but |
| 2                                                                                                                                                                                                                                                                          | unable to carry out any work activities. Up and about more than 50% of  waking hours.                                                                                             |
| 3                                                                                                                                                                                                                                                                          | In bed >50% of the time. Capable of only limited self-care, confined to bed  or chair more than 50% of waking hours.                                                              |
| 4                                                                                                                                                                                                                                                                          | 100% bedridden. Completely disabled. Cannot carry on any self-care.  Totally confined to bed or chair.                                                                            |
| 5                                                                                                                                                                                                                                                                          | Dead.                                                                                                                                                                             |
| *As published in Am. J. Clin. Oncol.: Oken, M.M., Creech, R.H., Tormey, D.C., Horton, J.,  Davis, T.E., McFadden, E.T., Carbone, P.P.: Toxicity And Response Criteria Of The Eastern  Cooperative Oncology Group. Am J Clin Oncol 5:649-655, 1982. The Eastern Cooperative |                                                                                                                                                                                   |
untitled h1
appendix c response criteria per

The International Workshop on Chronic Lymphocytic Leukemia (IWCLL) included updated response criteria in their 2008 publication [14]. The response categories are:
- **Complete remission (CR)**, requiring absence of peripheral blood clonal lymphocytes by immunophenotyping, absence of lymphadenopathy, absence of hepatomegaly or splenomegaly, absence of constitutional symptoms and satisfactory blood counts
- **Complete remission with incomplete marrow recovery (CRi)**, defined as CR above, but without normal blood counts  
- **Partial remission (PR)**, defined as ≥ 50% fall in lymphocyte count, ≥ 50% reduction in
lymphadenopathy or ≥ 50% reduction in liver or spleen, together with improvement in peripheral blood counts
- **Progressive disease (PD)**, defined as ≥ 50% rise in lymphocyte count to > 5 x109/L, ≥ 50% increase in lymphadenopathy, ≥ 50% increase in liver or spleen size, Richter's transformation, or new cytopenias due to CLL  
- **Stable disease**, defined as not meeting criteria for CR, CRi, PR or PD
Protocol <\#>