Clonal Evolution and Transcriptomic Analysis of Chronic Lymphocytic Leukemia Treated with Ibrutinib

Disease progression has been increasingly appreciated with the use of ibrutinib to treat chronic lymphocytic leukemia (CLL). Understanding the pattern of clonal evolution and transcriptomic changes during the early treatment period with ibrutinib may provide insight into the mechanisms of resistance. We performed whole exome sequencing on sequential samples with matched germline controls from 61 patients with CLL during the first 12 months of ibrutinib monotherapy or ibrutinib in combination with rituximab. Additionally, RNA sequencing was done on a subset of 14 patients treated with ibrutinib monotherapy. The presence of clonal shifts was associated with an increased risk of disease progression, suggesting that resistant clones are more likely to emerge in CLL with greater evolutionary capacity.This cohort was later augmented with additional data (including data from 15 additional patients). In total, this second set of data contained whole exome sequencing (31 samples), RNA sequencing (6 samples) and reduced representation bisulfite sequencing (67 samples) for CLL samples and used them to identify expression subtypes of CLL. In an integrative analysis of genetic, transcriptomic, and epigenetic data, incorporating known and newly identified subtypes of CLL, we built new models to improve patient prognostication.]]>
Eligibility for ibrutinib monotherapy study Inclusion criteria: Cohort 1: Treated and untreated patients age 65 or older and need for therapy. Cohort 2: Treated (maximum accrual n=16) and untreated (n=27, evaluable) patients at least 18 years old with 17p deletion or p53 expression by immunohistochemistry or p53 mutation by sequencing analysis. Men and women with histologically confirmed disease. Active disease Eastern Cooperative Oncology Group (ECOG) performance status of less than or equal to 2. ANC greater than 500/microL, platelets greater than 30,000/microL. Agreement to use contraception during the study and for 90 days after the last dose of study drug if sexually active and able to bear children. Willing and able to participate in all required evaluations and procedures in this study protocol including swallowing capsules without difficulty. Ability to understand the purpose and risks of the study and provide signed and dated informed consent and authorization to use protected health information (in accordance with national and local subject privacy regulations). Exclusion criteria: Previous radiotherapy, radioimmunotherapy, biological therapy, chemotherapy, or treatment with an investigational product fpr CCL treatement in the last 4 weeks (i.e. intravenous immunoglobulin). Transformed CLL Autoimmune hemolytic anemia or thrombocytopenia requiring steroid therapy. Impaired hepatic function: Total bilirubin greater than or equal to 1.5 times upper limit of normal unless dute to Gilbert's disease, AST/ ALT greater than or equal to 2.5 times institutional upper limit of normal unless due to infiltration of the liver. Impaired renal funtion: Creatinine greater than or equal to 2.0 mg/dL or GFR less than or equal to 50ml/min. Life-threatening illness, medical condition or organ system dysfunction which, in the investigator's opinion, could compromise the subject's safety, interfere with the absorption or metabolism of PCI-32765 PO, or put the study outcomes at undue risk. Concomitant immunotherapy, chemotherapy, radiotherapy, corticosteroids (at dosages equivalent to prednisone > 20 mg/day), or experimental therapy. Active Hepatitis B infection HIV infection Female patients: Current pregnancy or unwilling to take oral contraceptives or refrain from pregnancy if of childbearing potential or currently breastfeeding. Male patients who are unwilling to follow the contraception requirements described in this protocol. Psychiatric illness/social situations that would limit the patient's ability to tolerate and/or comply with study requirements. Unable to understand the investigational nature of the study or give informed consent. Individuals < 18 yrs old. Known hypersensitivity to any component of PCI-32765. Any prior therapy with PCI 32765 or any other BTK inhibitors. Requires anticoagulation with warfarin. Requires treatment with strong CY3A4/5 and/or CYP2D6 inhibitors (unless no alternative is available). Eligibility for ibrutinib plus rituximab study Inclusion criteria: Patients must have a diagnosis of high-risk CLL/SLL and be previously treated with up to 3 lines of prior therapy. High-risk CLL and high-risk SLL is defined by the presence of a 17p deletion or 11q deletion or TP53 mutation. Any CLL and SLL patient who has a short remission duration of less than 3 years after prior first-line chemo-immunotherapy, such as the FCR regimen, also fulfills criteria of high-risk CLL/SLL, regardless of the presence or absence of cytogenetic abnormalities. CLL and SLL patients with 17p deletion or TP53 mutation will not be required to have received any prior therapy, given the poor outcome of CLL/SLL patients to standard frontline chemo-immunotherapy, such patients will be eligible if they are untreated or if they have received up to 3 lines of prior therapy. Patients must have an indication for treatment by 2008 IWCLL Criteria. Patients age > 18 years at the time of signing informed consent. Understand and voluntarily sign an informed consent. Be able to comply with study procedures and follow-up examinations. ECOG/WHO performance status of 0-1. Patients of childbearing potential must be willing to practice highly effective birth control (e.g., condoms, implants, injectables, combined oral contraceptives, some intrauterine devices [IUDs], sexual abstinence, or sterilized partner) during the study and for 30 days after the last dose of study drug. Women of childbearing potential include any female who has experienced menarche and who has not undergone successful surgical sterilization (hysterectomy, bilateral tubal ligation, or bilateral oophorectomy) or is not postmenopausal. Post menopause is defined as follows: Amenorrhea >/= 12 consecutive months without another cause and a documented serum follicle stimulating hormone (FSH) level > 35 mIU/mL; a male of childbearing potential is any male that has not been surgically sterilized. Adequate renal and hepatic function as indicated by all of the following: Total bilirubin 30 mL/min, as calculated by the Cockcroft-Gault equation unless disease related. Free of prior malignancies for 3 years with exception of currently treated basal cell, squamous cell carcinoma of the skin, or carcinoma in situ of the cervix or breast. A Urine Pregnancy Test (within 7 days of Day 1) is required for women with childbearing potential. Exclusion criteria: Pregnant or breast-feeding females. Treatment including chemotherapy, chemo-immunotherapy, monoclonal antibody therapy, radiotherapy, high-dose corticosteroid therapy (more than 60 mg prednisone or equivalent daily), or immunotherapy within 21 days prior to enrollment or concurrent with this trial. Investigational agent received within 30 days prior to the first dose of study drug or have previously taken PCI-32765. If received any investigational agent prior to this time point, drug-related toxicities must have recovered to Grade 1 or less prior to first dose of study drug. Systemic fungal, bacterial, viral, or other infection not controlled (defined as exhibiting ongoing signs/symptoms related to the infection and without improvement, despite appropriate antibiotics or other treatment). Patients with uncontrolled Autoimmune Hemolytic Anemia (AIHA) or autoimmune thrombocytopenia (ITP). Patients with severe hematopoietic insufficiency, as defined by an absolute neutrophil count of less than 500/micro-L and/or a platelet count of less than 30,000/micro-L at time of screening for this protocol. Any other severe concurrent disease, or have a history of serious organ dysfunction or disease involving the heart, kidney, liver or other organ system that may place the patient at undue risk to undergo therapy with PCI-32765 and rituximab. Significant cardiovascular disease such as uncontrolled or symptomatic arrhythmias, congestive heart failure, or myocardial infarction within 6 months of screening, or any Class 3 or 4 cardiac disease as defined by the New York Heart Association Functional Classification. Significant screening ECG abnormalities including left bundle branch block, 2nd degree AV block type II, 3rd degree block, bradycardia, and QTc > 470 msec. Any serious medical condition, laboratory abnormality, or psychiatric illness that places the subject at unacceptable risk if he/she were to participate in the study. History of stroke or cerebral hemorrhage within 6 months. Evidence of bleeding diathesis or coagulopathy. Major surgical procedure, open biopsy, or significant traumatic injury within 28 days prior to Day 1, anticipation of need for major surgical procedure during the course of the study. Minor surgical procedures, fine needle aspirations or core biopsies within 7 days prior to Day 1. Bone marrow aspiration and/or biopsy are allowed. Serious, non-healing wound, ulcer, or bone fracture. Treatment with Coumadin. Patients who recently received Coumadin must be off Coumadin for at least 7 days prior to start of the study. Any chemotherapy (e.g., bendamustine, cyclophosphamide, pentostatin, or fludarabine), immunotherapy (e.g., alemtuzumab, or ofatumumab), bone marrow transplant, experimental therapy, or radiotherapy is prohibited during therapy on this study. Use of medications known to prolong QTc interval or that may be associated with Torsades de Pointes (refer to Appendix F) are prohibited within 7 days of starting study drug and during study-drug treatment. Requires treatment with strong CYP3A4/5 and/or CYP2D6 inhibitors. ]]>