Cytogenetic Abnormalities Following CAR T Cell Therapy for B-Cell Malignancies
Authors: Kim Na Hyun , Khamissi Fatima , Bone Kathleen , Kopp Nathan , Longo Walter , Johnson Bryon D. , Kearl Tyce , Hematti Peiman , Hamadani Mehdi , Fenske Timothy S. , Shah Nirav N. 
Published: December 2024

Introduction:
CD19 based CAR T cell therapy has become a standard of care treatment for patients with relapsed B-cell malignancies. Recently there has been increased focus on the development of secondary malignancies post CAR T cell therapy. As part of completed and ongoing clinical trials with bispecific LV20.19 CAR T cells at the Medical College of Wisconsin, all patients underwent a baseline bone marrow biopsy and at minimum repeat biopsy at day 28. Those with marrow involvement had repeat bone marrow biopsies at pre-specified times points until 2-years post-CAR T. We now evaluate these patients for development of new cytogenetic abnormalities post CAR T cell therapy as part of long-term follow-up of these trial patients.
Methods:
We performed a retrospective review of patients who received a next generation bispecific (LV20.19) CAR T-cell product on clinical trial (NCT03019055, NCT04186520). All patients received fludarabine and cyclophosphamide combinations as part of lymphodepletion. A baseline marrow aspirate and biopsy prior to CAR T and on day 28 after CAR T therapy was obtained on all patients. We evaluated the presence of cytogenetic changes found on all bone marrow samples collected following CAR T therapy. Adults with R/R diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), mantle cell lymphoma (MCL) or chronic lymphocytic leukemia (CLL) were included. Descriptive and survival analyses using the Kaplan-Meier methodology were performed. Median overall survival (OS) was estimated from the date of CAR T treatment to death or last follow-up.
Results:
From November 1, 2017 to July 1, 2024 a total of 96 patients who received LV20.19 CAR T therapy on clinical trials were evaluated for presence of cytogenetic abnormalities post-CAR. We identified 21 patients (22%) with new cytogenetic abnormalities after LV20.19 CAR T cell therapy. Among this subset, the median age was 64 years (46-75) and 86% (n=18) were male sex. The most common B-cell malignancy was DLBCL in 43% of patients (n=9) followed by CLL in 28% (n=6). 8 patients (38%) had a prior autologous stem cell transplant.
The most common cytogenetic findings identified included loss of Y in 6 patients and abnormalities within chromosome 7 (including translocation, loss of 7, and del 7q) in 8 patients. Other abnormalities identified included del(5q) (n=1), del(20q) (n=1), t(1;12) with del(2) (n=1), t(5;19) (n=1), t(3;6) (n=1), +15 +Y (n=1), del(1) (n=1). The cytogenetic abnormalities disappeared on subsequent marrows in patients with 7q (n=1), t(7;14) n=1, t(1;12) and del 2 (n=1), and +15 (n=1). The median time from LV20.19 CAR T cell therapy to discovery of the abnormality was 8 months (1 month-24 months). Despite the presence of cytogenetic abnormalities only 5 of the 21 patients developed morphologic evidence of myelodysplastic syndrome. 4 of the 5 patients passed due to either MDS related or allogeneic transplant related complications. The median OS for the 21 patients with cytogenetic abnormalities was 60 months.
Conclusions
Cytogenetic abnormalities were common in the bone marrow in patients receiving LV20.19 CAR T cell therapy as part of a clinical trial. However, most findings did not correlate with development of a new hematological malignancy, and others were transient in nature with no clinical consequence. These data demonstrate the importance of long-term follow-up of CAR T cell therapy patients given evolving cytogenetic abnormalities post-treatment.