KMT2A Rearrangements Are Associated with Lineage Switch Following CD19 Targeting CAR T-Cell Therapy
Authors: Lamble Adam J. , Myers Regina M. , Taraseviciute Agne , John Samuel , Yates Bonnie , Steinberg Seth M. , Sheppard Jennifer , Kovach Alexandra E. , Wood Brent L. , Borowitz Michael , Stetler-Stevenson Maryalice , Yuan Constance M. , Pillai Vinodh , Foley Toni , Chung Perry , Chen Lee , Lee Daniel W. , Annesley Colleen , DiNofia Amanda M. , Grupp Stephan A. , Verneris Michael R , Gore Lia , Laetsch Theodore W. , Bhojwani Deepa , Brown Patrick A. , Pulsipher Michael A. , Rheingold Susan R. , Gardner Rebecca A , Shah Nirali N. 
Published: November 2021

Abstract
Introduction: Chimeric antigen receptor (CAR) T-cells redirected against CD19 have demonstrated remarkable clinical activity in children and adults with relapsed/refractory (r/r) B-cell malignancies. The risk of lineage switch (LS) following CD19-directed therapies has been well documented but has been primarily limited to case reports. Additionally, the risk of subsequent malignant neoplasms (SMN) following CAR T-cells has not yet been described. Distinguishing LS (B-ALL to myeloid malignancy) from a therapy-related myeloid neoplasm is both clinically and biologically relevant. The former emerges from a highly refractory leukemic clone, likely resistant to salvage therapy, whereas the latter represents a new malignancy that can be associated with long-term survival.
Methods: We conducted a multicenter, retrospective review of children and young adults with r/r B-acute lymphoblastic leukemia (B-ALL) who received either commercial tisagenlecleucel or 1 of 3 investigational murine-based CD19-CAR constructs on clinical trials at 7 US centers between 2012-2019. Patients diagnosed with B-ALL before age 25 years were included and patients who had received any prior CAR product were excluded.
Results: Of 420 CAR-treated patients, with a median follow-up of 30.1 months, 12 (2.9%) experienced LS and 6 (1.4%) developed a SMN (Table). The median time to diagnosis of LS following CAR T-cell infusion was significantly shorter compared to diagnosis of SMN (65.5 days vs. 883.5 days; p=0.005).
Eleven of 12 patients (91.7%) with LS converted to acute myeloid leukemia (AML). One patient converted to mixed phenotype acute leukemia, B/myeloid type. The leukemia of 10 of 12 patients with LS harbored cytogenetics similar to those at initial diagnosis. For the remaining 2 patients with LS, cytogenetics were unavailable, but the leukemias were considered LS by the treating institution.
KMT2Ar rearrangement (KMT2Ar) was a predominant cytogenetic abnormality seen in patients with LS. Overall, 38 of 420 patients (9%) had a KMT2Ar. KMT2Ar was present in 9 of 12 (75%) patients with LS compared to 20 of 408 (7.1%) non-LS patients (p&lt;0.001). Patients with LS were younger at initial diagnosis compared to the remaining cohort (median age, 1.6 years vs. 7.7 years; p=0.001), reflecting the inherent association between KMT2Ar and infant ALL. Otherwise, there were no significant differences in gender, prior hematopoietic stem cell transplant (HSCT), prior blinatumomab exposure, or CAR response.
Within the KMT2Ar cohort, 31 (81.6%) patients achieved a complete remission post-CAR. Eight of these patients received a consolidative HSCT (representing 4 first and 4 second HSCTs). No KMT2Ar patient experienced a post-HSCT LS and 3 are alive with a median follow-up of 1164 days post-CAR. In contrast, of the 23 KTM2Ar patients who did not receive HSCT post-CAR, 7 developed LS and 14 are alive with a median follow-up of 864 days post-CAR. Relative contraindications to post-CAR HSCT included a prior HSCT (n=11) or early LS (n=5). Of the 7 CAR non-responding patients with KMT2Ar, 2 (28.6%) had rapid emergence of LS by the first restaging timepoint. There are no long-term survivors following LS, regardless of KMT2A status, dying a median of 123 days (range, 36-594 days) after diagnosis of LS.
The 6 SMNs were cholangiocarcinoma, synovial sarcoma, malignant melanoma and 3 therapy-related myeloid neoplasms (MDS/AML), distinguished from LS based on loss of original cytogenetics. Notably, 4/6 (67%) patients that developed a SMN had received an allogeneic HSCT prior to development of SMN. Four patients (67%) remain alive and in remission with a median follow-up of 304 days after diagnosis of SMN, including 2 patients with MDS/AML.
Conclusions: In the largest series of pediatric patients treated with CAR T-cell therapy, we show that LS occurs in 2.9% of children. The presence of a KMT2Ar was the biggest risk factor, with 23.7% of these patients experiencing LS. We found that LS can occur very early in a patient's post CAR T-cell course, and despite a variety of treatment approaches, the outcomes for these patients are dismal. Given the predisposition to LS, the role for consolidative HSCT in KMT2Ar patients warrants further study. Limited by a short follow-up period, we saw SMNs in only 1.4% of our patients. Causality is unknown and likely unrelated to CAR-T, but this further supports the long-term safety of CAR T-cells in children with B-ALL.
Figure 1 Figure 1.

Disclosures
Borowitz: Amgen, Blueprint Medicines: Honoraria. Lee: Harpoon Therapeutics: Consultancy; Amgen: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; Kite Pharma: Other: trial funding; Gilead: Other: trial funding. Grupp: Novartis, Adaptimmune, TCR2, Cellectis, Juno, Vertex, Allogene and Cabaletta: Other: Study steering committees or scientific advisory boards; Novartis, Roche, GSK, Humanigen, CBMG, Eureka, and Janssen/JnJ: Consultancy; Novartis, Kite, Vertex, and Servier: Research Funding; Jazz Pharmaceuticals: Consultancy, Other: Steering committee, Research Funding. Verneris: jazz: Other: advisory board; Novartis: Other: advisory board; Fate Therapeutics: Consultancy. Gore: Mirati: Current equity holder in publicly-traded company; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy, Current equity holder in publicly-traded company, Honoraria, Membership on an entity's Board of Directors or advisory committees; Roche/Genentech: Consultancy, Honoraria; Clovis: Current equity holder in publicly-traded company; Celgene: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; Sanofi Paris: Current equity holder in publicly-traded company; Anchiano: Current equity holder in publicly-traded company; Blueprint Medicines: Current equity holder in publicly-traded company. Brown: Novartis: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Kura: Membership on an entity's Board of Directors or advisory committees; KIte: Membership on an entity's Board of Directors or advisory committees. Pulsipher: Equillium: Membership on an entity's Board of Directors or advisory committees; Adaptive: Research Funding; Jasper Therapeutics: Honoraria. Rheingold: Pfizer: Research Funding; Optinose: Other: Spouse's current employment. Gardner: BMS: Patents & Royalties; Novartis: Consultancy.