KMT2A Rearrangements Are Associated with Lineage Switch Following CD19 Targeting CAR T-Cell Therapy

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<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.

Epigenetic regulator genes direct lineage switching in MLL/AF4 leukemia

“…Whilst these therapies target lineage specific surface markers, lineageswitched (pre-)leukaemic progenitor populations escape epitope recognition and provide a potential clonal source for the relapse 60 . As recognition of lineage switching following eg CD19 CAR-T cell therapy grows, two recent studies have highlighted the particular vulnerability of patients with MLLr ALL 54,61,62 . Given the increasing use of advanced immunological therapies, a detailed understanding of the molecular processes underlying lineage determination and switching will be critical for developing new strategies to avoid this route to clinical relapse.…”

Potent preclinical activity of FLT3-directed chimeric antigen receptor T-cell immunotherapy against <i>FLT3</i>- mutant acute myeloid leukemia and <i>KMT2A</i>-rearranged acute lymphoblastic leukemia

“…However, given recent reporting of FLT3i resistance mechanisms in patients with FLT3-mutant AML, such TKI-based therapies may not be curative for all patients. 36 Patients with KMT2A-R ALL are also known to be at particularly high risk of lymphoid-tomyeloid lineage switch following CD19CART immunotherapy 15,17 when compared to conventional chemotherapy or immunotherapy with the CD19xCD3 bispecific T-cell engager blinatumomab. 37 This lineage switch predilection presents a unique barrier to cure of these highrisk patients via CD19CART, as well as an opportunity for alternative therapeutic approaches.…”

“…Patients with KMT2A-R ALL are at increased risk for lineage switch to AML following CD19CART versus those with non-KMT2A-R ALL. 15,17 To assess the activity of FLT3CART in this setting, we created a pair of ALL and AML PDX models from an adolescent with primary chemotherapy-refractory KMT2A-AFF1 B-ALL who developed lineage-switched CD19-negative KMT2A-AFF1 AML approximately three weeks after tisagenlecleucel administration and was resistant to all further chemoimmunotherapy. In these preclinical studies, FLT3CART equipotently inhibited leukemia proliferation in vivo in both KMT2A-R ALL (Figure 4A) and AML (Figure 4B) PDX models, despite a marked reduction in FLT3 surface antigen density after lineage switch (Figure 4C).…”

“…15 Despite high rates of initial remission, approximately 50% of patients treated with CD19CART will relapse again within two years, often due to target antigen loss and/or lineage switch in KMT2A-R ALL. 13,[15][16][17] This phenomenon has led to appreciable interest in alternative strategies that may prevent target antigen escape and increase long-term cure rates, including CAR T cells directed at alternative leukemia cell surface antigens (e.g., TSLPR, BAFFR) and bispecific CAR T cells that recognize and target multiple antigens simultaneously. 18 Initial studies of dual-targeting CD19xCD22 CAR T cells demonstrated robust anti-leukemia activity in preclinical B-ALL models, 19 and current clinical phase 1 trials of these bispecific immunotherapies (NCT03241940, NCT03289455, NCT03330691, NCT03448393) have reported exciting early results.…”

CAR-T Cells Shoot for New Targets: Novel Approaches to Boost Adoptive Cell Therapy for B Cell-Derived Malignancies

“…Moreover, lineage reprogramming in these cases was found to be correlated with the aberration of genes encoding Pax5, EBF1, or FLT3. The phenomenon of lineage switch is one of the causes of resistance to CD19 CAR-T therapy, mainly in mixed lineage leukemia (MLL)-rearranged B-ALL [ 111 , 112 , 113 ], however, one case was also detected in a Philadelphia chromosome-positive B-ALL patient [ 114 ]. Recent studies showed that a similar situation can also occur in lymphomas.…”