DNA Damage Repair Pathway Variants Are Frequent in Patients Undergoing CAR-T Cell Therapy for Lymphoma and Associated with Increased Risk of Myeloid Neoplasia Post Cytotoxic Therapy

Background

Specific cancer therapy exposure can promote expansion of clonal haematopoiesis (CH) in a gene-dependent manner, contributing to myeloid neoplasia post cytotoxic therapy (MN-pCT). Longer term follow-up for chimeric antigen receptor-T cell therapy (CAR-T) has revealed that MN-pCT following CAR-T is relatively common (2-year cumulative incidence of 5-10%), with short latency (<12 months) and is associated with poor survival. This finding warrants specific recognition and surveillance considering the rapid adoption of CAR-T in frontline treatment setting. The study aims to (1) characterize the baseline frequency and natural history of CH variants (vars) detected prior to CAR-T and (2) investigate the relationship between baseline CH and risk of MN-pCT as well as late cytopenia.

Methods

Patients (pts) with large B cell lymphoma (LBCL) treated with CAR-T between April 2019 and December 2023 at Peter MacCallum Cancer Centre and Royal Melbourne Hospital were included. Genomic DNA isolated from blood and/or bone marrow from all patients prior to CAR-T cell infusion were analysed by targeted next-generation sequencing covering the coding regions and flanking splice sites of 80 commonly mutated genes in hematological cancers. VAF cut-off was 0.5%.

Results

In this cohort, 173 pts received CAR-T therapy (63% Axicabtagene ciloleucel, 37% Tisagenlecleucel) for relapsed refractory LBCL. Median pt age was 64 years (range: 22-82, 44% 65 years), 61% were male. Median lines of prior therapy were 2 (range: 1-6) and 32% had an autologous hematopoietic stem cell transplant. At baseline, prior to CAR-T infusion, 91 (66%) of 138 pts with available samples had vars identified. Fifty-nine pts (43%) had CH according to the WHO definition (VAF>=2%). Vars involving DNMT3A, TET2 or ASXL1 (DTA) were found in 54% pts and 49% had vars involving the DNA damage repair (DDR) pathway, such as TP53 or PPM1D. The commonest CH vars at baseline were DNMT3A (49 pts, 54%), TP53 (24 pts, 26%), PPM1D (24 pts, 26%), TET2 (13 pts, 14%) and ASXL1 (7 pts, 8%). Of the total 176 variants, almost half (48%, n=84) were detected at VAF<2%, followed by 35% (n=62) detected between VAF 2-10% and 17% (n=30) with VAF>10%. The median number of vars per pt was 1 (range 1-6), with 1 var detected in 57%, 2 vars in 29% and 3+ vars in 14%. Among pts with TP53 vars, 2 or more TP53 vars were found in 17%.

With a median follow-up of 19.9 months (range: 0.6-62.2) by the cut-off date (31-MAY-2024), 10 (6%) pts have so far developed MN-pCT (5 AML, 5 MDS). The cumulative incidence of MN-pCT was 2% at 1 year, 3% at 2 years and 11% at 3 years, with death from LBCL as a competing risk. Median latency to development of MN-pCT from CAR-T infusion was 24.7 months (range: 3.7-40.7). At MN-pCT, 90% (n=9) had DDR mutations (7 TP53, 1 PPM1D, 1 TP53 & PPM1D), and 60% (n=6) pts had complex karyotype involving del(5q), monosomy 7 and del(17p). 75% DDR mutations detected at time of MN-pCT had the same var identified in tissue prior to CAR-T infusion. For patients with TP53 var detected prior to CAR-T infusion, there is a trend towards increased risk for developing MN-pCT (OR 3.2, 95% CI 0.9-11.3, p=0.07). Overall survival after MN-pCT was poor (median OS of 8.2 months; range 1.2-10.9). Late cytopenias, defined as Gr 3 or higher cytopenias at >90 days, were observed in 18% patients with CH prior to CAR-T (n=16; 6 neutropenia, 10 thrombocytopenia). Presence of DDR CH prior to CAR-T was associated with late thrombocytopenia (OR 3.9, 95% CI 1.1-13.5, p=0.04) based on logistic regression. Serial samples were available from 6 pts with MN-pCT (3 AML, 3 MDS). One patient had baseline TP53 Y220C with VAF 4.2% prior to CAR-T, which expanded to 14.8% at Month 1 post CAR-T and subsequently developed loss of heterozygosity with VAF 90.2% at time of AML pCT 2 years after CAR-T infusion.

Conclusion
Incidental CH var involving the DDR pathway is a frequent finding prior to CAR-T infusion (49%). Baseline DDR var is associated with MN-pCT and late thrombocytopenia. There is an increasing risk of MN-pCT between the 2^nd and 3^rd year following CAR-T infusion. These findings support consideration of a molecularly-informed risk management plan in patients undergoing CAR-T therapy.