Mutation Spectrum, Characteristics and Impact of Mutation Profiling on Prognosis, Outcome and Treatment Responses in Patients (pts) with Mantle Cell Lymphoma

Background: Genomic profiles of mantle cell lymphoma (MCL) are associated with clinical outcomes. BTKi Resistance in MCL can be predicted with mutation profile. Identifying these patients (pts) early can help guide therapy decisions and predict outcomes. We describe results from a clinical NGS based assay with a customized 162-gene panel in routine work-ups of MCL pts.

Materials and Methods: We reviewed data from MCL patients who underwent CLIA approved lymphoma gene panel testing at MDACC from October 2020 until the end of June 2022. Data on treatment response, outcomes, and patient characteristics were collected. Mutation panel testing was conducted on various patient samples. Genomic DNA was isolated from fresh bone marrow (BM) aspirate, formalin-fixed paraffin-embedded (FFPE) tissues, fine needle aspirate (FNA) and peripheral blood (PB) specimens. Sequencing was performed using the Illumina NextSeq platform (Illumina, San Diego, CA). Variant calling was performed using Agilent SureCall software v4.1 and post-variant call analysis and annotation were performed using an in-house bioinformatics pipeline (OncoSeek v 1.1). Analytical sensitivity of the assay was established at 2% using a per base coverage cut-off of 200x. The assay was performed in cases with >10% lymphoma cells in the sample.

Results: We included 227 MCL pts in this study: 129 treatment naïve and 97 with prior therapies. The distribution of patients according to the sample type included: BM (n=107), FFPE (n=50; 24 lymph node, 20 GI tract, and 6 miscellaneous tissues), FNA from involved nodal and non-nodal tissues (n=50) and PB (n=20). Baseline pt features included a median age of 67 years (range, 38-88 years). There were 164 men and 63 women. Histomorphology was classic in 165 pts, blastoid in 31, pleomorphic in 19 and blastoid/pleomorphic in 2. Ten pts had unclear histomorphology. Ki-67% in involved tissues was evaluable in 180 pts (in 47 pts Ki-67% was not available). Ki-67% was high (>=30%) in 98 and low in 82 biopsy specimens. Among the 97 previously treated pts, 47 had BTKi refractory disease. Twenty-three pts were treated with standard of care brexucabtagene autoleucel (CART). The spectrum of gene mutations is depicted by both previously untreated and pts with prior therapy in figure-1A. The most common mutated genes were: ATM (51.5%), TP53 (29.5%), KMT2D (21.1%), CCND1 (19.3%), BIRC3 (16.2%), NSD2 (11.4%), SMARCA4 (10.1%), UBR5 (9%), NOTCH1 (8.3%), CARD11 (7%), SAMHD1 (7%), NFKB1E (6.6%), SP140 (6.6%), S1PR1 (6.6%), DNMT3A (6%), NOTCH2 (6%), IGLL5 (6%), TRAF2 (5%), TET2 (5%). Unlike chronic lymphocytic leukemia, mutations of BTK (n=5; 2%) and PLCg (n=4; 2%) were rare. BTK mutations included missense mutations: C481Y, C481R, T474I and 2 with L528W. All patients with BTK mutations were resistant to prior BTKi and 4/5 died with refractory disease. Additional mutations of prognostic interest in other lymphomas were detected at very low frequency (<3%) and included CDKN2A, CD79b, MYD88, MEF2B, MAP3K14, Rb1, PAX5, SPEN, SF3B1, DIS3. We also evaluated pt survival from the date of gene panel testing and noted that TP53 mutant MCL pts had significantly inferior survival. We further divided the pts based on >=3 mutations (n=77) vs < 3 mutations (n=150) and identified that pts with a higher number of mutations had inferior survival, P <0.0001 (Figure 1C). Pts with SMARCA4 and TRAF2 mutations also demonstrated shorter survival compared to those which were wild type (not shown). Twenty-three pts received CART therapy and 7 had progressed and 16 have not. The distribution of mutations before CART in the two groups was not significantly different. Among the 47 BTKi refractory MCL, the frequency of certain mutations was higher: TP53 (49%), ATM (55%), KMT2D (31%), CCND1 (23%), 10% each for SMARCA4, NSD2 and SP140. Currently, we are utilizing this test to evaluate and include pts with high risk MCL on our clinical trials in MCL and treat with risk stratified treatments.

Conclusion: The clinical NGS-based assay for MCL pts at our institution has proven to have prognostic significance. Resistant MCL pts exhibit a preponderance of mutations involving TP53, epigenetic modifier and chromatin regulator genes. Comprehensive risk stratification of pts early on and during therapy is very useful and improves patient care, helps design next generation clinical trials and improves our understanding of the biology of resistant MCL in the BTKi and CART era.