Integrating genomic features for prognosis in Chinese patients with B-cell lymphoma following chimeric antigen receptor T-cell therapy

Despite advancements in CAR-T therapy, over half of the lymphoma patients still face drug resistance or relapse. Seventy-nine Chinese patients with B-cell lymphoma provided 192 serum samples for circulating tumor DNA (ctDNA) detection to identify the genomic features linked to prognosis during CAR-T cell therapy. Patients in complete remission and noncomplete remission groups were analyzed, and those with >10 ctDNA gene mutations before CAR-T cell therapy had significantly worse overall survival and progression-free survival rates than those with fewer mutations. MYD88, FAT1, and BTG2 mutations were correlated with poorer OS, whereas MUC16 mutations were correlated with better OS. Patients with TP53 mutation pretreatment had significantly lower CR rates than those without TP53 mutations (33.3% vs. 68.1%, P=0.02). However, TP53 mutation pretreatment did not affect long-term patient survival. All patients with TP53 mutations 4 weeks after CAR-T cell therapy failed to achieve CR, with poorer OS (1-year OS rate: 37.5% vs. 66.4%; 2-year OS rate: 12.5% vs. 56.3%, P=0.0023). Among patients with CR, those with BCR mutations at 4 weeks post-treatment exhibited poorer OS (2-year OS rate: 40.9% vs. 76.1%, P=0.035). One week after CAR-T cell therapy, patients without CDKN2A, CBLB, APC, SPEN, KMT2D, CARD11, FOXO1, or PDGFRB mutations were more likely to achieve CR (76.6% vs. 28.6%, P<0.001) and had better OS (1-year OS rate: 81.5% vs. 38.9%, 2-year OS rate: 62.2% vs. 5%, P<0.001) and PFS (1-year PFS rate: 67.2% vs. 0%, P<0.001). This study evaluated the genomic features and screened a gene set to predict CAR-T cell therapy efficacy in B-cell lymphoma, aiding clinicians in accurately evaluating efficacy and treatment decision-making.