Abstract
Background: Tumor-intrinsic molecular features informing risk and resistance mechanisms in large-B-cell lymphoma (LBCL) treated with CD19-directed chimeric antigen receptor T-cells (CAR-T) are lacking. TP53 has been implicated in aberrant apoptosis signaling and immune evasion. We hypothesized that TP53-alterations are detrimental in LBCL treated with CD19-CAR-T.
Methods: Patients with relapsed/refractory LBCL treated with CD19-CAR-T were included. Targeted next-generation sequencing (NGS) encompassing protein-coding exons of over 400 genes (MSK-IMPACT) was performed on pre-CAR-T tumor samples in a subset of patients. Response and survival rates by tumor-intrinsic histological, cytogenetic, and molecular markers were assessed. Interactions between genomic aberrations and cellular pathways that could contribute to CAR-T resistance were studied using publicly available datasets with genomic and transcriptomic profiling.
Results: We included 136 adults with LBCL treated with CD19-CAR-T. (axicabtagene-ciloleucel [70, 51%], tisagenlecleucel [38, 28%], lisocabtagene-maraleucel [28. 21%]). Patients were heavily pre-treated (≥4 treatment lines [58%]) and primarily categorized as diffuse large B-cell lymphoma (DLBCL)-NOS (79%) followed by double/triple hit high-grade lymphoma (12%). DLBCL transformed from follicular lymphoma, high KI67-index, germinal center B-cell cell of origin, and double expressor phenotype were highly represented (43%, 47%, 50%, and 40%, respectively). Outcomes in the complete cohort echoed pivotal trials: best overall response rate 78% (Fig. A), median overall survival (OS) 22.7 months (95%CI 14.8-NR), median progression-free survival 6.2 months (3.3-12.3). A subset of 76 patients had tumor NGS profiling. Clinical features and CR and OS rates were similar across patients with and without NGS. TP53 genomic alterations were common (28, 37%). A total of 26 TP53 mutations (22 missense; 2 in-frame deletions; 2 splice sites) were identified in 23 patients. An additional five patients had TP53 homozygous deletions (i.e., copy number alterations). Two patients had concurrent TP53 mutations and homozygous deletions. Among tumor-intrinsic factors, only TP53-alterations were predictive of complete response (CR) in univariable and multivariable logistic regression; no association was observed with histological and cytogenetic features (Fig. B). TP53-alterations were also predictive of OS in univariable and multivariable Cox regression (Fig. C-D; 1-year OS in TP53-altered (48% [95% CI 32 - 71]) vs. wild-type (75% [64 - 89]), p = 0.039). Notably, in TP53-altered LBCL, axicabtagene-ciloleucel therapy was associated with superior OS compared to aggregated 41BB products (HR 3.40 [1.19-9.66]) in multivariable Cox regression adjusted for age, performance status, and primary refractory disease (Fig. E).
Transcriptomic analysis of publicly available samples from newly diagnosed LBCL patients (n=562) demonstrated that TP53-alterations are associated with dysregulation of pathways related to CAR-T cell cytotoxicity, including downregulation of interferon and death receptor pathway genes, and reduced CD8 T-cell tumor infiltration (Fig. F-H).
Conclusions: We show, for the first time, that TP53 alterations are a valuable prognostic and potentially predictive marker in LGBL CD19-CAR-T recipients. Gene expression profiling suggests that TP53 alterations result in an immunosuppressive tumor-microenvironment and impaired apoptosis signaling, which could lead to decreased CAR-T efficacy.
Shouval: Medexus: Consultancy. Batlevi: Life Sciences: Consultancy; Kite Pharma: Consultancy; Juno/Celgene: Consultancy; GLG Pharma: Consultancy; Pfizer: Current holder of individual stocks in a privately-held company; Medscape: Honoraria; BMS: Current holder of individual stocks in a privately-held company; Seattle Genetics: Consultancy; Memorial Sloan Kettering Cancer Center: Current Employment; Moderna: Current holder of individual stocks in a privately-held company; Regeneron: Current holder of individual stocks in a privately-held company; Viatris: Current holder of individual stocks in a privately-held company; Karyopharm: Consultancy; TG Therapeutics: Consultancy; ADC Therapeutics: Consultancy; Dava Oncology: Honoraria; Bayer: Research Funding; TouchIME: Honoraria; Xynomic: Research Funding; Roche/Genentech: Research Funding; Novartis: Research Funding; Epizyme: Research Funding; Janssen: Research Funding; Autolus: Research Funding. Dahi: Kite / Gilead: Membership on an entity's Board of Directors or advisory committees. Giralt: AMGEN: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; SANOFI: Membership on an entity's Board of Directors or advisory committees; PFIZER: Membership on an entity's Board of Directors or advisory committees; JENSENN: Membership on an entity's Board of Directors or advisory committees; GSK: Membership on an entity's Board of Directors or advisory committees; JAZZ: Membership on an entity's Board of Directors or advisory committees; CELGENE: Membership on an entity's Board of Directors or advisory committees; Actinnum: Membership on an entity's Board of Directors or advisory committees. Salles: Janssen: Consultancy; Novartis: Consultancy; Epizyme: Consultancy, Honoraria; Miltneiy: Consultancy; Regeneron: Consultancy, Honoraria; Incyte: Consultancy; Ipsen: Consultancy; Kite/Gilead: Consultancy; Morphosys: Consultancy, Honoraria; Velosbio: Consultancy; Takeda: Consultancy; Loxo: Consultancy; Genentech/Roche: Consultancy; Rapt: Consultancy; Genmab: Consultancy; Allogene: Consultancy; Debiopharm: Consultancy; BMS/Celgene: Consultancy; Beigene: Consultancy; Abbvie: Consultancy, Honoraria; Bayer: Honoraria. Sauter: Bristol-Myers Squibb: Research Funding; GSK: Consultancy; Genmab: Consultancy; Precision Biosciences: Consultancy; Kite/Gilead: Consultancy; Celgene: Consultancy, Research Funding; Gamida Cell: Consultancy; Novartis: Consultancy; Spectrum Pharmaceuticals: Consultancy; Juno Therapeutics: Consultancy, Research Funding; Sanofi-Genzyme: Consultancy, Research Funding. Scordo: i3 Health: Other: Speaker; Kite - A Gilead Company: Membership on an entity's Board of Directors or advisory committees; Angiocrine Bioscience: Consultancy, Research Funding; Omeros Corporation: Consultancy; McKinsey & Company: Consultancy. Shah: Amgen: Research Funding; Janssen Pharmaceutica: Research Funding. van den Brink: Seres: Other: Honorarium, Intellectual Property Rights, Research Fundingand Stock Options; Ceramedix: Other: has consulted, received honorarium from or participated in advisory boards ; Merck & Co, Inc: Honoraria; WindMILTherapeutics: Honoraria; MagentaTherapeutics: Honoraria; Da Volterra: Other: has consulted, received honorarium from or participated in advisory boards; Pluto Therapeutics: Current holder of stock options in a privately-held company, Other: has consulted, received honorarium from or participated in advisory boards ; GlaskoSmithKline: Other: has consulted, received honorarium from or participated in advisory boards; Forty-Seven, Inc.: Honoraria; Lygenesis: Other: has consulted, received honorarium from or participated in advisory boards ; Rheos: Honoraria; Pharmacyclics: Other; Kite Pharmaceuticals: Other; Frazier Healthcare Partners: Honoraria; Priothera: Research Funding; Wolters Kluwer: Patents & Royalties; Juno Therapeutics: Other; DKMS (nonprofit): Other; Notch Therapeutics: Honoraria; Nektar Therapeutics: Honoraria; Synthekine (Spouse): Other: has consulted, received honorarium from or participated in advisory boards; Novartis (Spouse): Other: has consulted, received honorarium from or participated in advisory boards; Jazz Pharmaceuticals: Honoraria; Therakos: Honoraria; Amgen: Honoraria. Perales: Nektar Therapeutics: Honoraria, Other; MorphoSys: Honoraria; Miltenyi Biotec: Honoraria, Other; Merck: Honoraria; Medigene: Honoraria; Kite/Gilead: Honoraria, Other; Karyopharm: Honoraria; Incyte: Honoraria, Other; Equilium: Honoraria; Cidara: Honoraria; Celgene: Honoraria; Bristol-Myers Squibb: Honoraria; NexImmune: Honoraria; Novartis: Honoraria, Other; Omeros: Honoraria; Sellas Life Sciences: Honoraria; Servier: Honoraria; Takeda: Honoraria. Palomba: Kite Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Pharmacyclics: Membership on an entity's Board of Directors or advisory committees.
