Prognostic impact of HLA‐I neoantigen‐specific CD8+ T cells in limited‐stage follicular lymphoma

Abstract

Introduction: Follicular lymphoma (FL) is the most common indolent NHL. Recently, we demonstrated in limited and advanced stage FL (LSFL, ASFL), that patients with longer remissions had raised clonally expanded intratumoral CD8+ T cells (Tobin, JCO 2019). Durable remissions occur in ∼50% of LSFL patients whereas ASFL is incurable. However, little is known regarding the immunological features associated with this difference. We hypothesized HLA-I neoantigen (neoAg)-specific CD8+ T cells may play a role. Methods: The discovery cohort comprised 101 patients with diagnostic paraffin embedded tissue from the TROG99.03 LSFL clinical trial (MacManus, JCO 2018), in which stage I/II patients were randomized to involved field radiation (IFRT) only or combined modality therapy between 2000 and 2012 (PET from 2006). Contemporaneous validation cohorts were (a) AusLSFL: 60 PET staged, stage I FL patients from Australia (treatment miscellaneous), and (b) CanLSFL: 60 PET staged, stage I FL patients drawn principally from Canada (IFRT only). Digital gene expression (NanoString), targeted sequencing (330 genes), and germline HLA-typing was performed. Mutations observed by sequencing were used to predict neoAgs in TROG99.03 tissues using 8 algorithms (PVACseq) and filtered according to strong binding affinity to HLA-I over wild-type (TESLA consortium guidelines; Wells, Cell 2020). Results: CD8A gene expression was tested for prognostic significance. In TROG99.03, elevated intratumoral CD8A (by MaxStat) was associated with ∼2-fold improvement in PFS for all patients: HR 0.45 (CI: 0.77–0.26, p = 0.0053) and stage I only patients: HR 2.4 (CI: 1.2–4.6, p = 0.036). In keeping with a relationship between CD8+ T cell infiltration and tumor antigen presentation, raised expression of NLRC5 (a transcriptional HLA-I activator) was also associated with superior PFS: HR 0.48 (CI: 0.99–0.24, p = 0.024). CD8A significance was confirmed in both validation cohorts (whereas NLRC5 was validated in AusLSFL only). In keeping with recent IHC CD8 protein data (Los-de Vries, Bld Adv 2022), CD8A gene expression was raised in stage I LSFL vs. 68 ASFL patients treated with immunochemotherapy (p = 0.02). Mutational profiling was concordant with published LSFL data, with CREBBP and KMT2DA most frequent. NeoAg calling methods including functional assays for neoAg peptide binding were confirmed in a separate cohort of fresh FL tissues. 59% of TROG99.03 tissues had ≥1 neoantigens detected. Importantly, unsupervised hierarchical clustering showed 2-fold enrichment of samples with neoantigens among those with high vs. low HLA-I. Conclusions: Raised CD8A is associated with favorable prognosis in LSFL. Our data suggests disease control involves populations of expanded HLA-I neoAg-specific T cells. These findings have implications for novel immunotherapeutic strategies designed to increase the rate of durable remissions. The research was funded by: National Health and Medical Research Council, Australia; Leukaemia Foundation; Mater Foundation Keywords: Diagnostic and Prognostic Biomarkers, Indolent non-Hodgkin lymphoma, Microenvironment Conflicts of interests pertinent to the abstract. C. Keane Honoraria: Takeda, Roche, AZ, MSD, Beigene C. Cheah Consultant or advisory role: Roche, Janssen, Gilead, AstraZenecca, Lilly, TG therapeutics, Beigene, Novartis, Menarini, Daizai, Abbvie, Genmab. BMS Honoraria: BMS, Roche, Abbvie; MSD, Lilly R. Kridel Research funding: Abbvie Educational grants: Eisai M. K. Gandhi Research funding: Beigene, Janssen