Toward Personalized Lymphoma Immunotherapy: Identification of Common Driver Mutations Recognized by Patient CD8+ T Cells

Abstract

Purpose: A fundamental challenge in the era of next-generation sequencing (NGS) is to design effective treatments tailored to the mutational profiles of tumors. Many newly discovered cancer mutations are difficult to target pharmacologically; however, T-cell-based therapies may provide a valuable alternative owing to the exquisite sensitivity and specificity of antigen recognition. To explore this concept, we assessed the immunogenicity of a panel of genes that are common sites of driver mutations in follicular lymphoma, an immunologically sensitive yet currently incurable disease.Experimental Design: Exon capture and NGS were used to interrogate tumor samples from 53 patients with follicular lymphoma for mutations in 10 frequently mutated genes. For 13 patients, predicted mutant peptides and proteins were evaluated for recognition by autologous peripheral blood T cells after in vitro priming.Results: Mutations were identified in 1-5 genes in 81% (43/53) of tumor samples. Autologous, mutation-specific CD8 þ T cells were identified in 23% (3/13) of evaluated cases.T-cell responses were directed toward putative driver mutations in CREBBP and MEF2B. Responding T cells showed exquisite specificity for mutant versus wild-type proteins and recognized lymphoma cells expressing the appropriate mutations.Responding T cells appeared to be from the na€ ve repertoire, as they were found at low frequencies and only at single time points in each patient. Conclusions: Patients with follicular lymphoma harbor rare yet functionally competent CD8 þ T cells specific for recurrent mutations. Our results support the concept of using NGS to design individualized immunotherapies targeting common driver mutations in follicular lymphoma and other malignancies. Clin CancerRes; 22(9); 2226-36. Ó2015 AACR.

Development of a gene panel for next-generation sequencing of clinically relevant mutations in cell-free DNA from cancer patients

“…The SiRe panel detects the appearance of resistance mutations such as EGFR p.T790M (Figure 3). Finally, the non-synonymous mutation burden correlates with a good response to immunotherapy in NSCLC (Rizvi et al , 2015) and other tumours, and NGS has been proposed as a tool with which to design customised immunotherapies that target common driver mutations (Nielsen et al , 2016). Our panel, which covers several exons in frequently mutated genes, can be useful also in this setting.…”

The oncogenic membrane protein LMP1 sequesters TRAF3 in B-cell lymphoma cells to produce functional TRAF3 deficiency

“…34,[61][62][63] One challenge to this approach is determining which of the many mutations typically found are changes driving tumor growth, survival, and/or metastasis and should be prioritized for targeted therapies. 64,65 It is also increasingly appreciated that nongenetic changes in tumors have a significant impact on pathogenesis. In addition to epigenetic alterations, abnormal cellular localization and expression of specific proteins can make important contributions.…”

Mutational Analysis of Gene Fusions Predicts Novel MHC Class I–Restricted T-Cell Epitopes and Immune Signatures in a Subset of Prostate Cancer

“…Monocyte-derived dendritic cell (DC) cultures were generated as previously described [36]. Briefly, healthy donor PBMC were plated in 6 well plates (10 7 cells/well) and non-adherent cells removed after 90 and 150 minutes at 37 °C.…”

“…T cells were re-stimulated with irradiated (50 Gy) peptide-pulsed PBMC and polyI:C after 11 days and expanded with 240 IU/mL IL-2, 20 ng/mL IL-15, and 20 ng/mL IL-7 for two weeks. T cell cultures were rested for 3 days in 10 ng/mL IL-7 and screened for TMPRSS2:ERG reactivity by interferon-γ (IFNγ) ELISPOT as described [36]. Individual reactive cultures were expanded using irradiated (50 Gy) allogeneic feeder cells (PBMC) supplemented with OKT3 (30 ng/mL) and IL-2 (300 IU/mL) for 2 weeks.…”