Abstract 163P
Background
Links between the tumor mutational signature, myeloid and tumor-infiltrating lymphocytes (TIL) phenotype and functional states are lacking in malignant pleural mesothelioma (MPM). We performed multi-omic profiling of the tumor immune microenvironment (TIME) of epithelioid MPM cases to provide insights that could drive novel therapeutic avenues in future studies.
Methods
MPM tumor tissue from patients who underwent surgical resection was confirmed by a pathologist as epithelioid histological type. Flow cytometry, cytokine profiing and TIL expansion was performed ex vivo. Twenty-two tumor samples were processed for bulk RNA-seq with 15 matched cases profiled for WES. Single cell(sc) RNA-seq with matched scTCR-seq was performed on 9 tumor cases. Analysis was performed using in-house set open-source pipelines with downstream analysis in R. Statistical significance was determined using BH adjusted p-value and +/-1 log2FC with Wilcoxon Sum Ranking test for differentially expressed genes (adjusted p-value significance: 0 ≤ *** < 0.001 ≤ ** < 0.01).
Results
BAP1 was the dominant mutation identified in the analyzed cohort (SNV (6/22, 27.3%), CNV (3/15, 20%)). Median tumor mutation burden was low (0.80) and no HLA loss of heterozygosity was identified. scRNA-seq profiling identified clusters of highly proliferative, effector memory CD8+ TIL that contained hyper and highly expanded clones. TIL expressed a high degree of checkpoint receptors (PD-1***, LAG3***, TIM3***) which was confirmed by flow cytometry, and the transcription factor, TOX***. Treg clusters and suppressive myeloid cell types were identified which could limit immune responses against the tumor. CCL22, IP-10 and sCD25 were detected in the tumor tissue. Expanded TIL showed a loss of polyfunctional cytokine secretion but retained production of IFNγ.
Conclusions
Hyper and highly expanded TCRs were identified suggesting potential anti-tumor response despite having a dysfunctional, highly proliferative phenotype and a highly suppressive TIME. Our ongoing efforts are focused on receptor-ligand interaction predictions as well as identifying predicted neo-antigens.
Clinical trial identification
IRB: LAB08-0380.
Legal entity responsible for the study
University of Texas MD Anderson Cancer Center.
Funding
A. Dillon & L. Bourg Mesothelioma Endowment, Fleming Endowed Professorship, Re & RM Kennedy Lung Cancer Fund.
Disclosure
C. Haymaker: Financial Interests, Personal, Advisory Board: Regeneron; Financial Interests, Personal, Other, Consulting: Avenge; Financial Interests, Personal, Other, Stock options as a member of the Scientific Advisory Board: Briacell; Financial Interests, Institutional, Research Grant: Iovance, Dragonfly, BTG, Sanofi, Avenge, KSQ; Non-Financial Interests, Personal, Advisory Role, Co-Chair of SAB: Mesothelioma Applied Research Foundation. J. Zhang: Financial Interests, Institutional, Research Grant: Merck, Johnson and Johnson, Novartis, AstraZeneca, GenePlus, Innovent, Catalyst, Henlius, Summit, Hengrui; Financial Interests, Personal, Advisory Role: Merck, Johnson and Johnson, Novartis, AstraZeneca, GenePlus, Innovent, Catalyst, Henlius, Summit, Hengrui. A.S. Tsao: Financial Interests, Personal, Advisory Board: Genentech, BMS, Eli Lilly, Roche, Novartis, Ariad, EMD Serono, Merck, Seattle Genetics, AstraZeneca, Boehringer Ingelheim, GSK, Pfizer, Gilead Sciences, Inc., Summit Therapeutics; Financial Interests, Institutional, Research Grant: Ariad, AstraZeneca, BMS, Boehringer Ingelheim, Eli Lilly, Epizyme, Genentech, Merck, Millennium, Novartis, Polaris, Settle Genetics. All other authors have declared no conflicts of interest.