Identification and characterization of immunogenic neoantigens in biliary cancer (BC) and pancreatic cancer (PC).

Authors

Francesca Battaglin

Francesca Battaglin

Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA

Francesca Battaglin , Andrew Elliott , Joanne Xiu , Sandra Algaze , Jingyuan Wang , Priya Jayachandran , Shivani Soni , Karam Ashouri , Alexandra Wong , Pooja Mittal , Jae Ho Lo , Lesly Torres-Gonzalez , Wu Zhang , Benjamin Adam Weinberg , Sanjay Goel , Emil Lou , Anthony B. El-Khoueiry , Heinz-Josef Lenz

Organizations

Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, Caris Life Sciences, Irving, TX, Caris Life Sciences, Phoenix, AZ, Ruesch Center for The Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, University of Minnesota, Minneapolis, MN

Research Funding

Partly supported by National Cancer Institute (grant number P30CA014089), Gloria Borges WunderGlo Foundation, Dhont Family Foundation, Gene Gregg Pancreas Research Fund, San Pedro Peninsula Cancer Guild
Daniel Butler Research Fund, V foundation for cancer research, Victoria and Philip Wilson Research Fund, Fong research project and Ming Hsieh research fund

Background: Recognition of tumor neoantigens by autologous T cells activates immune surveillance and has been reported to promote sensitivity to immune checkpoint inhibitors (ICI) in mismatch repair deficient (MMRd)/microsatellite instability high (MSI-H) tumors. Neoantigen-targeted reactivity has also been reported in microsatellite stable (MSS) tumors. Neoantigens are emerging targets for novel immunotherapy strategies, including tumor vaccines, in BC and PC. We aimed to comprehensively assess the spectrum of immunogenic neoantigens in BC and PC. Methods: 3728 tumor specimens (1389 BC; 2339 PC) tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing on DNA (720-gene panel) and RNA (whole transcriptome) were analyzed. MSI status was determined by immunohistochemistry of MMR protein and/or NGS. Immune epitope prediction was performed on translated peptide sequences harboring detected mutations using the NetMHCpan v4.0 method in the Immune Epitope Database, with HLA genotyping performed using arcasHLA. Immune/stromal cell abundance in the tumor microenvironment (TME) was quantified using the MCP Counter method. Gene expression profiles were analyzed for a transcriptional signature predictive of response to immunotherapy (T cell-inflamed signature, TIS). Results: MMRd/MSI-H rate was 1.8% in BC and 1.4% in PC. 117219 unique peptide:allele interactions with predicted binding-level affinity for patient-specific HLA alleles were identified (48781 in BC; 71182 in PC). MMRd/MSI-H tumors had higher neoantigen load at all affinity levels compared to MSS. Only 4 recurrent neoantigens with binding affinity (observed in >10 samples) were identified in BC and derived from mutations in KRAS (3/4) and IDH1 (1/4), while 78 were found in PC, mostly associated with mutations in KRAS (53/78) and TP53 (16/78). The frequency of individual neoantigens was particularly low in MSS BC (< 2%). Across both cancer types, TIS scores positively correlated with the abundance of immune cell populations in the TME, notably cytotoxic lymphocytes (r > 0.40). Recurrent neoantigens associated with highest average TIS scores resulted from mutation of KRAS (G12D/V, 1.8%/1.5% of samples, respectively) in BC yet mean TIS scores were low (~60th percentile overall). Similarly, TP53 (Y220C/R273C, 0.6%/0.7%, respectively) and CDKN2A (multiple variants, 0.5%) were associated with the highest yet relatively low mean TIS scores in MSS PC (~73th percentile) compared to mean TIS scores associated with MSH3 (K383fs, 12%) and KRAS (G12D, 12%) in MMRd/MSI-H PC (~90th percentile). Conclusions: This is the largest study to investigate the landscape of immunogenic neoantigens in BC and PC. The frequency of high-level binding affinity neoantigens was relatively low and associated with relatively lower TIS scores in MSS tumors, which may contribute to the immunogenic cold TME characterizing these tumor types.

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Abstract Details

Meeting

2024 ASCO Gastrointestinal Cancers Symposium

Session Type

Poster Session

Session Title

Poster Session B: Cancers of the Pancreas, Small Bowel, and Hepatobiliary Tract

Track

Pancreatic Cancer,Hepatobiliary Cancer,Neuroendocrine/Carcinoid,Small Bowel Cancer

Sub Track

Tumor Biology, Biomarkers, and Pathology

Citation

J Clin Oncol 42, 2024 (suppl 3; abstr 552)

DOI

10.1200/JCO.2024.42.3_suppl.552

Abstract #

552

Poster Bd #

F19

Abstract Disclosures

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