Identification and characterization of immunogenic neoantigens in colorectal cancer (CRC).

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 , Anthony F. Shields , Richard M. Goldberg , John Marshall , Emil Lou , 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, Karmanos Cancer Institute, Wayne State University, Detroit, MI, West Virginia University Cancer Institute and the Mary Babb Randolph Cancer Center, Morgantown, WV, Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 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: Presentation of neoantigens, short peptides derived from tumor-specific somatic mutations, by HLA molecules triggers the activation of anti-tumor immune response. Recognition of neoantigens by autologous T cells promotes 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, and neoantigens are emerging targets for tumor vaccines and adoptive cell therapy. Here, we aimed to comprehensively assess the spectrum of immunogenic neoantigens in CRC to identify new subpopulations for these therapeutic strategies. Methods: 7,053 CRC 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 proteins 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 estimated from RNA expression profiles using MCP-Counter. Gene expression profiles were analyzed for a transcriptional signature predictive of response to immunotherapy (T cell-inflamed signature, TIS). Results: 6,600,005 unique peptide:allele interactions were tested, of which 368,468 (5.6%) were predicted neoantigens with patient-specific HLA alleles, including 16,184 (0.25%) with high affinity. MMRd/MSI-H tumors (6.9%) had higher neoantigen load at all affinity levels compared to MSS, with 10,243 (63.3%) and 5,621 (34.7%) of the predicted high affinity neoantigens exclusively associated with MSS and MMRd/MSI-H, respectively. 32 recurrent high affinity neoantigens were identified in > 10 samples, most frequently derived from APC mutations in MSS tumors (78% of recurrent neoantigens), and from RNF43 (25%), ASXL1 (20%), and KMT2D (15%) in MMRd/MSI-H. TIS scores positively correlated with the abundance of various immune cell populations in the TME, notably cytotoxic lymphocytes (r = 0.46). Among the recurrent high affinity neoantigens, those with the highest mean TIS scores (> 90th percentile) resulted from mutation of MSH3 (K383fs, 5.1%) and KMT2D (multiple variants, 2.8%) in MMRd/MSI-H CRC, while those in MSS CRC derived from SOX9 (multiple variants, 0.2%) and APC (multiple variants, 0.7%) but were not associated with increased mean TIS scores (~55th percentile). Conclusions: This is one of the largest studies to investigate the landscape of immunogenic neoantigens in CRC. We were able to identify candidate recurrent peptides with high HLA binding affinity and an association with a positive TIS signature supporting the role of neoantigens as potential cancer immunotherapy targets.

Disclaimer

This material on this page is ©2024 American Society of Clinical Oncology, all rights reserved. Licensing available upon request. For more information, please contact licensing@asco.org

Abstract Details

Meeting

2024 ASCO Gastrointestinal Cancers Symposium

Session Type

Poster Session

Session Title

Poster Session C: Cancers of the Colon, Rectum, and Anus

Track

Colorectal Cancer,Anal Cancer

Sub Track

Translational Research

Citation

J Clin Oncol 42, 2024 (suppl 3; abstr 161)

DOI

10.1200/JCO.2024.42.3_suppl.161

Abstract #

161

Poster Bd #

K9

Abstract Disclosures

Similar Abstracts

Abstract

2024 ASCO Gastrointestinal Cancers Symposium

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

First Author: Francesca Battaglin

Abstract

2024 ASCO Gastrointestinal Cancers Symposium

LMTK3 gene expression and the molecular landscape of colorectal cancer (CRC).

First Author: Lesly Torres-Gonzalez

First Author: Katherine K Benson