Diagnostic tool to identify and treat DNA repair deficient gastroesophageal adenocarcinomas

Background and aims DNA repair deficiency is a common feature of cancer. Homologous recombination (HR) and nucleotide excision repair (NER) are the two most frequently disabled DNA repair pathways in solid tumors. HR deficient breast, ovarian, pancreatic and prostate cancers respond well to platinum chemotherapy and PARP inhibitors. However, the frequency of DNA repair pathway deficiency in gastric and esophageal adenocarcinoma (GEA) still lacks diagnostic and functional validation. Furthermore, whether DNA repair deficient GEA have enhanced responsiveness to platinum chemotherapy and sensitivity to PARP inhibitors is not well characterized. Methods Using whole exome and genome sequencing data, we measured various HR deficiency-associated mutational signatures in patient specimen of gastric, esophageal and colorectal cancer specimens and gastric cancer cell lines. Gold-standard immunofluorescence assays were used to confirm HR and NER deficiency in cancer cell lines. The relationship between PARP inhibitor treatment and tumor response was evaluated in patients with gastric cancer. Drug sensitivity was determined using standard in vitro cell culture assays. Single-cell RNA-sequencing was performed to evaluate gastric cancer response to commonly used chemotherapeutics. Results We found that a significant subset of GEA, but very few colorectal tumors, show evidence of HR deficiency by mutational signature analysis (HRD score). Gastric cancer cell lines with high HRD mutational signature scores demonstrated functional HR deficiency by RAD51 assay and increased sensitivity to platinum and PARP inhibitors. There was a positive association between HRD scores and tumor response in patients with gastric cancer treated with a PARP inhibitor on a clinical trial. A gastric cancer cell line with strong sensitivity to cisplatin showed HR proficiency but exhibited NER deficiency by DDB2 proteo-probe assay. Single-cell RNA-sequencing revealed that, in addition to inducing general apoptosis, cisplatin treatment triggered ferroptosis in a NER-deficient gastric cancer, which may explain the outlier sensitivity. Conclusion A subset of upper gastrointestinal tumors have genomic features of HR and NER deficiency and therefore may be more likely to benefit from platinum chemotherapy and PARP inhibition. ### Competing Interest Statement JMC received research funding to his institution from Merus, Roche, and Bristol Myers Squibb. He received research funding from Merck, Astrazeneca, Arcus Biosciences, Apexigen, Esperas Pharma, Bayer, and Tesaro; received advisory board honorarium from Syros Pharmaceuticals and Blueprint Medicines. Z. Szallasi is an inventor on a patent used in the myChoice HRD assay. NS. Sethi is a consultant for Astrin Biosciences. * 5-FU : Fluorouracil CCLE : Cancer Cell Line Encyclopedia COAD : Colon adenocarcinoma DDB2 : DNA damage-binding protein 2 ESCA : Esophageal carcinoma GDC : Genomic Data Commons GEA : Gastric and esophageal adenocarcinoma GG-NER : Global genome-nucleotide excision repair HR : Homologous recombination LOH : Loss of heterogeneity LST : Large-scale State Transitions NER : Nucleotide excision repair PARP : Poly (ADP-ribose) polymerase scRNA-seq : Single cell RNA sequencing STAD : Stomach Adenocarcinoma TAI : Telomeric Allelic Imbalances TCGA : The Cancer Genome Atlas TC-NER : Transcription coupled-nucleotide excision repair VCF : Variant Call Format WES : Whole exome sequenced WGS : Whole genome sequencing XPC : XPC Complex Subunit, DNA Damage Recognition and Repair Factor