Dynamic phospho-proteogenomic analysis of gastric cancer cells suggests host immunity provides survival benefit

The mainstay of advanced gastric cancer (GC) therapy is DNA-damaging drugs. Using proteogenomic analysis of a panel of eight GC cell lines, we identified genetic alterations and signaling pathways, potentially associated with resistance to DNA-damaging drugs. Notably, 5-fluorouracil (5FU) resistance was associated with PD-L1 expression, but not established GC subtypes. In publicly available cohort data, PD-L1 expression was associated with a reduced risk of GC progression. In addition to PD-L1, expression of inflammatory genes induced by lymphocyte cytokines was consistently associated with prolonged survival in GC. In our validation cohort, total lymphocyte count (TLC) predicted a better relapse-free survival rate in GC patients with 5FU-based adjuvant chemotherapy than those with surgery alone. Moreover, TLC+ patients who had no survival benefit from adjuvant chemotherapy were discriminated by IκBα expression. Collectively, our results suggest that 5FU resistance observed in cell lines may be overcome by host immunity or by combination therapy with immune checkpoint blockade. ### Competing Interest Statement T.I.: Grant/Research Support, Nippon Kayaku, Chugai Pharmaceutical, Daiichi Sankyo, Taiho Pharmaceutical, Otsuka Pharmaceutical, Quantdetect Inc.; Consultation, Quantdetect Inc. A.Y-A.: Consultation, PCL Japan, Kotobiken Medical Laboratories, LSI Medience, Quantdetect Inc. H.H.: Grant/Research Support, LSI Medience Co.; Consultation, Quantdetect, Inc. J.W.: Consultation, Baylor College of Medicine; Stock/Options/Financial, Theralink Technologies Inc. V.E.: Consultation, TheraLink Technologies, Inc.; Royalty distributions from patents licensed from George Mason University. Y.Sasaki: Grant/Research Support from Eli Lilly Japan. E.P.III.: Grant/Research Support, Springworks Therapeutics, Inc., Deciphera Pharmaceuticals, Genentech/Roche, Inc; Consultation, Ceres Nanosciences, Inc., Theralink Technologies, Inc., Perthera, Inc.; Stock/Options/Financial, Ceres Nanosciences, Inc., Theralink Technologies, Inc., Perthera, Inc. G.B.M.: Grant/Research Support, AstraZeneca, Zentalis, Nanostring, Ionis (Provision of tool compounds); Scientific Advisory Board/Consultant, Amphista, Astex, AstraZeneca, Biodyne, BlueDot, Chrysallis Biotechnology, Ellipses Pharma, GSK, ImmunoMET, Infinity, Ionis, Leapfrog Bio, Lilly, Medacorp, Nanostring, Neophore, Nuvectis, Pangea, PDX Pharmaceuticals, Qureator, Roche, Rybodyne, Signalchem Lifesciences, Tarveda, Turbine, Zentalis Pharmaceuticals; Stock/Options/Financial, Bluedot, Biodyne, Catena Pharmaceuticals, ImmunoMet, Nuvectis, RyboDyne, SignalChem, Tarveda, Turbine; and Licensed Technologies, HRD assay to Myriad Genetics and DSP to Nanostring. S.S.N.: Grant/Research Support, Array Jet, Taiho Pharmaceuticals, Boehringer-Ingelheim, Geninus, and Thermo Fisher Scientific; Honorarium, Chugai Pharmaceuticals and MSD; Consultation, Mills Institute for Personalized Care (MIPC); Advisor, CLEA Japan; and CEO, Quantdetect, Inc. The other authors declare no competing interests. ### Funding Statement This work was supported by JSPS KAKENHI (JP16K18458, JP25462034, JP16H01578, and 16H06279); grant from the Keiryokai Research Foundation (Y118 and 131); NCI Grant (CA16672); and NHI Grant (R50CA221675). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The multi-center study protocol was approved by the Institutional Review Board (IRB) of Iwate Medical University (H24-132, HGH24-12, and HG2020-018), where all analysis was carried out. Ethical approval for conducting this study was given by all IRB committees of all 12 participating institutions listed in the Northern Japan Gastric Cancer Study Consortium (Nishizuka et al., J Surg Oncol, 2018; Ohmori et al., J Surg Oncol, 2019; Koizumi et al., J Natl Cancer Inst, 2022). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Targeted gene sequencing and RNA sequencing data have been deposited in the DNA Data Bank of Japan (DDBJ) via the Bioinformation and DDBJ Center under data set identifier DRA011072 (). RPPA data is available at The University of Texas MD Anderson Cancer Center RPPA Data Repository under data set identifier TCPA00000007 (). Cohort data for advanced GC patients from the Northern Japan Gastric Cancer Study Consortium are available upon request.