63O - Transcriptional features of stage IIT4N0/III colon cancer associated with residual disease and ctDNA status after surgery in the PEGASUS trial

Background

Post-surgical detection of circulating tumor DNA (ctDNA), a surrogate for minimal residual disease (MRD) in colon cancer (CC) adjuvant setting, has been investigated in the PEGASUS trial (NCT04259944). MRD positive (MRD+) status distinguishes patients at high risk of relapse from MRD negative (MRD-) ones, potentially cured by surgery alone, with no defined biological or molecular characteristics linked to these CC prognostic groups thus far.

Methods

Global mRNA sequencing was performed by 3’-end RNA sequencing on FFPE tumor resections of patients enrolled in the PEGASUS trial, to compare MRD+ (ctDNA+ with/without relapse and ctDNA- with relapse) versus MRD- (ctDNA- without relapse) cases. MRD status was tested by hypergeometric distribution analysis for differential enrichment in molecular subtypes (CMS and CRIS classifiers) and stromal populations (estimated by EPIC), and for differential Hallmark Pathways expression by GSEA. An ensemble classifier of MRD+ vs. MRD- cases using penalized linear regression, gradient boosting and random forest was also trained (10-fold cross-validation nested to a leave-one-out test of performance).

Results

RNA was extracted and successfully sequenced from 152 FFPE samples. MRD+ cases (n=43) were enriched in stromal (CMS4, p = 0.004; fibroblasts, p = 0.004) and cancer cell-intrinsic (CRIS-D, p = 0.0008; CRIS-A, p = 0.02) traits, and depleted in CMS1 (p = 0.019) and CMS2 (p = 0.0022) classes. The performance of the ensemble classifier on the left-out samples was 0.738 Accuracy, 0.76 Precision, 0.898 Recall, 0.823 F1. GSEA pathway analysis for differential expression and pathway enrichment analysis for the signatures of the ensemble classifier concordantly highlighted traits associated with stroma and tissue remodeling.

Conclusions

Detection of MRD post-surgery correlates with distinct transcriptional characteristics of the primary tumor, indicating intrinsic properties of cancer cells and heightened interactions with the tumor microenvironment. For the first time, these observations highlight significant biological diversity in tumors of patients with similar outward characteristics.

Clinical trial identification

IFOM-CPT005/2019/PO004; EudraCT 2019-002074-32; NCT04259944.

Editorial acknowledgement

Legal entity responsible for the study

IFOM - the AIRC Institute of Molecular Oncology.

Funding

AIRC.

Disclosure

S. Lonardi: Financial Interests, Personal, Advisory Board: Amgen, Merck Serono, Lilly, Servier, AstraZeneca, MSD, Incyte, Daiichi Sankyo, Bristol Myers Squibb, Astellas, GSK, Takeda, Bayer, Rottapharm; Financial Interests, Personal, Invited Speaker: Pierre Fabre, GSK, Roche, Servier, Amgen, Bristol Myers Squibb, Incyte, Lilly, Merck Serono, MSD, AstraZeneca; Financial Interests, Institutional, Coordinating PI: Amgen, Merck Serono, Bayer, Roche, Lilly, AstraZeneca, Bristol Myers Squibb; Non-Financial Interests, Member of Board of Directors, Italian No-Profit Oncology Research Foundation supporting academic Clinical trials: GONO Foundation. N. Tarazona Llavero: Financial Interests, Personal, Advisory Board: Merck, Guardant Health, Grifols; Financial Interests, Personal, Invited Speaker: Merck, Pfizer, Servier, Amgen; Financial Interests, Institutional, Funding: Natera Inc, Guardant Health; Non-Financial Interests, Member: SEOM Committee. C. Montagut Viladot: Financial Interests, Personal, Advisory Board: Merck Serono, Roche; Financial Interests, Personal, Invited Speaker: Merck Serono, Pierre Fabre, Guardant Health, Amgen; Financial Interests, Institutional, Royalties: Biocartis; Financial Interests, Institutional, Coordinating PI: Merck Serono; Non-Financial Interests, Member: TTD (Grupo Tratamiento Tumores Digestivos). A. Sartore Bianchi: Financial Interests, Personal, Invited Speaker: Amgen, Bayer, Pierre Fabre; Financial Interests, Personal, Advisory Board: Servier, Takeda. M.E. Elez Fernandez: Financial Interests, Personal, Advisory Board: Hoffman La - Roche, Servier, Amgen, Merck Serono, Sanofi, Bayer, Pierre Fabre, MSD, Takeda, Boehringer Ingelheim, Cure Teq AG, Repare Therapeutics Inc., RIN Institute Inc., Janssen; Financial Interests, Personal, Invited Speaker: Organon, Novartis, Pfizer, BMS, Lilly, Medscape; Financial Interests, Personal, Other, Educational training: Seagen International GmbH; Financial Interests, Institutional, Funding: Hoffmann-La Roche Ltd, Sanofi Aventis Recherche & Développement, Amgen Inc., Boehringer Ingelheim, Novartis Farmacéutica SA, Bristol Myers Squibb International Corporation, BeiGene, HalioDX SAS, Janssen-Cilag SA, Merck Health KGAA, Merck Sharp & Dohme de España SA, PharmaMar SA, Servier, Taiho Pharma USA Inc, Hutchison MediPharma International, Menarini, Merus NV, Pfizer, Mirati, Array Biopharma Inc, AstraZeneca Pharmaceuticals LP, Celgene International SARL, Debiopharm International SA, Genentech Inc, MedImmune, AbbVie Deutschland Gmbh & Co KG, Bayer Pharma AG, Bioncotech Therapeutics, S.L., Biontech Rna Pharmacuticals GMBH, Biontech Small Molecules GMBH, Boehringer Ingelheim de España S.A., Daiichi Sankyo, Inc, Gercor, Hutchinson Medipharma Limited, Iovance Biotherapeutics, Inc., Janssen Research & Development, Menarini Ricerche SPA, Merck, Sharp & Dohme De España S.A., Nouscom SRL., Pledpharma AB, Redx Pharma PLC, Scandion Oncology, Seattle Genetics Inc., Sotio A.S., Wntresearch AB; Non-Financial Interests, Other, Coordinator of the SEOM +MIR Section of Residents and Young Assistants: Sociedad Española de Oncología Médica (SEOM); Non-Financial Interests, Other, Speaker of the ESMO Academy: European Society for Medical Oncology (ESMO); Non-Financial Interests, Other, Volunteer member of the ASCO Annual Meeting Scientific Program Committee: Developmental Therapeutics – Immunotherapy: American Society of Clinical Oncology (ASCO); Non-Financial Interests, Leadership Role, Member of the Scientific Program Committee and Developmental Therapeutics-Immunotherapy Track Leader, 2023-2024 term: American Society for Clinical Oncology (ASCO); Non-Financial Interests, Other, Member of the Scientific Committee 2024: European Society for Medical Oncology (ESMO); Other, Travel, accommodations, expenses.: Roche, Merck Serono, Sanofi, Amgen, Array BioPharma, Servier, Bristol Myers Squibb. C. Santos Vivas: Financial Interests, Personal, Advisory Board: Amgen; Financial Interests, Personal, Invited Speaker: Amgen; Non-Financial Interests, Leadership Role, Clinical trial coordinator: Merck; Other, Travel grant: Merck, MSD, Amgen. M. Mandalà: Financial Interests, Personal, Advisory Board: MSD, Novartis, Sanofi, BMS, Pierre Fabre; Financial Interests, Personal, Invited Speaker: Sun Pharma. A. Cervantes: Financial Interests, Institutional, Advisory Board: Merck Serono, Amgen, Roche, Transgene, AnHeart Therapeutics, AbbVie, GSK; Financial Interests, Institutional, Invited Speaker: Amgen, Roche, Merck Serono, Foundation Medicine; Financial Interests, Personal, Other, Associate Editor: Annals of Oncology, ESMO Open; Financial Interests, Personal, Other, Editor in Chief: Cancer Treatment Reviews; Financial Interests, Institutional, Research Grant, Principal Investigator: Actuate Therapeutic, Amgen, Astellas Pharma, BeiGene, Bayer, AstraZeneca, BMS, Amcure, FibroGen, Lilly, Genentech, MedImmune, Merck Serono, Novartis, Natera, MSD, Servier, Sierra Oncology, Adaptimmune, Takeda, Affimed, Roche, Seamless, Gilead, Janssen, F. STAR Therapeutics, Ribon Therapeutics; Non-Financial Interests, Other, Scientific Director: INCLIVA Biomedical Research Institute. S. Siena: Financial Interests, Personal, Advisory Board, Advisory Board Member: Agenus, AstraZeneca, BMS, Checkmab, Daiichi Sankyo, GSK, Novartis, Seagen, T-One-Therapeutics, Merck, MSD. A. Bardelli: Financial Interests, Personal, Other, Receipt of honoraria or consultation fees: Guardant Health, Inivata; Financial Interests, Personal, Advisory Board, Scientific Advisory Board: Inivata, Neophore; Financial Interests, Personal, Advisory Board, Roche/Genentech Global CRC Advisory Board: Roche; Financial Interests, Personal, Stocks/Shares, Stock shareholder: Neophore, Kither; Financial Interests, Institutional, Research Grant, Receipt of grants/research supports: Neophore, AstraZeneca, Boehringer Ingelheim. All other authors have declared no conflicts of interest.