43P - A redesigned cell atlas of colon cancers to better assess their cellular composition

Background

Colon cancer (CC) exhibits inter- and intra-tumor heterogeneity, corresponding to a diversity of cellular composition. Published atlases of CC cells diverge in granularity and tumor cell (TC) types. They do not guarantee reliable deconvolution of bulk and spatial RNAseq data, they were not constructed for this purpose. Here, we propose a redesigned single-cell (sc) atlas of CCs constructed to enable robust deconvolution of CC transcriptome data, either bulk or spatial.

Methods

We reanalyzed two scRNAseq series totaling 600k cells obtained from the tumors of 120 CC patients, together with four reference series totaling 275k immune and stromal cells of various types. We randomly derived two subsets from these data, then performed a multi-step top-down unsupervised clustering analysis independently on each subset. We determined non-TC types using standard integration methods. We classified TCs according to normal epithelial cells (NECs) signatures to overcome the difficulties usually encountered when integrating TC data (impact of copy number variations and cell cycle activity).

Results

We grouped cells from CC samples at the first level according to their main lineage. We then independently analyzed mesenchymal/endothelial, lymphoid, and myeloid cell groups, each with a corresponding reference dataset. This identified the expected cell types for the lymphoid and myeloid lineages and, among others, 8 fibroblast subsets for the mesenchymal group. For NECs, we identified enterocytes, goblet, BEST4, enteroendocrine (EE), tuft, transit amplifying, and LGR5 stem cells. Applied to TCs, NEC expression signatures enabled us to distinguish undifferentiated TCs from differentiated TCs, the latter expressing markers from either enterocytes, goblet, EE, or tuft cells. This classification of TCs is associated with CMS and MMR status on our bulk RNAseq data (3000 samples). Deconvolution of our bulk and spatial RNAseq data with this atlas shows promising results.

Conclusions

We built a ready-to-use consensus cellular atlas of CC that improves the accuracy of deconvolution methods to infer cellular composition, a source of biomarkers in bulk RNAseq data to predict prognosis and response to treatment.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

M. Sroussi.

Funding

Has not received any funding.

Disclosure

C. Gallois: Financial Interests, Institutional, Invited Speaker: Sanofi Genzyme; Financial Interests, Institutional, Advisory Board: Servier, Pierre Fabre, Merck; Financial Interests, Institutional, Other, French congress invitation: MSD; Financial Interests, Institutional, Other, Congress invitation: Amgen. O. Bouche: Financial Interests, Personal, Advisory Board: Amgen, Merck, Apmonia Therapeutics, Deciphera, Astellas, Takeda; Financial Interests, Personal, Invited Speaker: Servier, Pierre Fabre, Bayer. T. Aparicio: Financial Interests, Personal, Invited Speaker, 2022: Servier; Financial Interests, Personal, Invited Speaker, 3 Conferences: Pierre Fabre; Financial Interests, Personal, Advisory Board, 2 Board in 2022 and 2023: BMS; Financial Interests, Personal, Invited Speaker, 1 conference: MSD; Non-Financial Interests, Leadership Role, 2021-2024: Fédération Francophone de Cancérologie Digestive. J. Taieb: Financial Interests, Personal, Advisory Board: MSD, Astellas, Merck, Servier, Pierre Fabre, Amgen, BMS, Novartis, Pfizer, Sanofi, Rottapharm, Takeda, Takeda; Financial Interests, Personal, Invited Speaker: Amgen, BMS, Merck, MSD, Novartis; Financial Interests, Personal, Invited Speaker, symposia: Astellas; Financial Interests, Personal, Other, steering committee of clinical trial: Novartis; Non-Financial Interests, Leadership Role, President of the scientific committee of the ARCAD foundation until end 2022: ARCAD Foundation; Non-Financial Interests, Leadership Role, Chair of the ARCAD pancreas research group: ARCAD Foundation; Non-Financial Interests, Leadership Role, Member of the administrative council, the scientific committee, the executive board and responsible for the international relationships/partnership for FFCD in the prodige intergroup: Federation Francophone de Cancerologie Digestive (FFCD); Non-Financial Interests, Other, steering committee of clinical trials: Pfizer, Servier. P. Laurent-Puig: Financial Interests, Personal, Invited Speaker: Amgen, Sanofi; Financial Interests, Personal, Advisory Board: Biocartis, Pierre Fabre; Financial Interests, Personal, Ownership Interest: Methys DX; Financial Interests, Institutional, Research Grant, PI of translational research: Federation francophone de cancerologie digestive; Non-Financial Interests, Leadership Role: President of canceropole ile de france. All other authors have declared no conflicts of interest.