Single-cell transcriptomics reveals stage- and side-specificity of gene modules in colorectal cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38826219", "kind": "science-record", "revision": 3, "content_hash": "sha256:bb46cf8c3bc907a5425789cdc2b3c13c59d2e2be95c384e31a44625772acb3cf", "created_at": "2026-11-01T19:20:47Z", "updated_at": "2026-11-01T21:33:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Single-cell transcriptomics reveals stage- and side-specificity of gene modules in colorectal cancer.", "doi": "10.21203/rs.3.rs-4402565/v1", "pmid": "38826219", "authors": ["Sara Rahiminejad", "Kavitha Mukund", "Mano Ram Maurya", "Shankar Subramaniam"], "journal": "Research square", "year": 2024, "abstract": "BACKGROUND: An understanding of mechanisms underlying colorectal cancer (CRC) development and progression is yet to be fully elucidated. This study aims to employ network theoretic approaches to analyse single cell transcriptomic data from CRC to better characterize its progression and sided-ness.\nMETHODS: We utilized a recently published single-cell RNA sequencing data (GEO-GSE178341) and parsed the cell X gene data by stage and side (right and left colon). Using Weighted Gene Co-expression Network Analysis (WGCNA), we identified gene modules with varying preservation levels (weak or strong) of network topology between early (pT1) and late stages (pT234), and between right and left colons. Spearman's rank correlation (ρ) was used to assess the similarity or dissimilarity in gene connectivity.\nRESULTS: Equalizing cell counts across different stages, we detected 13 modules for the early stage, two of which were non-preserved in late stages. Both non-preserved modules displayed distinct gene connectivity patterns between the early and late stages, characterized by low ρ values. One module predominately dealt with myeloid cells, with genes mostly enriched for cytokine-cytokine receptor interaction potentiallystimulating myeloid cells to participate in angiogenesis. The second module, representing a subset of epithelial cells, was mainly enriched for carbohydrate digestion and absorption, influencing the gut microenvironment through the breakdown of carbohydrates. In the comparison of left vs. right colons, two of 12 modules identified in the right colon were non-preserved in the left colon. One captured a small fraction of epithelial cells and was enriched for transcriptional misregulation in cancer, potentially impacting communication between epithelial cells and the tumor microenvironment. The other predominantly contained B cells with a crucial role in maintaining human gastrointestinal health and was enriched for B-cell receptor signalling pathway.\nCONCLUSIONS: We identified modules with topological and functional differences specific to cell types between the early and late stages, and between the right and left colons. This study enhances the understanding of roles played by different cell types at different stages and sides, providing valuable insights for future studies focused on the diagnosis and treatment of CRC.", "claims": [{"id": "claim-method", "statement": "Spearman’s rank correlation (ρ) was used to assess the similarity or dissimilarity in gene connectivity.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38826219", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Spearman’s rank correlation (ρ) was used to assess the similarity or dissimilarity in gene connectivity."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset analyzed in the current study is available in the Gene Expression Omnibus (GEO) repository with the accession code GSE178341 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178341].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38826219", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "The dataset analyzed in the current study is available in the Gene Expression Omnibus (GEO) repository with the accession code GSE178341 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178341]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified modules with topological and functional differences specific to cell types between the early and late stages, and between the right and left colons.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38826219", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "We identified modules with topological and functional differences specific to cell types between the early and late stages, and between the right and left colons."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified modules with topological and functional differences specific to cell types between the early and late stages, and between the right and left colons.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38826219"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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