Single-Cell Sequencing of Hepatocellular Carcinoma Reveals Cell Interactions and Cell Heterogeneity in the Microenvironment.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34992435", "kind": "science-record", "revision": 5, "content_hash": "sha256:efe95b4be09bc21f1d8b2770429bc7f4a94eb570b5e5673c9d70386254861d51", "created_at": "2026-11-01T17:36:42Z", "updated_at": "2026-11-01T22:48:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Single-Cell Sequencing of Hepatocellular Carcinoma Reveals Cell Interactions and Cell Heterogeneity in the Microenvironment.", "doi": "10.2147/IJGM.S338090", "pmid": "34992435", "authors": ["Xinyao Li", "Lei Wang", "Liusong Wang", "Zanjie Feng", "Cijun Peng"], "journal": "International journal of general medicine", "year": 2021, "abstract": "BACKGROUND: Hepatocellular carcinoma (HCC) is the main histological subtype of liver cancer, which has the characteristics of poor prognosis and high fatality rate. Single-cell sequencing can provide quantitative and unbiased characterization of cell heterogeneity by analyzing the molecular profile of the whole genome of thousands of single cells. Thus, the purpose of this study was to identify novel prognostic markers for HCC based on single-cell sequencing data.\nMETHODS: Single-cell sequencing of 21 HCC samples and 256 normal liver tissue samples in the GSE124395 dataset was collected from the Gene Expression Omnibus (GEO) database. The quality-controlled cells were grouped by unsupervised cluster analysis and identified the marker genes of each cell cluster. Hereafter, these cell clusters were annotated by singleR and CellMarker according to the expression patterns of the marker genes. Pseudotime analysis was performed to construct the trajectory of cell evolution and to define hub genes in the evolution process. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to explore the potential regulatory mechanism of hub genes in HCC. Next, the differential expression of hub genes and the correlation of the expression of these genes with patients' survival and diagnosis were investigated in The Cancer Genome Atlas (TCGA) database.\nRESULTS: A total of 9 clusters corresponding to 9 cell types, including NKT cells, hepatocytes, endothelial cells, Kupffer cells, EPCAM+ cells, cancer cells, plasma cells (B cells), immature B cells, and myofibroblasts were identified. We screened 63 key genes related to cell differentiation through trajectory analysis, which were enriched in the process of coagulation. Ultimately, we identified 10 survival-related hub genes in the TCGA database, namely ALDOB, APOC3, APOH, CYP2E1, CYP3A4, GC, HRG, LINC01554, PDK4, and TXN.\nCONCLUSION: In conclusion, ALDOB, APOC3, APOH, CYP2E1, CYP3A4, GC, HRG, LINC01554, PDK4, and TXN may serve as hub genes in the diagnosis and prognosis for HCC.", "claims": [{"id": "claim-method", "statement": "The Kaplan-Meier curve was used for the survival analysis of 36 differentially expressed hub genes, and the difference between survival curves of the two groups was tested by a Log rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34992435", "locator": "sections[10] \"Statistical Analysis\" paragraph 2", "quote": "The Kaplan-Meier curve was used for the survival analysis of 36 differentially expressed hub genes, and the difference between survival curves of the two groups was tested by a Log rank test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data from GEO is shared and available to the public, and there are no ethical concerns.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34992435", "locator": "sections[20] \"Ethical Statement\" paragraph 2", "quote": "The data from GEO is shared and available to the public, and there are no ethical concerns."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Ultimately, we identified 10 survival-related hub genes in the TCGA database, namely ALDOB, APOC3, APOH, CYP2E1, CYP3A4, GC, HRG, LINC01554, PDK4, and TXN.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34992435", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Ultimately, we identified 10 survival-related hub genes in the TCGA database, namely ALDOB, APOC3, APOH, CYP2E1, CYP3A4, GC, HRG, LINC01554, PDK4, and TXN."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Ultimately, we identified 10 survival-related hub genes in the TCGA database, namely ALDOB, APOC3, APOH, CYP2E1, CYP3A4, GC, HRG, LINC01554, PDK4, and TXN.", "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:34992435"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE124395"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE124395"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34992435", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/IJGM.S338090", "sha256": 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