Single-Cell RNA Sequencing Revealed That the Enrichment of TPI1+ Malignant Hepatocytes Was Linked to HCC Metastasis and Immunosuppressive Microenvironment.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38410699", "kind": "science-record", "revision": 4, "content_hash": "sha256:4caaa1582bf2dca02bef17404fee72a9d7036c21c6c9c44b88614b08f1aa3a38", "created_at": "2026-11-01T19:20:21Z", "updated_at": "2026-11-01T22:53:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Single-Cell RNA Sequencing Revealed That the Enrichment of TPI1+ Malignant Hepatocytes Was Linked to HCC Metastasis and Immunosuppressive Microenvironment.", "doi": "10.2147/JHC.S453249", "pmid": "38410699", "authors": ["Yuxin Liang", "Deyuan Zhong", "Qinyan Yang", "Yuan Tang", "Yingying Qin", "Yuhao Su", "Xiaolun Huang", "Jin Shang"], "journal": "Journal of hepatocellular carcinoma", "year": 2024, "abstract": "Background: Tumor metastasis is the leading cause of high mortality in hepatocellular carcinoma (HCC). The metastasis-related HCC microenvironment is characterized by high heterogeneity. Single-cell RNA sequencing (scRNA-seq) may aid in determining specific cell clusters involved in regulating the immune microenvironment of HCC.\nMethods: The scRNA-seq data of 10 HCC samples were collected from the Gene Expression Omnibus (GEO) database GSE124395. Correlations between key gene expression and clinicopathological data were determined using public databases. HCC tissues and matched tumor-adjacent and normal tissue samples were obtained by surgical resection at Sichuan Cancer Hospital. Immune cell infiltration analysis was performed and verified by immunohistochemistry and immunofluorescent staining.\nResults: Nine malignant hepatocyte clusters with different marker genes and biological functions were identified. C3_Hepatocyte-SERF2 and C6_Hepatocyte-IL13RA2 were mainly involved in the regulation of the immune microenvironment, which was also a significant pathway in regulating HCC metastasis. Key genes in malignant hepatocyte clusters that associated with HCC metastasis were further screened by LASSO regression analysis. TPI1, a key gene in C6_Hepatocyte-IL13RA2 and HCC metastasis, could participate in regulating the HCC immune microenvironment in The Cancer Genome Atlas (TCGA) and Tumor Immune Estimation Resource (TIMER) databases. Moreover, immunohistochemistry analysis demonstrated that TPI1 expression was positively correlated with HCC metastasis and poor prognosis, while negatively correlated with CD8+ T cell infiltration. The negative correlation between TPI1 expression and CD8+ T cell infiltration was further confirmed by immunofluorescence staining.\nConclusion: In summary, a cluster of TPI1+ malignant hepatocytes was associated with the suppression of CD8+ T cell infiltration and HCC metastasis, providing novel insights into potential biomarkers for immunotherapy in HCC.", "claims": [{"id": "claim-method", "statement": "The Wilcox test was performed to determine differentially expressed genes (DEGs) according to the criteria of P value < 0.05 and log2 fold change > 0.58.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38410699", "locator": "sections[4] \"Identification of Hepatocyte Subsets and Differential Expressed Metastasis-Related Genes\" paragraph 2", "quote": "The Wilcox test was performed to determine differentially expressed genes (DEGs) according to the criteria of P value < 0.05 and log2 fold change > 0.58."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data supporting the findings of our study are available from the corresponding author under reasonable requirements.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38410699", "locator": "sections[17] \"Data Sharing Statement\" paragraph 2", "quote": "The data supporting the findings of our study are available from the corresponding author under reasonable requirements."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A cluster of TPI1+ malignant hepatocytes was associated with the suppression of CD8+ T cell infiltration and HCC metastasis, providing novel insights into potential biomarkers for immunotherapy in HCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38410699", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "In summary, a cluster of TPI1+ malignant hepatocytes was associated with the suppression of CD8+ T cell infiltration and HCC metastasis, providing novel insights into potential biomarkers for immunotherapy in HCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A cluster of TPI1+ malignant hepatocytes was associated with the suppression of CD8+ T cell infiltration and HCC metastasis, providing novel insights into potential biomarkers for immunotherapy in HCC.", "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:38410699"], "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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Single-cell RNA sequencing (scRNA-seq) may aid in determining specific", "ollection and Tissue Samples The single-cell RNA-sequencing data, including 10 HCC tissue samples, were", "group (TNM stage IIIB-IV). In addition, the transcriptome data and corresponding clinicopathological a"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Single-Cell RNA Sequencing Revealed That the Enrichment of TPI1+ Malign", "ment is characterized by high heterogeneity. Single-cell RNA sequencing (scRNA-seq) may aid in determining specific", "h heterogeneity. Single-cell RNA sequencing (scRNA-seq) may aid in determining specific cell cluste", "immune microenvironment of HCC. Methods: The scRNA-seq data of 10 HCC samples were collected from t"], "order_basis": "paper_text_order:0", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ation analysis was performed and verified by immunohistochemistry and immunofluorescent staining. Results: Nin", "mation Resource (TIMER) databases. Moreover, immunohistochemistry analysis demonstrated that TPI1 expression w", "med and verified by immunohistochemistry and immunofluorescent staining. Results: Nine malignant hepatocyte", "T cell infiltration was further confirmed by immunofluorescence staining. 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