scRNA-Seq Analysis Revealed CAFs Regulating HCC Cells via PTN Signaling.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39582814", "kind": "science-record", "revision": 3, "content_hash": "sha256:77fc2f959e53a60e1862e58e7d6ed87035b4aeb75dffa733fc4d488a23d5a5c6", "created_at": "2026-11-01T20:29:50Z", "updated_at": "2026-11-01T22:13:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "scRNA-Seq Analysis Revealed CAFs Regulating HCC Cells via PTN Signaling.", "doi": "10.2147/JHC.S493675", "pmid": "39582814", "authors": ["Wenxian Lin", "Lizhu Tang", "Chenyi Zhuo", "Xiuli Mao", "Jiajia Shen", "Shaoang Huang", "Shangyang Li", "Yujuan Qin", "Ju Liao", "Yuhong Chen", "Xiamin Zhang", "Yuting Li", "Jian Song", "Lingzhang Meng", "Xiaofeng Dong", "Yueyong Li"], "journal": "Journal of hepatocellular carcinoma", "year": 2024, "abstract": "Background: Cancer-associated fibroblasts (CAFs) play a pivotal role in shaping the microenvironment of hepatocellular carcinoma (HCC). However, the mechanisms through which CAFs influence the progression of HCC remain incompletely understood.\nMethods: Single-cell RNA sequencing datasets (GSE158723 and GSE112271) were retrieved from the Gene Expression Omnibus (GEO) database at the National Center for Biotechnology Information (NCBI) and analyzed using R software. Our analysis suggested that CAFs may promote liver cancer cell development, possibly through the interaction of pleiotrophin (PTN) and syndecan-2 (SDC2). Clinical samples from HCC patients were collected and processed into frozen sections and single-cell suspensions for Masson staining, immunofluorescence staining, and flow cytometry. Additionally, Huh7 liver cancer cells and LO2 normal liver cells were cultured and subjected to immunofluorescence assays using cell slides.\nResults: The proportion of CAFs in cancerous tissues was higher than in adjacent non-cancerous tissues, and pleiotrophin (PTN) expression was elevated in cancer tissues compared to adjacent tissues. These findings aligned with the results of the single-cell RNA sequencing (scRNA-seq) analysis. Furthermore, SDC2 expression was significantly upregulated in Huh7 liver cancer cells compared to LO2 normal liver cells.\nDiscussion: This study suggests that CAFs may contribute to HCC progression via the PTN/SDC2 signaling pathway. Our findings provide deeper insights into the interactions between CAFs and HCC cells within the tumor microenvironment (TME).", "claims": [{"id": "claim-method", "statement": "For comparison between the two groups, unpaired Student’s T-tests were used for the normally distributed data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39582814", "locator": "sections[8] \"Statistical Analysis\" paragraph 2", "quote": "For comparison between the two groups, unpaired Student’s T-tests were used for the normally distributed data."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data and materials are provided along with the manuscript.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39582814", "locator": "sections[17] \"Data Sharing Statement\" paragraph 2", "quote": "Data and materials are provided along with the manuscript."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper retrieved the GSE158723 and GSE112271 single-cell RNA sequencing datasets from NCBI GEO and analyzed them using R software.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39582814", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Single-cell RNA sequencing datasets (GSE158723 and GSE112271) were retrieved from the Gene Expression Omnibus (GEO) database at the National Center for Biotechnology Information (NCBI) and analyzed using R software."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper retrieved the GSE158723 and GSE112271 single-cell RNA sequencing datasets from NCBI GEO and analyzed them using R software.", "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:39582814"], "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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Methods: Single-cell RNA sequencing datasets (GSE158723 and GSE112271) were retr", "ese findings aligned with the results of the single-cell RNA sequencing (scRNA-seq) analysis. Furthermore, SDC2 expr", "e results of the single-cell RNA sequencing (scRNA-seq) analysis. Furthermore, SDC2 expression was"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ncompletely understood. Methods: Single-cell RNA sequencing datasets (GSE158723 and GSE112271) were retr", "aligned with the results of the single-cell RNA sequencing (scRNA-seq) analysis. Furthermore, SDC2 expr"], "order_basis": "paper_text_order:293", "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": ["single-cell suspensions for Masson staining, immunofluorescence staining, and flow cytometry. Additionally,", "l liver cells were cultured and subjected to immunofluorescence assays using cell slides. Results: The propo", "ator at 37°C) and made into cell slides, and immunofluorescence staining was performed using antibodies SDC2", "ted HCC via PTN/SDC2 signaling. We performed immunofluorescent staining on Lo2 and Huh-7 cell lines, found"], "order_basis": "paper_text_order:785", "id": "assay:3"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["n staining, immunofluorescence staining, and flow cytometry. Additionally, Huh7 liver cancer cells and L", "y significant with p<0.05 (Figure 4E and F). Flow cytometry analysis of clinical HCC samples showed the"], "order_basis": "paper_text_order:818", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Shanghai) Co., LTD, product number: ORC0100) cell lines were cultured (The cell density and growth status of the r", "passed into a T25 culture bottle at 1:2 and cultured in a 5%CO2 incubator at 37°C) and made into cel", "TD, product number: ORC0100) cell lines were cultured (The cell density and growth status of the r"], "order_basis": "paper_text_order:2704", "id": "assay:5"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["For comparison between the two groups, unpaired Student’s T-tests were used for the normally distributed data."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}