Endothelial-specific genes TMTC1, RPS6KA2, and F8 are downregulated in hypertrophic cardiomyopathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41392291", "kind": "science-record", "revision": 4, "content_hash": "sha256:de961d6cea441135f6838051bfdc9595c31148b5878bd92a098128c20d85d6b4", "created_at": "2026-11-01T20:31:24Z", "updated_at": "2026-11-01T22:57:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Endothelial-specific genes TMTC1, RPS6KA2, and F8 are downregulated in hypertrophic cardiomyopathy.", "doi": "10.1186/s40001-025-03670-5", "pmid": "41392291", "authors": ["Pingge Tian", "Lei Xu", "Fan Zou", "Qian Jia", "Yangjian Liu", "Jin Chen", "Pengzhen Wang"], "journal": "European journal of medical research", "year": 2025, "abstract": "BACKGROUND: Hypertrophic cardiomyopathy (HCM) is a common inherited heart disease characterized by left ventricular hypertrophy and excessive myocardial contraction. Endothelial cells (ECs) play a key role in the pathogenesis of HCM, and their secreted growth factors regulate the growth and function of cardiomyocytes. However, the specific molecular mechanisms and biomarkers associated with endothelial dysfunction in HCM remain unclear.\nMETHODS: Single-cell RNA sequencing (scRNA-seq) data were downloaded from the Gene Expression Omnibus (GEO) database (GSE255296), and bulk RNA sequencing data were obtained from GSE249925 and GSE180313. The scRNA-seq data were processed using the Seurat package for cell type annotation and batch effect removal. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed, and pathway activity was evaluated using the AUCell algorithm. SCENIC was applied to construct transcription factor-specific regulatory networks. Differential gene expression analysis was conducted using the limma package, and key genes were determined by intersecting differentially expressed genes (DEGs) with EC-specific highly expressed genes. The diagnostic efficacy of these key genes was assessed via receiver operating characteristic (ROC) curve analysis. The mRNA expression of genes in HUVECs treated with or without angiotensin II (Ang II) was assessed using qPCR. Cell viability was determined using the CCK-8 assay, and cell invasive ability was evaluated through Transwell assays to investigate the regulatory effect of TMTC1 overexpression on Ang II-induced injury in HUVECs.\nRESULTS: Seven major cell types were identified, with cardiomyocytes and ECs being the main cell populations in HCM. KEGG enrichment analysis revealed significant activation of pathways such as the transforming growth factor-beta (TGF-β) signaling pathway in ECs. High-activity transcription factors NFIB, MECOM, and FLI1 were identified in ECs, whose target genes were enriched in processes related to cell morphogenesis. Three key genes-TMTC1, RPS6KA2, and F8-were selected based on differential expression and EC specificity. These genes were lowly expressed in HCM and exhibited high diagnostic efficacy, with area under the curve (AUC) values > 0.7. Ultimately, the CCK-8 assay results indicated that Ang II inhibited the viability of HUVECs, and this inhibitory effect could be reversed by the overexpression of TMTC1 (oe-TMTC1). Furthermore, Transwell assays indicated that Ang II impaired cellular migration, and this impairment could be restored by oe-TMTC1.\nCONCLUSION: The identified key genes and pathways provide new targets for therapeutic intervention and contribute to a deeper understanding of the pathogenesis of HCM.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) between HCM and healthy control groups were identified and analyzed using the limma package, with the screening criteria for differential genes set as p.adj < 0.05 and |log2 fold change (FC)|> log2(1.5) [23].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41392291", "locator": "sections[8] \"Differential gene analysis\" paragraph 2", "quote": "Differentially expressed genes (DEGs) between HCM and healthy control groups were identified and analyzed using the limma package, with the screening criteria for differential genes set as p.adj < 0.05 and |log2 fold change (FC)|> log2(1.5) [23]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41392291", "locator": "sections[28] \"Data availability\" paragraph 2", "quote": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Three key genes—TMTC1, RPS6KA2, and F8—were selected based on differential expression and EC specificity.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41392291", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Three key genes—TMTC1, RPS6KA2, and F8—were selected based on differential expression and EC specificity."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Three key genes—TMTC1, RPS6KA2, and F8—were selected based on differential expression and EC specificity.", "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:41392291"], "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:GSE180313"], "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:GSE180313"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41392291", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40001-025-03670-5", "sha256": 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METHODS: Single-cell RNA sequencing (scRNA-seq) data were downloaded from the Ge", "nclear. METHODS: Single-cell RNA sequencing (scRNA-seq) data were downloaded from the Gene Expressi", "e obtained from GSE249925 and GSE180313. The scRNA-seq data were processed using the Seurat package"], "order_basis": "paper_text_order:506", "id": "assay:1"}, {"role": "data_generation", "definition_id": "clinical_trial", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ysis. The mRNA expression of genes in HUVECs treated with or without angiotensin II (Ang II) was assessed using q"], "order_basis": "paper_text_order:1394", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["t angiotensin II (Ang II) was assessed using qPCR. Cell viability was determined using the CCK"], "order_basis": "paper_text_order:1461", "id": "assay:3"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["PCR. Cell viability was determined using the CCK-8 assay, and cell invasive ability was evaluat", "he curve (AUC) values > 0.7. Ultimately, the CCK-8 assay results indicated that Ang II inhibite"], "order_basis": "paper_text_order:1507", "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": ["ican Type Culture Collection (ATCC) and were cultured in Vascular Cell Basal Medium (PCS-100-030, ATC", "ican Type Culture Collection (ATCC) and were cultured in Vascular Cell Basal Medium (PCS-100-030,"], "order_basis": "paper_text_order:3714", "id": "assay:5"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed genes (DEGs) between HCM and healthy control groups were identified and analyzed using the limma package, with the screening criteria for differential genes set as p.adj < 0.05 and |log2 fold change (FC)|> log2(1.5) [23]."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}