Identification of the distinctive role of DPT in dilated cardiomyopathy: a study based on bulk and single-cell transcriptomic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34733953", "kind": "science-record", "revision": 4, "content_hash": "sha256:33560359c7a861640753d041d3d69b36ffe9f6e1964b34e86450186303c225bf", "created_at": "2026-11-01T17:36:24Z", "updated_at": "2026-11-01T22:05:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the distinctive role of DPT in dilated cardiomyopathy: a study based on bulk and single-cell transcriptomic analysis.", "doi": "10.21037/atm-21-2913", "pmid": "34733953", "authors": ["Yang Lu", "Qiongfeng Wu", "Jie Liao", "Shaoshao Zhang", "Kai Lu", "Shuaitao Yang", "Yuwei Wu", "Qian Dong", "Jing Yuan", "Ning Zhao", "Yimei Du"], "journal": "Annals of translational medicine", "year": 2021, "abstract": "BACKGROUND: Dilated cardiomyopathy (DCM) is a common cause of heart failure. Cardiac remodeling is the main pathological change in DCM, yet the molecular mechanism is still unclear. Therefore, the present study aims to find potential crucial genes and regulators through bulk and single-cell transcriptomic analysis.\nMETHODS: Three microarray datasets of DCM (GSE57338, GSE42955, GSE79962) were chosen from gene expression omnibus (GEO) to analyze the differentially expressed genes (DEGs). LASSO regression, SVM-RFE, and PPI network methods were then carried out to identify key genes. Another dataset (GSE116250) was used to validate these findings. To further identify DCM-associated specific cell types, transcription factors, and cell-cell interaction networks, GSEA, SCENIC, and CellPhoneDB were conducted on public datasets for single-cell RNA sequencing analysis of DCM (GSE109816 and GSE121893). Finally, reverse transcription-polymerase chain reaction (RT-PCR), western blot, and immunohistochemical were performed to validate DPT expression in fibroblasts and DCM.\nRESULTS: There were 281 DEGs between DCM and non-failing donors. CCL5 and DPT were identified to be key genes and both genes had a 0.844 area under the receiver operating curve (AUC) in the validation dataset. Further single-cell sequencing analysis revealed three main findings: (I) DPT was mainly expressed in fibroblasts and was significantly upregulated in DCM fibroblasts; (II) DPT+ fibroblasts were involved in the organization of the extracellular matrix (ECM) and collagen fibrils and were regulated by the transcription factor STAT3; and (III) DPT+ fibroblasts had high interactions with endothelial cells through including Ephrin-Eph, ACKR-CXCL, and JAG-NOTCH signal pathways. RT-PCR, western blot, and immunohistochemical confirmed that DPT was highly expressed and co-localized with Vimentin and p-STAT3 in DCM patients. STAT3 inhibitor S3I-201 reduced the expression of DPT in mouse cardiac fibroblasts.\nCONCLUSIONS: DPT could be used as a diagnostic marker and therapeutic target of DCM. DPT+ fibroblasts could be a novel regulator of the cardiac remodeling process in DCM.", "claims": [{"id": "claim-method", "statement": "P values were evaluated by Wilcoxon rank-sum test in R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34733953", "locator": "sections[5] \"Screening and verification of key genes\" paragraph 3", "quote": "P values were evaluated by Wilcoxon rank-sum test in R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Sharing Statement: Available at https://dx.doi.org/10.21037/atm-21-2913", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34733953", "locator": "sections[27] \"Footnotes\" paragraph 2", "quote": "Data Sharing Statement: Available at https://dx.doi.org/10.21037/atm-21-2913"}], "state": "complete"}, {"id": "claim-target-result", "statement": "CCL5 and DPT were identified as key genes for dilated cardiomyopathy, and both had an AUC of 0.844 in the validation dataset.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34733953", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "CCL5 and DPT were identified to be key genes and both genes had a 0.844 area under the receiver operating curve (AUC) in the validation dataset."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "CCL5 and DPT were identified as key genes for dilated cardiomyopathy, and both had an AUC of 0.844 in the validation dataset.", "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:34733953"], "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: Three microarray datasets", "conducted on public datasets for single-cell RNA sequencing analysis of DCM (GSE109816 and GSE121893). F"], "order_basis": "paper_text_order:66", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["cell transcriptomic analysis. METHODS: Three microarray datasets of DCM (GSE57338, GSE42955, GSE7996"], "order_basis": "paper_text_order:423", "id": "assay:2"}, {"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": ["honeDB were conducted on public datasets for single-cell RNA sequencing analysis of DCM (GSE109816 and GSE121893). F", "Methods Analysis of scRNA-seq dataset The raw count and metadata of GSE109"], "order_basis": "paper_text_order:926", "id": "assay:3"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["cription-polymerase chain reaction (RT-PCR), western blot, and immunohistochemical were performed to v", "CXCL, and JAG-NOTCH signal pathways. RT-PCR, western blot, and immunohistochemical confirmed that DPT"], "order_basis": "paper_text_order:1063", "id": "assay:4"}, {"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": ["e chain reaction (RT-PCR), western blot, and immunohistochemical were performed to validate DPT expression in", "H signal pathways. RT-PCR, western blot, and immunohistochemical confirmed that DPT was highly expressed and"], "order_basis": "paper_text_order:1081", "id": "assay:5"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["tor S3I-201 reduced the expression of DPT in mouse cardiac fibroblasts. CONCLUSIONS: DPT could"], "order_basis": "paper_text_order:2057", "id": "assay:6"}, {"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": ["P values were evaluated by Wilcoxon rank-sum test in R."], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}