Identification of a Novel Gene Correlated With Vascular Smooth Muscle Cells Proliferation and Migration in Chronic Thromboembolic Pulmonary Hypertension.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34858201", "kind": "science-record", "revision": 5, "content_hash": "sha256:f6258e303dd674969e3876b8f644abfa02e7c6e4c75d4311ce8502668fd534c8", "created_at": "2026-11-01T17:36:33Z", "updated_at": "2026-11-01T22:47:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a Novel Gene Correlated With Vascular Smooth Muscle Cells Proliferation and Migration in Chronic Thromboembolic Pulmonary Hypertension.", "doi": "10.3389/fphys.2021.744219", "pmid": "34858201", "authors": ["Feng Wang", "Congrui Sun", "Xiaoshuo Lv", "Mingsheng Sun", "Chaozeng Si", "Yanan Zhen", "Jing Guo", "Weiliang Sun", "Zhidong Ye", "Jianyan Wen", "Peng Liu"], "journal": "Frontiers in physiology", "year": 2021, "abstract": "Objective: Chronic thromboembolic pulmonary hypertension (CTEPH) is characterized by thrombofibrotic obstruction of the proximal pulmonary arteries, which result in vascular remodeling of the distal pulmonary artery. While the cellular and molecular mechanisms underlying CTEPH pathogenesis remain incompletely understood, recent evidence implicates vascular remodeling. Here, we identify the molecular mechanisms that contribute to vascular remodeling in CTEPH. Methods: Microarray data (GSE130391) for patients with CTEPH and healthy controls were downloaded from the Gene Expression Omnibus (GEO) and screened for differentially expressed genes (DEGs). DEGs were functionally annotated using Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. A protein-protein interaction (PPI) network was constructed to identify hub genes. Finally, pulmonary artery samples were harvested from patients with CTEPH (n = 10) and from controls (n = 10) and primary vascular smooth muscle cells (VSMCs) were cultured. Effects of the proto-oncogene FOS on VSMC proliferation and migration were assessed using expression and knockdown studies. Results: We detected a total of 292 DEGs, including 151 upregulated and 141 downregulated genes. GO analysis revealed enrichment of DEGs in biological processes of signal transduction, response to lipopolysaccharide, signal transduction, and myeloid dendritic cell differentiation. Molecular function analysis revealed enrichment in tumor necrosis factor (TNF)-activated receptor activity, transcriptional activator activity, and protein homodimerization activity. The expression of TNF-α and its receptor (sTNFR1 and sTNFR2) were significantly higher in CTEPH group, compared with control group. KEGG pathway analysis revealed enrichment in salmonella infection, pathways in cancer, osteoclast differentiation, and cytokine-cytokine receptor interaction. Hub genes in the PPI included FOS, suggesting an important role for this gene in vascular remodeling in CTEPH. Primary VSMCs derived from patients with CTEPH showed increased FOS expression and high proliferation and migration, which was attenuated by FOS inhibition. In control VSMCs, TNF-α treatment increased proliferation and migration, which FOS inhibition likewise attenuated. Conclusion: TNF-α drives CTEPH pathogenesis by promoting VSMC proliferation and migration via increased FOS expression. These results advance our understanding of the molecular mechanisms of vascular remodeling in CTEPH, and may inform the development of new therapeutic targets.", "claims": [{"id": "claim-method", "statement": "The Bioconductor project was used to analyze the high-throughput genomic data, with DEGs between control and CTEPH samples identified using the limma package. A t-test was used to calculate DEG p-values, with an adjusted p-value cut off of 0.05 and the | log FC| > 1.0 as the filter criteria.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34858201", "locator": "sections[5] \"Identification of Differentially Expressed Genes\" paragraph 2", "quote": "The Bioconductor project was used to analyze the high-throughput genomic data, with DEGs between control and CTEPH samples identified using the limma package. A t-test was used to calculate DEG p-values, with an adjusted p-value cut off of 0.05 and the | log FC| > 1.0 as the filter criteria."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34858201", "locator": "sections[29] \"Data Availability Statement\" paragraph 2", "quote": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We detected a total of 292 DEGs, including 151 upregulated and 141 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34858201", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We detected a total of 292 DEGs, including 151 upregulated and 141 downregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We detected a total of 292 DEGs, including 151 upregulated and 141 downregulated genes.", "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:34858201"], "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:GSE130391"], "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:GSE130391"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34858201", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fphys.2021.744219", "sha256": "sha256:910291584a2e98e739beafbe5de8f4ed716a875ca181c1c56ae1e67ea074aaa1", "bytes": 35744, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fphys.2021.744219", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8632225", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE130391", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE130391", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE130391", "version": null, "note": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3737373", "GSM3737374", "GSM3737375", "GSM3737376", "GSM3737377", "GSM3737378", "GSM3737379", "GSM3737380", "GSM3737381", "GSM3737382", "GSM3737383", "GSM3737384", "GSM3737385", "GSM3737386", "GSM3737387", "GSM3737388", "GSM3737389", "GSM3737390", "GSM3737391", "GSM3737392", "GSM3737393", "GSM3737394"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Comparing CTEPH to Control and IPAH pulmonary arteries", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE130391 not downloaded", "asset:data:geo:GSE130391 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Bioconductor project was used to analyze the high-throughput genomic data, with DEGs between control and CTEPH samples identified using the limma package. 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