The gene expression of CALD1, CDH2, and POSTN in fibroblast are related to idiopathic pulmonary fibrosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38370408", "kind": "science-record", "revision": 3, "content_hash": "sha256:7c879a7228a31f0c8c7dfa11339536401839d985d6dd8e7db51adeb25aedcfec", "created_at": "2026-11-01T19:20:18Z", "updated_at": "2026-11-01T22:11:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The gene expression of CALD1, CDH2, and POSTN in fibroblast are related to idiopathic pulmonary fibrosis.", "doi": "10.3389/fimmu.2024.1275064", "pmid": "38370408", "authors": ["Shufei Wu", "Mengying Liu", "Mingrui Zhang", "Xu Ye", "Huimin Gu", "Cheng Jiang", "Huihui Zhu", "Xiaoling Ye", "Qi Li", "Xinmei Huang", "Mengshu Cao"], "journal": "Frontiers in immunology", "year": 2024, "abstract": "Introduction: Idiopathic pulmonary fibrosis (IPF) is characterized by progressive lung dysfunction due to excessive collagen production and tissue scarring. Despite recent advancements, the molecular mechanisms remain unclear.\nMethods: RNA sequencing identified 475 differentially expressed genes (DEGs) in the TGF-β1-induced primary lung fibrosis model. Gene expression chips GSE101286 and GSE110147 from NCBI gene expression omnibus (GEO) database were analyzed using GEO2R, revealing 94 DEGs in IPF lung tissue samples. The gene ontology (GO) and pathway enrichment, Protein-protein interaction (PPI) network construction, and Maximal Clique Centrality (MCC) scoring were performed. Experimental validation included RT-qPCR, Immunohistochemistry (IHC), and Western Blot, with siRNA used for gene knockdown. A co-expression network was constructed by GeneMANIA.\nResults: GO enrichment highlighted significant enrichment of DEGs in TGF-β cellular response, connective tissue development, extracellular matrix components, and signaling pathways such as the AGE-RAGE signaling pathway and ECM-receptor interaction. PPI network analysis identified hub genes, including FN1, COL1A1, POSTN, KIF11, and ECT2. CALD1 (Caldesmon 1), CDH2 (Cadherin 2), and POSTN (Periostin) were identified as dysregulated hub genes in both the RNA sequencing and GEO datasets. Validation experiments confirmed the upregulation of CALD1, CDH2, and POSTN in TGF-β1-treated fibroblasts and IPF lung tissue samples. IHC experiments probed tissue-level expression patterns of these three molecules. Knockdown of CALD1, CDH2, and POSTN attenuated the expression of fibrotic markers (collagen I and α-SMA) in response to TGF-β1 stimulation in primary fibroblasts. Co-expression analysis revealed interactions between hub genes and predicted genes involved in actin cytoskeleton regulation and cell-cell junction organization.\nConclusions: CALD1, CDH2, and POSTN, identified as potential contributors to pulmonary fibrosis, present promising therapeutic targets for IPF patients.", "claims": [{"id": "claim-method", "statement": "apply GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) to conduct differential analyses of IPF compared to normal lung tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38370408", "locator": "sections[5] \"Microarray datasets collection and processing\" paragraph 2", "quote": "apply GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) to conduct differential analyses of IPF compared to normal lung tissues."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data presented in the study are deposited in the NCBI SRA repository, accession number PRJNA842213.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38370408", "locator": "sections[21] \"Data availability statement\" paragraph 2", "quote": "The data presented in the study are deposited in the NCBI SRA repository, accession number PRJNA842213."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Gene expression chips GSE101286 and GSE110147 from NCBI gene expression omnibus (GEO) database were analyzed using GEO2R, revealing 94 DEGs in IPF lung tissue samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38370408", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Gene expression chips GSE101286 and GSE110147 from NCBI gene expression omnibus (GEO) database were analyzed using GEO2R, revealing 94 DEGs in IPF lung tissue samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Gene expression chips GSE101286 and GSE110147 from NCBI gene expression omnibus (GEO) database were analyzed using GEO2R, revealing 94 DEGs in IPF lung tissue samples.", "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:38370408"], "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: RNA sequencing identified 475 differentially expressed gene", "tified as dysregulated hub genes in both the RNA sequencing and GEO datasets. Validation experiments con", "logy (GO) and pathway enrichment analysis of RNAseq-DEGs. Bubble size indicates counts of respec", "illustrating functional relationships among RNAseq-DEGs and GO terms. To further explore the fu"], "order_basis": "paper_text_order:297", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["performed. Experimental validation included RT-qPCR, Immunohistochemistry (IHC), and Western Blo", "rformed. Experimental validation included RT-qPCR, Immunohistochemistry (IHC), and Western Blo", "ation of CALD1, CDH2, and POSTN knockdown by RT-qPCR. (B) Validation of CALD1, CDH2, and POSTN kn", "used to amplify the human transcripts during RT-qPCR.Click here for additional data file. Supplem"], "order_basis": "paper_text_order:781", "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": ["d. Experimental validation included RT-qPCR, Immunohistochemistry (IHC), and Western Blot, with siRNA used for", "tion included RT-qPCR, Immunohistochemistry (IHC), and Western Blot, with siRNA used for gene", "ted fibroblasts and IPF lung tissue samples. IHC experiments probed tissue-level expression p", "ntary Table 3Antibodies for western blot and IHC.Click here for additional data file. Supplem"], "order_basis": "paper_text_order:789", "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": ["ded RT-qPCR, Immunohistochemistry (IHC), and Western Blot, with siRNA used for gene knockdown. A co-ex", "ion of collagen I and α-SMA was confirmed by western blot analysis, with three biological replicates f", "tured under original magnification ×200. (B) Western blot analysis of Collagen I and α-SMA expression", "ation of CALD1, CDH2, and POSTN knockdown by western blot. Each gene was knocked down using two differ"], "order_basis": "paper_text_order:821", "id": "assay:4"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": [", and Western Blot, with siRNA used for gene knockdown. A co-expression network was constructed by", "xpression patterns of these three molecules. Knockdown of CALD1, CDH2, and POSTN attenuated the exp", "histochemistry (IHC), and Western Blot, with siRNA used for gene knockdown. A co-expression net", "ta file. Supplementary Figure 2Validation of Knockdown Efficacy and Assessment of Cellular Response"], "order_basis": "paper_text_order:840", "id": "assay:5"}, {"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": ["bility were assessed by Cell Counting Kit-8 (CCK8) after siRNAs knockdown. p >0.05. (D).Wester"], "order_basis": "paper_text_order:10887", "id": "assay:6"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}