To detect potential pathways and target genes in infantile Pompe patients using computational analysis.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35411297", "kind": "science-record", "revision": 3, "content_hash": "sha256:ecbf611239754bc7308351508bdef2162185b60549c30e4cacd7bdd7bd0192ff", "created_at": "2026-11-01T18:14:13Z", "updated_at": "2026-11-01T21:27:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "To detect potential pathways and target genes in infantile Pompe patients using computational analysis.", "doi": "10.34172/bi.2022.23467", "pmid": "35411297", "authors": ["Aynur Karadağ Gürel", "Selçuk Gürel"], "journal": "BioImpacts : BI", "year": 2022, "abstract": "Introduction: Pompe disease (PD) is a disease caused by pathogenic variations in the GAA gene known as glycogen storage disease type II, characterized by heart hypertrophy, respiratory failure, and muscle hypotonia, leading to premature death if not treated early. The only treatment option, enzyme replacement therapy (ERT), significantly improves the prognosis for some patients while failing to help others. In this study, the determination of key genes involved in the response to ERT and potential molecular mechanisms were investigated. Methods: Gene Expression Omnibus (GEO) data, accession number GSE38680, containing samples of biceps and quadriceps muscles was used. Expression array data were analyzed using BRB-Array Tools. Biceps group patients did not receive ERT, while quadriceps received treatment with rhGAA at 0, 12, and 52 weeks. Differentially expressed genes (DEGs) were deeply analyzed by DAVID, GO, KEGG and STRING online analyses, respectively. Results: A total of 1727 genes in the biceps group and 1198 genes in the quadriceps group are expressed differently. It was observed that DEGs were enriched in the group that responded poorly to ERT in the 52nd week. Genes frequently changed in the weak response group; the expression of 530 genes increased and 1245 genes decreased compared to 0 and 12 weeks. The GO analysis demonstrated that the DEGs were mainly involved in vascular smooth muscle contraction, lysosomes, autophagy, regulation of actin cytoskeleton, inflammatory response, and the WNT signaling pathway. We also discovered that the WNT signaling pathway is highly correlated with DEGs. Several DEGs, such as WNT11, WNT5A, CTNNB1, M6PR, MYL12A, VCL, TLN, FYN, YES1, and BCL2, may be important in elucidating the mechanisms underlying poor response to ERT. Conclusion: Early diagnosis and treatment of PD are very important for the clinic of the disease. As a result, it suggests that the enriched genes and new pathways emerging as a result of the analysis may help identify the group that responds poorly to treatment and the outcome of the treatment. Obtained genes and pathways in neonatal screening will guide diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "The DEGs between biceps and quadriceps samples were identified using the unpaired t test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35411297", "locator": "sections[4] \"Microarray data preprocessing and identification of DEG analysis\" paragraph 3", "quote": "The DEGs between biceps and quadriceps samples were identified using the unpaired t test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profiling data with the series number GSE38680 was obtained from the public functional genomics data repository GEO (https://www.ncbi.nlm.nih.gov/geo/), which is based on the Affymetrix Human Genome U133 plus 2.0 Array.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35411297", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "The gene expression profiling data with the series number GSE38680 was obtained from the public functional genomics data repository GEO (https://www.ncbi.nlm.nih.gov/geo/), which is based on the Affymetrix Human Genome U133 plus 2.0 Array."}], "state": "complete"}, {"id": "claim-target-result", "statement": "At week 52, 2,243 genes differed between poor and positive ERT responders, including 739 upregulated and 1,504 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35411297", "locator": "sections[15] \"Comparison – according to clinical response after ERT- Quadriceps 0, 12, and 52. Week’s poor response vs. positive response\" paragraph 2", "quote": "When the gene expression profiles are compared, there were variations in 530 genes (247 up-283 down) in 0 week between those who did not respond and those who did, with variations in expression profiles for 507 genes (339 up-168 down) in the 12th week and 2243 genes (739 up-1504 down) in the 52nd week (Table 2)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "At week 52, 2,243 genes differed between poor and positive ERT responders, including 739 upregulated and 1,504 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:35411297"], "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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