HSPA13 gene and microRNA-155: relationship between Down syndrome and Alzheimer's disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40959651", "kind": "science-record", "revision": 3, "content_hash": "sha256:ec83a0982a0ba59e2810569b215be6b26ea797e897dd788d244ba6e65cf308af", "created_at": "2026-11-01T20:31:03Z", "updated_at": "2026-11-01T22:14:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "HSPA13 gene and microRNA-155: relationship between Down syndrome and Alzheimer's disease.", "doi": "10.1590/1980-5764-DN-2024-0239", "pmid": "40959651", "authors": ["Fabiana de Campos Gomes", "Beatriz Pavarino Bertelli", "Conceição Pinheiro de Souza", "Daniel Ramos de Oliveira Santos", "João Simão de Melo-Neto", "Érika Cristina Pavarino", "Eny Maria Goloni-Bertollo"], "journal": "Dementia & neuropsychologia", "year": 2025, "abstract": "Gene dysregulation in trisomy 21 can cause disorders of genes that are members of the heat-shock proteins (HSPs) family and contribute to the early onset of Alzheimer's disease (AD) in Down syndrome (DS).\nObjective: Investigate in silico differently expressed genes (DEGs) of HSPs and the interaction with microRNAs (miRNAs) located in human chromosome 21 (Hsa21).\nMethods: Two transcriptome libraries of human brain samples, datasets GSE5390 (DS) and GSE33000 (DA), were extracted from the Gene Expression Omnibus (GEO) and analyzed via GEO2R. DEGs with p-values (Adj p-values) <0.05 were analyzed via STRING. MiRNAs were identified in the miRbase database and analysis of their potential regulation on DEGs was performed using the DIANA tools.\nResults: HSPE1, HSP90B1, HSPB8 and HSPA13 genes showed a different expression pattern in the transcriptomes of DS. The HSPA13 and HSPA2 genes showed an altered expression profile in the DS and AD datasets. In the predicted protein-protein interactions (PPI), we identified the interaction of HSPE1, HSP90B1, HSPB8 and HSPA13 with other HSP proteins. The miRNA encoded by Hsa21 (hsa-miR-155-5p) interacted with the HSPA13 gene.\nConclusion: The results suggest that certain genes encoding members of the HSP family, and in particular the interaction between miR-155-5p and HSPA13, may be associated with AD in DS.", "claims": [{"id": "claim-method", "statement": "For the GEO2R analyses, we applied the following options: adjust the p values via the Benjamini & Hochberg false discovery rate method with a cutoff <0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40959651", "locator": "sections[8] \"Data analysis\" paragraph 2", "quote": "For the GEO2R analyses, we applied the following options: adjust the p values via the Benjamini & Hochberg false discovery rate method with a cutoff <0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are publicly available at Gene Expression Omnibus (GEO) repository (https://www.ncbi.nlm.nih.gov/gds) of the National Center for Biotechnology Information (NCBI).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40959651", "locator": "sections[15] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The datasets generated and/or analyzed during the current study are publicly available at Gene Expression Omnibus (GEO) repository (https://www.ncbi.nlm.nih.gov/gds) of the National Center for Biotechnology Information (NCBI)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "After FDR analysis, four HSP genes were significantly different in the DS transcriptome.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40959651", "locator": "sections[10] \"Identification of differently expressed genes and the heat shock proteins expression profile\" paragraph 6", "quote": "After FDR analysis, only four genes, including HSPE1, HSP90B1, HSPB8 (encoded on chromosome 12) and HSPA13 (encoded on chromosome 21), were significantly different (Figure 2A)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "After FDR analysis, four HSP genes were significantly different in the DS transcriptome.", "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:40959651"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40959651", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1590/1980-5764-DN-2024-0239", "sha256": "sha256:a703d184ec6e3f35a35ce22e0af9e291ca7c7183daaeeb51e0536f39d6eabeaf", "bytes": 23046, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1590/1980-5764-DN-2024-0239", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12435772", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R analysis with p-value adjustment using the Benjamini & Hochberg false discovery rate method at a cutoff of <0.05", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For the GEO2R analyses, we applied the following options: adjust the p values via the Benjamini & Hochberg false discovery rate method with a cutoff <0.05."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["GSE5390 - ID: 2941", "GSE33000 - ID: 200033000"], "resolved_accessions": [], "statements": ["The datasets generated and/or analyzed during the current study are publicly available at Gene Expression Omnibus (GEO) repository (https://www.ncbi.nlm.nih.gov/gds) of the National Center for Biotechnology Information (NCBI)."], "basis": "The paper names GSE5390 - ID: 2941, GSE33000 - ID: 200033000, but the accession does not resolve in the repository (no reason recorded, no reason recorded), so the data cannot be reached from here. 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