Can Wharton jelly derived or adipose tissue derived mesenchymal stem cell can be a treatment option for duchenne muscular dystrophy? Answers as transcriptomic aspect.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32929392", "kind": "science-record", "revision": 3, "content_hash": "sha256:0c77c7ba2bb5b08ad97049a41fe4adbff975dc74bd682cbc92b087708cc9124d", "created_at": "2026-11-01T17:34:05Z", "updated_at": "2026-11-01T21:23:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "partial", "title": "Can Wharton jelly derived or adipose tissue derived mesenchymal stem cell can be a treatment option for duchenne muscular dystrophy? Answers as transcriptomic aspect.", "doi": null, "pmid": "32929392", "authors": ["Eda Sun", "Erdal Karaoz"], "journal": "American journal of stem cells", "year": 2020, "abstract": "INTRODUCTION: Mesenchymal stem cells (MSCs) are able to differentiate into several cell lineages including skeletal muscle. In addition to their differentiation capacities, they have the ability to transfer their content genomic information horizontally through their exosomes and fusion abilities, as we have shown in our previous clinic study on Duchenne Muscular Dystrophy (DMD) patients, dystrophin expression increased after MSC treatment. Therefore, this study aimed to compare the transcriptomic properties of Wharton's jelly derived (WJ-) MSC and Adipose tissue (AT-) derived MSC, which are the two most preferred sources in MSC treatments applied in DMD.\nMETHODS: Both MSC cell lines obtained from ATCC (PCS-500-010; PCS-500-011) were characterized by flow cytometry then WJ-MSC and AT-MSC cell lines were sequenced via RNA-SEQ. R language was used to obtain the differentially expressed genes (DEGs) and differentially expressed miRNAs, respectively. Additionally, in order to support the results of our study, a gene expression profile data set of DMD patients (GSE1004) were acquired from Gene Expression Omnibus (GEO) database.\nRESULTS: Here, we demonstrated that activated WNT signaling and downregulated TGF-β pathways under the control of decreased mir-24 which are involved in myogenic differentiation are differentially expressed in WJ-MSC. We have shown that the expression of mir-199a-5p, which is known to increase in exosomes of DMD patients, is less in WJ-MSC. Additionally, we have shown activated PI3K/Akt pathway, which is controlling mitochondria transfer via Tunnelling Nanotube as a new perspective in cellular therapies in myodegenerative diseases, in WJ-MSC more than in AT-MSCs.\nCONCLUSION: Summing up, WJ-MSC, which we recommend as an appropriate source candidate due to its immune-regulation properties, stands forward as a preferable source in the cellular treatment of DMD patients due to its transcriptomic aspect.", "claims": [{"id": "claim-method", "statement": "R language was used to obtain the differentially expressed genes (DEGs) and differentially expressed miRNAs, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32929392", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "R language was used to obtain the differentially expressed genes (DEGs) and differentially expressed miRNAs, respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Additionally, in order to support the results of our study, a gene expression profile data set of DMD patients (GSE1004) were acquired from Gene Expression Omnibus (GEO) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32929392", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Additionally, in order to support the results of our study, a gene expression profile data set of DMD patients (GSE1004) were acquired from Gene Expression Omnibus (GEO) database."}], "state": "complete"}], "gaps": ["doi"]}, "experiment": {"state": "complete", "objective": "", "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:32929392"], "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:GSE1004"], "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:GSE1004"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32929392", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": null, "sha256": "sha256:39ff252dd6a021ab265242eb36d4a352ad76f93355b6d7997c86690dca2955a8", "bytes": 1964, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "32929392", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7486554", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE1004", "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=GSE1004", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE1004", "version": null, "note": "Additionally, in order to support the results of our study, a gene expression profile data set of DMD patients (GSE1004) were acquired from Gene Expression Omnibus (GEO) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Additionally, in order to support the results of our study, a gene expression profile data set of DMD patients (GSE1004) were acquired from Gene Expression Omnibus (GEO) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM15807", "GSM15822", "GSM15823", "GSM15824", "GSM15825", "GSM15826", "GSM15827", "GSM15828", "GSM15829", "GSM15830", "GSM15831", "GSM15832", "GSM15833", "GSM15834", "GSM15835", "GSM15836", "GSM15837", "GSM15838", "GSM15839", "GSM15840", "GSM15841", "GSM15842", "GSM15843", "GSM15844"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "8300;91", "taxon": "Homo sapiens", "title": "Molecular profiles (HG-U95A) of dystrophin-deficient and normal human muscle", "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:GSE1004 not downloaded", "asset:data:geo:GSE1004 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "R language", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "R language was used to obtain the differentially expressed genes (DEGs) and differentially expressed miRNAs, respectively."}}], "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (R language), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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