Co-expression network of mRNA and DNA methylation in first-episode and drug-naive adolescents with major depressive disorder.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36911124", "kind": "science-record", "revision": 4, "content_hash": "sha256:30dc9aebe8c2bcbec7e18fd6ebc56785547fad0b67fd912d4be89a8e51fc3f0a", "created_at": "2026-11-01T19:01:32Z", "updated_at": "2026-11-01T22:51:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Co-expression network of mRNA and DNA methylation in first-episode and drug-naive adolescents with major depressive disorder.", "doi": "10.3389/fpsyt.2023.1065417", "pmid": "36911124", "authors": ["Yuanmei Tao", "Hang Zhang", "Meijiang Jin", "Hanmei Xu", "Shoukang Zou", "Fang Deng", "Lijuan Huang", "Hong Zhang", "Xiaolan Wang", "Xiaowei Tang", "Zaiquan Dong", "Yanping Wang", "Li Yin"], "journal": "Frontiers in psychiatry", "year": 2023, "abstract": "Objective: We explored the DNA methylation and messenger RNA (mRNA) co-expression network and hub genes in first-episode, drug-naive adolescents with major depressive disorder (MDD). To preliminarily explore whether adolescent MDD has unique mechanisms compared with adult MDD.\nMethods: We compared DNA methylation and mRNA profiles of peripheral blood mononuclear cells from four first-episode and drug-naive adolescents with MDD and five healthy adolescent controls (HCs). We performed differential expression analysis, constructed co-expression network, and screened the hub genes. And enrichment analysis was performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We also downloaded DNA methylation and mRNA datasets of adults with MDD (GSE113725/GSE38206) from the GEO database, and performed differential expression and enrichment analysis.\nResults: Our clinical data showed that 3034 methylation sites and 4190 mRNAs were differentially expressed in first-episode, drug-naive adolescents MDD patients compared with HCs. 19 hub genes were screened out according to the high degree value in the co-expression network. The results from the GEO database showed that compared with adult HCs, there were 290 methylation sites and 127 mRNAs were differentially expressed in adult MDD patients.\nConclusion: Compared with adolescent HCs and adult MDD patients, the DNA methylation and mRNA expression patterns of first-episode, drug-naive adolescent MDD patients were different. The co-expression network of DNA methylation and mRNA and the screened hub genes may play an important role in the pathogenesis of MDD in first-episode, drug-naive adolescents. Compared with adult MDD, adolescent MDD is more enriched in metabolism in terms of function and pathways.", "claims": [{"id": "claim-method", "statement": "The DESeq2 package of R (version 4.1.0) was used to screen the differentially expressed mRNAs between MDD patients and healthy controls based on the transcript expression level satisfying |log2FoldChange| > 1 and p < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36911124", "locator": "sections[8] \"mRNA\" paragraph 2", "quote": "The DESeq2 package of R (version 4.1.0) was used to screen the differentially expressed mRNAs between MDD patients and healthy controls based on the transcript expression level satisfying |log2FoldChange| > 1 and p < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36911124", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Compared with adolescent HCs and adult MDD patients, the DNA methylation and mRNA expression patterns of first-episode, drug-naive adolescent MDD patients were different.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36911124", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Compared with adolescent HCs and adult MDD patients, the DNA methylation and mRNA expression patterns of first-episode, drug-naive adolescent MDD patients were different."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Compared with adolescent HCs and adult MDD patients, the DNA methylation and mRNA expression patterns of first-episode, drug-naive adolescent MDD patients were different.", "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:36911124"], "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:GSE113725"], "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:GSE113725"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36911124", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fpsyt.2023.1065417", "sha256": "sha256:a37c404a9208ee544b4ee1ac00bef497207cf3aea60f578ea44a61f7adf5cb60", "bytes": 35805, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fpsyt.2023.1065417", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9995926", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE113725", "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=GSE113725", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE113725", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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