Transcriptomic profiling of hepatic tissues for drug metabolism genes in nonalcoholic fatty liver disease: A study of human and animals.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36686439", "kind": "science-record", "revision": 3, "content_hash": "sha256:c011d94da912b036fd2791168f23359cf17cc6f94aa5b097678a758f683bc0de", "created_at": "2026-11-01T19:01:14Z", "updated_at": "2026-11-01T22:08:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptomic profiling of hepatic tissues for drug metabolism genes in nonalcoholic fatty liver disease: A study of human and animals.", "doi": "10.3389/fendo.2022.1034494", "pmid": "36686439", "authors": ["Li Chen", "Lu Chen", "Xu Li", "Lin Qin", "Yan Zhu", "Qianru Zhang", "Daopeng Tan", "Yuqi He", "Yu-He Wang"], "journal": "Frontiers in endocrinology", "year": 2022, "abstract": "Background: Drug metabolism genes are involved in the in vivo metabolic processing of drugs. In previous research, we found that a high-fat diet affected the transcript levels of mouse hepatic genes responsible for drug metabolism.\nAims: Our research intends to discover the drug metabolism genes that are dysregulated at the transcriptome level in nonalcoholic fatty liver disease (NAFLD).\nMethods: We analyzed the transcriptome for drug metabolism genes of 35 human liver tissues obtained during laparoscopic cholecystectomy. Additionally, we imported transcriptome data from mice fed a high-fat diet in previous research and two open-access Gene Expression Omnibus (GEO) datasets (GSE63067 and GSE89632). Then, using quantitative real-time polymerase chain reaction (qRT-PCR), we cross-linked the differentially expressed genes (DEGs) in clinical and animal samples and validated the common genes.\nResults: In this study, we identified 35 DEGs, of which 33 were up-regulated and two were down-regulated. Moreover, we found 71 DEGs (39 up- and 32 down-regulated), 276 DEGs (157 up- and 119 down-regulated), and 158 DEGs (117 up- and 41 down-regulated) in the GSE63067, GSE89632, and high-fat diet mice, respectively. Of the 35 DEGs, nine co-regulated DEGs were found in the Venn diagram (CYP20A1, CYP2U1, SLC9A6, SLC26A6, SLC31A1, SLC46A1, SLC46A3, SULT1B1, and UGT2A3).\nConclusion: Nine significant drug metabolism genes were identified in NAFLD. Future research should investigate the impacts of these genes on drug dose adjustment in patients with NAFLD.\nClinical Trial Registration: http://www.chictr.org.cn, identifier ChiCTR2100041714.", "claims": [{"id": "claim-method", "statement": "The screening criteria for DEGs were as follows: P-value <0.05 and |fold change|>1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36686439", "locator": "sections[13] \"3.3 Differentially expressed genes\" paragraph 2", "quote": "The screening criteria for DEGs were as follows: P-value <0.05 and |fold change|>1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The data presented in the study are deposited in the ArrayExpress repository, accession number E-MTAB-12445. 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:36686439", "locator": "sections[18] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The data presented in the study are deposited in the ArrayExpress repository, accession number E-MTAB-12445. 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": "Nine significant drug metabolism genes were identified in NAFLD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36686439", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "Nine significant drug metabolism genes were identified in NAFLD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Nine significant drug metabolism genes were identified in NAFLD.", "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:36686439"], "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:E-MTAB-12445"], "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:E-MTAB-12445"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36686439", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fendo.2022.1034494", "sha256": "sha256:19d14b727d1e922c5338c6b0989603e1b545cb04ac96d688ab53a5f77360e4f3", "bytes": 47763, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fendo.2022.1034494", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9845619", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:E-MTAB-12445", "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=E-MTAB-12445", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "E-MTAB-12445", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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Additionally, we imported transcriptome data from mice fed a high-fat diet in previo", "ize and high false positive rate of a single transcriptome analysis, it may be difficult to obtain reli"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d: Drug metabolism genes are involved in the in vivo metabolic processing of drugs. In previous r", "h-fat diet affected the transcript levels of mouse hepatic genes responsible for drug metabolis", "develop a list of 612 drug metabolism genes in mice (9). Meanwhile, in the present study, from a", "oups are in red, and the HFD groups are blue in the mouse data. 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