{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T13:26:30Z","timestamp":1786973190074,"version":"build-2736575974"},"reference-count":69,"publisher":"SAGE Publications","issue":"10","license":[{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"funder":[{"name":"The Fifth Batch of National Outstanding Chinese Medicine Clinical Talent Training Program, State Administration of Traditional Chinese Medicine","award":["[2022] No. 1"],"award-info":[{"award-number":["[2022] No. 1"]}]},{"name":"Superior Specialized Department of Spleen and Stomach Diseases, State Administration of Traditional Chinese Medicine","award":["[2024] No. 90"],"award-info":[{"award-number":["[2024] No. 90"]}]}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["OMICS: A Journal of Integrative Biology"],"published-print":{"date-parts":[[2026,10,1]]},"abstract":"<jats:p>\n                    Inflammatory bowel disease (IBD) involves complex immunometabolic dysregulation. Mitochondria-associated endoplasmic reticulum membranes (MAMs) link metabolic adaptation and inflammatory signaling, but gene expression features associated with MAM-related transcriptomic states in IBD remain unclear. Public transcriptomic datasets were integrated with a curated MAM-related gene set and herbal target information. Differential expression analysis, weighted gene coexpression network analysis, and machine learning-assisted feature selection were used to identify candidate genes. A two-gene nomogram was constructed and evaluated in discovery and independent validation datasets. Functional enrichment, immune deconvolution, regulatory network prediction, molecular docking, 200-ns molecular dynamics simulations, and preliminary quantitative polymerase chain reaction validation were performed.\n                    <jats:italic toggle=\"yes\">LIMK1<\/jats:italic>\n                    and\n                    <jats:italic toggle=\"yes\">PKM<\/jats:italic>\n                    were identified as candidate transcriptomic signature genes associated with IBD status and MAM-related transcriptional states, showing discriminatory performance in independent datasets. Both genes were associated with cytokine\u2013cytokine receptor interaction and drug metabolism\u2013cytochrome P450 pathways and were linked to macrophage-related immune states. Structural analyses suggested stable predicted binding between\n                    <jats:italic toggle=\"yes\">PKM<\/jats:italic>\n                    and 1-(4-hydroxybenzyl)-4-methoxy-9,10-dihydrophenanthrene-2,7-diol and structurally plausible interactions between\n                    <jats:italic toggle=\"yes\">LIMK1<\/jats:italic>\n                    and palmatine. Preliminary tissue-level validation supported the disease-associated expression pattern of\n                    <jats:italic toggle=\"yes\">PKM<\/jats:italic>\n                    , whereas\n                    <jats:italic toggle=\"yes\">LIMK1<\/jats:italic>\n                    showed a consistent but nonsignificant upward trend.\n                    <jats:italic toggle=\"yes\">LIMK1<\/jats:italic>\n                    and\n                    <jats:italic toggle=\"yes\">PKM<\/jats:italic>\n                    may represent candidate transcriptomic signatures associated with MAM-related regulatory states in IBD. These findings should be interpreted as hypothesis-generating associations rather than evidence of MAM localization, functional causality, or therapeutic efficacy. Further protein-level and functional validation is required.\n                  <\/jats:p>","DOI":"10.1177\/15578100261472246","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T13:09:40Z","timestamp":1786540180000},"page":"609-630","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":0,"title":["<i>LIMK1<\/i>\n                    and\n                    <i>PKM<\/i>\n                    as Integratively Identified Transcriptomic Signatures in Inflammatory Bowel Disease"],"prefix":"10.1177","volume":"30","author":[{"given":"Houshu","family":"Tu","sequence":"first","affiliation":[{"name":"Jiangxi University of Chinese Medicine, Nanchang, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Menglin","family":"Chen","sequence":"additional","affiliation":[{"name":"Jiangxi University of Chinese Medicine, Nanchang, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Panpan","family":"Zhu","sequence":"additional","affiliation":[{"name":"Jiangxi University of Chinese Medicine, Nanchang, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5198-712X","authenticated-orcid":false,"given":"Ling","family":"He","sequence":"additional","affiliation":[{"name":"Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Hong","sequence":"additional","affiliation":[{"name":"Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, China."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2026,8,12]]},"reference":[{"key":"e_1_3_5_2_1","doi-asserted-by":"publisher","DOI":"10.54033\/cadpedv22n7-181"},{"key":"e_1_3_5_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09104-1"},{"key":"e_1_3_5_4_1","doi-asserted-by":"publisher","DOI":"10.1111\/apt.13736"},{"key":"e_1_3_5_5_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-023-09677-8"},{"key":"e_1_3_5_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/bies.202400184"},{"key":"e_1_3_5_7_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-7493-1_12"},{"key":"e_1_3_5_8_1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2026.1782885"},{"key":"e_1_3_5_9_1","doi-asserted-by":"publisher","DOI":"10.3390\/jcm12051830"},{"key":"e_1_3_5_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.phymed.2022.154131"},{"key":"e_1_3_5_11_1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2026.1801914"},{"key":"e_1_3_5_12_1","doi-asserted-by":"publisher","DOI":"10.1155\/2022\/8735551"},{"key":"e_1_3_5_13_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12920-023-01451-9"},{"key":"e_1_3_5_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13148-019-0730-1"},{"key":"e_1_3_5_15_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpsyg.2019.01507"},{"key":"e_1_3_5_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molmed.2019.09.009"},{"key":"e_1_3_5_17_1","doi-asserted-by":"publisher","DOI":"10.1161\/CIRCRESAHA.109.195883"},{"key":"e_1_3_5_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/nm.3189"},{"key":"e_1_3_5_19_1","doi-asserted-by":"publisher","DOI":"10.37349\/edd.2024.00062"},{"key":"e_1_3_5_20_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-7"},{"key":"e_1_3_5_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-31438-6"},{"key":"e_1_3_5_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-41028-9"},{"key":"e_1_3_5_23_1","doi-asserted-by":"publisher","DOI":"10.21037\/tcr-24-215"},{"key":"e_1_3_5_24_1","doi-asserted-by":"publisher","DOI":"10.1172\/JCI34610"},{"key":"e_1_3_5_25_1","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.161096"},{"issue":"6","key":"e_1_3_5_26_1","article-title":"Ulcerative colitis (primer)","volume":"1","author":"Kobayashi T","year":"2020","unstructured":"Kobayashi T, , Siegmund B, , Le Berre C, et al. 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