{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T18:47:41Z","timestamp":1769021261815,"version":"3.49.0"},"reference-count":40,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2025,3,29]],"date-time":"2025-03-29T00:00:00Z","timestamp":1743206400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82170686"],"award-info":[{"award-number":["82170686"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82200762"],"award-info":[{"award-number":["82200762"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["7254312"],"award-info":[{"award-number":["7254312"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004826","name":"Beijing Municipal Natural Science Foundation","doi-asserted-by":"publisher","award":["82170686"],"award-info":[{"award-number":["82170686"]}],"id":[{"id":"10.13039\/501100004826","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004826","name":"Beijing Municipal Natural Science Foundation","doi-asserted-by":"publisher","award":["82200762"],"award-info":[{"award-number":["82200762"]}],"id":[{"id":"10.13039\/501100004826","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004826","name":"Beijing Municipal Natural Science Foundation","doi-asserted-by":"publisher","award":["7254312"],"award-info":[{"award-number":["7254312"]}],"id":[{"id":"10.13039\/501100004826","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>(1) Background: the epigenetic mechanisms underlying the progression from acute kidney injury (AKI) to chronic kidney disease (CKD) remain poorly understood; (2) Methods: to investigate this process, we conducted genome-wide DNA methylation sequencing to map the epigenetic changes during the AKI-CKD transition in a mouse model. By integrating DNA methylome and transcriptome analyses, we identified genes and signaling pathways regulated by DNA methylation throughout this progression; (3) Results: our analysis identified four candidate genes\u2014Atp1a3, Ncf1, Lpl, and Slc27a2\u2014that were regulated by DNA methylation and strongly correlated with kidney disease prognosis. Additionally, we found that the PPAR signaling pathways, among others, were implicated in this process. Treatment with DNA methyltransferase inhibitors mitigated fibrosis and improved lipid metabolism in the kidneys during AKI-CKD progression; (4) Conclusions: this study provides the first comprehensive epigenetic map of the AKI-CKD transition. Our findings offer new insights into the epigenetic regulation of kidney disease progression and highlight potential therapeutic targets to prevent the transition from AKI to CKD.<\/jats:p>","DOI":"10.3390\/biom15040498","type":"journal-article","created":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T05:21:04Z","timestamp":1743398464000},"page":"498","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Integration of DNA Methylome and Transcriptome Analysis to Identify Novel Epigenetic Targets in the Acute Kidney Injury\u2013Chronic Kidney Disease Transition"],"prefix":"10.3390","volume":"15","author":[{"given":"Xumin","family":"Zheng","sequence":"first","affiliation":[{"name":"Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People\u2019s Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9454-2315","authenticated-orcid":false,"given":"Xinru","family":"Guo","sequence":"additional","affiliation":[{"name":"School of Medicine, Nankai University, Tianjin 300071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuhao","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People\u2019s Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaiting","family":"Zhuang","sequence":"additional","affiliation":[{"name":"Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People\u2019s Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Na","family":"Gong","sequence":"additional","affiliation":[{"name":"Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People\u2019s Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yifei","family":"Fu","sequence":"additional","affiliation":[{"name":"Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People\u2019s Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanjun","family":"Liang","sequence":"additional","affiliation":[{"name":"Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People\u2019s Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People\u2019s Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siyang","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People\u2019s Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenjuan","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People\u2019s Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiangmei","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People\u2019s Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guangyan","family":"Cai","sequence":"additional","affiliation":[{"name":"Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People\u2019s Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,3,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2616","DOI":"10.1016\/S0140-6736(15)60126-X","article-title":"International Society of Nephrology\u2019s 0by25 initiative for acute kidney injury (zero preventable deaths by 2025): A human rights case for nephrology","volume":"385","author":"Mehta","year":"2015","journal-title":"Lancet"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"3365","DOI":"10.1681\/ASN.2004090740","article-title":"Acute kidney injury, mortality, length of stay, and costs in hospitalized patients","volume":"16","author":"Chertow","year":"2005","journal-title":"J. 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