{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T20:46:16Z","timestamp":1781988376761,"version":"3.54.5"},"reference-count":46,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Gene"],"published-print":{"date-parts":[[2024,11]]},"DOI":"10.1016\/j.gene.2024.148599","type":"journal-article","created":{"date-parts":[[2024,5,21]],"date-time":"2024-05-21T16:07:46Z","timestamp":1716307666000},"page":"148599","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":4,"special_numbering":"C","title":["Landscape of extrachromosomal circular DNAs, transcriptome, and proteome analysis reveals insights into alcoholic liver cirrhosis"],"prefix":"10.1016","volume":"927","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-5359-1178","authenticated-orcid":false,"given":"Jingwen","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanyuan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-6590-0825","authenticated-orcid":false,"given":"Fei","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yadong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junying","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"6532","key":"10.1016\/j.gene.2024.148599_b0005","first-page":"887","volume":"371","author":"Andersson","year":"2021","journal-title":"In the zone for liver proliferation"},{"key":"10.1016\/j.gene.2024.148599_b0010","doi-asserted-by":"crossref","unstructured":"Biagini, G., Ballardini, G.J.J.o.h., 1989. Liver fibrosis and extracellular matrix 8(1), 115\u2013124.","DOI":"10.1016\/0168-8278(89)90170-0"},{"key":"10.1016\/j.gene.2024.148599_b0015","unstructured":"Chen, F.Z., You, L.J., Yang, F., et al., 2020. CNGBdb: china national genebank database 42(8), 799\u2013809."},{"issue":"1","key":"10.1016\/j.gene.2024.148599_b0020","first-page":"e3001522","volume":"20","author":"Chen","year":"2022","journal-title":"Rab2A regulates the progression of nonalcoholic fatty liver disease downstream of AMPK-TBC1D1 axis by stabilizing PPAR\u03b3."},{"issue":"1","key":"10.1016\/j.gene.2024.148599_b0025","first-page":"7","volume":"2","author":"Deshpande","year":"2014","journal-title":"Effect of alcohol consumption and oxidative stress and its role in DNA damage"},{"key":"10.1016\/j.gene.2024.148599_b0030","doi-asserted-by":"crossref","unstructured":"Dillon, L.W., Kumar, P., Shibata, Y., et al., 2015. Production of extrachromosomal microDNAs is linked to mismatch repair pathways and transcriptional activity 11(11), 1749-1759.","DOI":"10.1016\/j.celrep.2015.05.020"},{"issue":"1","key":"10.1016\/j.gene.2024.148599_b0035","volume":"1875","author":"Gillman","year":"2021","journal-title":"The role of DNA damage and repair in liver cancer"},{"key":"10.1016\/j.gene.2024.148599_b0040","doi-asserted-by":"crossref","unstructured":"Gu, J., Hong, R., Niu, G., et al., 2020. Down-regulation of DLG2 predicts an unfavorable prognosis and promotes the proliferation and migration of Hepatocellular Carcinoma. 2020.","DOI":"10.21203\/rs.3.rs-22758\/v1"},{"key":"10.1016\/j.gene.2024.148599_b0045","doi-asserted-by":"crossref","unstructured":"Guo, X., Chen, F., Gao, F., et al., 2020. CNSA: a data repository for archiving omics data. Database: the journal of biological databases and curation, 2020. doi: 10.1093\/database\/baaa055. PubMed PMID: 32705130; PubMed Central PMCID: PMCPMC7377928.eng.","DOI":"10.1093\/database\/baaa055"},{"key":"10.1016\/j.gene.2024.148599_b0050","doi-asserted-by":"crossref","unstructured":"Holt, S., Arrey, G., Regenberg, B.J.T.i.B.S., 2022. Did circular DNA shape the evolution of mammalian genomes? 2022.","DOI":"10.1101\/2022.06.22.497135"},{"issue":"1","key":"10.1016\/j.gene.2024.148599_b0055","first-page":"37","article-title":"Global epidemiology of alcohol-associated cirrhosis and HCC: trends","volume":"20","author":"Huang","year":"2023","journal-title":"Project. Risk Fact."},{"key":"10.1016\/j.gene.2024.148599_b0060","doi-asserted-by":"crossref","unstructured":"Jeon, S., Carrm R.J.J.o.L.R., 2016. Alcohol effects on hepatic lipid metabolism 61(4), 470\u2013479.","DOI":"10.1194\/jlr.R119000547"},{"key":"10.1016\/j.gene.2024.148599_b0065","doi-asserted-by":"crossref","unstructured":"Kang, Q., Sun, J., Wang, B., et al., 2023. Wine, beer and Chinese Baijiu in relation to cardiovascular health: the impact of moderate drinking 12(1), 1\u201313.","DOI":"10.1016\/j.fshw.2022.07.013"},{"key":"10.1016\/j.gene.2024.148599_b0070","doi-asserted-by":"crossref","unstructured":"Karsdal, M.A., Daniels, S.J., Holm Nielsen, S., et al., 2020. Collagen biology and non\u2010invasive biomarkers of liver fibrosis. 40(4), 736-750.","DOI":"10.1111\/liv.14390"},{"key":"10.1016\/j.gene.2024.148599_b0075","doi-asserted-by":"crossref","unstructured":"Khurana, A., Sayed, N., Allawadhi, P., et al., 2021. It\u2019s all about the spaces between cells: role of extracellular matrix in liver fibrosis, 9(8).","DOI":"10.21037\/atm-20-2948"},{"key":"10.1016\/j.gene.2024.148599_b0080","doi-asserted-by":"crossref","unstructured":"Lackner, C., Tiniakos, D.J.J.o.h., 2019. Fibrosis and alcohol-related liver disease 70(2), 294-304.","DOI":"10.1016\/j.jhep.2018.12.003"},{"issue":"5","key":"10.1016\/j.gene.2024.148599_b0085","first-page":"589","volume":"26","author":"Li","year":"2010","journal-title":"Fast and accurate long-read alignment with burrows-wheeler transform"},{"key":"10.1016\/j.gene.2024.148599_b0090","doi-asserted-by":"crossref","unstructured":"Li, R., Wang, Y., Li, J., et al., 2022. Extrachromosomal circular DNA (eccDNA): an emerging star in cancer 10(1), 1\u201313.","DOI":"10.1186\/s40364-022-00399-9"},{"key":"10.1016\/j.gene.2024.148599_b0095","doi-asserted-by":"crossref","unstructured":"Liao, Z., Jiang, W., Ye, L., et al., 2020. Classification of extrachromosomal circular DNA with a focus on the role of extrachromosomal DNA (ecDNA) in tumor heterogeneity and progression 1874(1), 188392.","DOI":"10.1016\/j.bbcan.2020.188392"},{"key":"10.1016\/j.gene.2024.148599_b0100","doi-asserted-by":"crossref","unstructured":"Ling, X., Han, Y., Meng, J., et al., 2021. Small extrachromosomal circular DNA (eccDNA): major functions in evolution and cancer 20(1), 1-15.","DOI":"10.1186\/s12943-021-01413-8"},{"issue":"4","key":"10.1016\/j.gene.2024.148599_b0105","first-page":"e817","volume":"12","author":"Lv","year":"2022","journal-title":"Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs"},{"issue":"11","key":"10.1016\/j.gene.2024.148599_b0110","first-page":"969","volume":"32","author":"Lyu","year":"2022","journal-title":"CRISPR FISHer enables high-sensitivity imaging of nonrepetitive DNA in living cells through phase separation-mediated signal amplification"},{"key":"10.1016\/j.gene.2024.148599_b0115","doi-asserted-by":"crossref","unstructured":"M.D. FS. Alcoholic cirrhosis and hepatocellular carcinoma. 2015:113-130.","DOI":"10.1007\/978-3-319-09614-8_7"},{"issue":"7","key":"10.1016\/j.gene.2024.148599_b0120","first-page":"2132","volume":"32","author":"Molin","year":"2020","journal-title":"The EccDNA replicon: a heritable, extranuclear vehicle that enables gene amplification and glyphosate resistance in Amaranthus palmeri"},{"key":"10.1016\/j.gene.2024.148599_b0125","unstructured":"Nielsen, M.J., Nedergaard, A.F., Sun, S., et al., 2013. The neo-epitope specific PRO-C3 ELISA measures true formation of type III collagen associated with liver and muscle parameters. 5(3), 303."},{"key":"10.1016\/j.gene.2024.148599_b0130","doi-asserted-by":"crossref","unstructured":"Nowak, A.J., Relja, B.J.I.J.o.M.S., 2020. The impact of acute or chronic alcohol intake on the NF-\u03baB signaling pathway in alcohol-related liver disease 21(24), 9407.","DOI":"10.3390\/ijms21249407"},{"key":"10.1016\/j.gene.2024.148599_b0135","doi-asserted-by":"crossref","unstructured":"Paulsen, T., Kumar, P., Koseoglu, M.M., et al., 2018. Discoveries of extrachromosomal circles of DNA in normal and tumor cells 34(4), 270\u2013278.","DOI":"10.1016\/j.tig.2017.12.010"},{"issue":"20","key":"10.1016\/j.gene.2024.148599_b0140","first-page":"11787","volume":"49","author":"Paulsen","year":"2021","journal-title":"MicroDNA levels are dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA damage"},{"key":"10.1016\/j.gene.2024.148599_b0145","doi-asserted-by":"crossref","unstructured":"Rahman, S.R., Roper, J.A., Grove, J.I., et al., 2022. Integrins as a drug target in liver fibrosis, 42(3), 507\u2013521.","DOI":"10.1111\/liv.15157"},{"issue":"1","key":"10.1016\/j.gene.2024.148599_b0150","first-page":"16","volume":"4","author":"Seitz","year":"2018","journal-title":"Alcoholic Liver Disease."},{"issue":"11","key":"10.1016\/j.gene.2024.148599_b0155","first-page":"2498","volume":"13","author":"Shannon","year":"2003","journal-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks"},{"key":"10.1016\/j.gene.2024.148599_b0160","doi-asserted-by":"crossref","unstructured":"Sin, S.T., Jiang, P., Deng, J., et al., 2020. Identification and characterization of extrachromosomal circular DNA in maternal plasma 117(3), 1658\u20131665.","DOI":"10.1073\/pnas.1914949117"},{"key":"10.1016\/j.gene.2024.148599_b0165","doi-asserted-by":"crossref","unstructured":"Singh, N.P., Khan, A.J.M.R.D.R., 1995. Acetaldehyde: genotoxicity and cytotoxicity in human lymphocytes 337(1), 9-17.","DOI":"10.1016\/0921-8777(95)00006-6"},{"issue":"D1","key":"10.1016\/j.gene.2024.148599_b0170","first-page":"D447","volume":"43","author":"Szklarczyk","year":"2015","journal-title":"STRING v10: protein\u2013protein interaction networks, integrated over the tree of life"},{"key":"10.1016\/j.gene.2024.148599_b0175","doi-asserted-by":"crossref","unstructured":"Tan, H.K., Yates, E., Lilly, K., et al., 2020. Oxidative stress in alcohol-related liver disease 12(7):332.","DOI":"10.4254\/wjh.v12.i7.332"},{"key":"10.1016\/j.gene.2024.148599_b0180","doi-asserted-by":"crossref","unstructured":"Vijayraghavan, S., Porcher, L., Mieczkowski, P.A., et al., 2022. Acetaldehyde makes a distinct mutation signature in single-stranded DNA 50(13), 7451\u20137464.","DOI":"10.1093\/nar\/gkac570"},{"key":"10.1016\/j.gene.2024.148599_b0185","unstructured":"Vos, T., Lim, S.S., Abbafati, C., et al., 2020. Global burden of 369 diseases and injuries in 204 countries and territories, 1990\u20132019: a systematic analysis for the Global Burden of Disease Study 2019 396 (10258), 1204-1222."},{"key":"10.1016\/j.gene.2024.148599_b0190","doi-asserted-by":"crossref","unstructured":"Wang, W.-J., Xiao, P., Xu, H.-Q., et al., 2019. Growing burden of alcoholic liver disease in China: a review 25(12), 1445.","DOI":"10.3748\/wjg.v25.i12.1445"},{"issue":"7784","key":"10.1016\/j.gene.2024.148599_b0195","first-page":"699","volume":"575","author":"Wu","year":"2019","journal-title":"Circular ecDNA promotes accessible chromatin and high oncogene expression"},{"key":"10.1016\/j.gene.2024.148599_b0200","doi-asserted-by":"crossref","unstructured":"Xu, W., Xu, Y.-n., Zhang, X., et al., 2020. Hepatic stem cell Numb gene is a potential target of Huang Qi Decoction against cholestatic liver fibrosis 10(1), 1-14.","DOI":"10.1038\/s41598-020-74324-1"},{"key":"10.1016\/j.gene.2024.148599_b0205","doi-asserted-by":"crossref","unstructured":"Xu, Y.-n., Xu, W., Zhang, X., et al., 2023. BM-MSCs overexpressing the Numb enhance the therapeutic effect on cholestatic liver fibrosis by inhibiting the ductular reaction. 14(1):45.","DOI":"10.1186\/s13287-023-03276-w"},{"key":"10.1016\/j.gene.2024.148599_b0210","unstructured":"Yan, H., Lu, X., Gao, Y., et al., 2015. Epidemiological investigation of fatty liver disease in Northwest China 622\u2013627."},{"key":"10.1016\/j.gene.2024.148599_b0215","doi-asserted-by":"crossref","unstructured":"Zhang, H., Liu, Z., Liu, S.J.M.I., 2016. HMGB1 induced inflammatory effect is blocked by CRISPLD2 via MiR155 in hepatic fibrogenesis 69:1\u20136.","DOI":"10.1016\/j.molimm.2015.10.018"},{"issue":"1","key":"10.1016\/j.gene.2024.148599_b0220","first-page":"1","volume":"12","author":"Zhang","year":"2021","journal-title":"Single-cell RNA-sequencing reveals the dynamic process and novel markers in porcine spermatogenesis"},{"key":"10.1016\/j.gene.2024.148599_b0225","doi-asserted-by":"crossref","unstructured":"Zhao, J., Qi, Y.-F., Yu, Y.-R.J.A.o.h., 2021. STAT3: A key regulator in liver fibrosis 21, 100224.","DOI":"10.1016\/j.aohep.2020.06.010"},{"key":"10.1016\/j.gene.2024.148599_b0230","doi-asserted-by":"crossref","unstructured":"Zhou, C., Li, S., Bin, K., et al., 2022. ITGA2 overexpression inhibits DNA repair and confers sensitivity to radiotherapies in pancreatic cancer 547, 215855.","DOI":"10.1016\/j.canlet.2022.215855"}],"container-title":["Gene"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0378111924004803?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0378111924004803?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,7,26]],"date-time":"2024-07-26T02:36:13Z","timestamp":1721961373000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0378111924004803"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11]]},"references-count":46,"alternative-id":["S0378111924004803"],"URL":"https:\/\/doi.org\/10.1016\/j.gene.2024.148599","relation":{},"ISSN":["0378-1119"],"issn-type":[{"value":"0378-1119","type":"print"}],"subject":[],"published":{"date-parts":[[2024,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Landscape of extrachromosomal circular DNAs, transcriptome, and proteome analysis reveals insights into alcoholic liver cirrhosis","name":"articletitle","label":"Article Title"},{"value":"Gene","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.gene.2024.148599","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"148599"}}