{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T02:34:57Z","timestamp":1791513297219,"version":"4.3.4"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T00:00:00Z","timestamp":1781049600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T00:00:00Z","timestamp":1786924800000},"content-version":"vor","delay-in-days":68,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Cuiying Innovation and Technology Youth Project","award":["2026B-018"],"award-info":[{"award-number":["2026B-018"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["82560153"],"award-info":[{"award-number":["82560153"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Cuiying Science and Technology Innovation General Project","award":["CY2023-MS-B09"],"award-info":[{"award-number":["CY2023-MS-B09"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Inflammation"],"DOI":"10.1007\/s10753-026-02521-7","type":"journal-article","created":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T16:24:39Z","timestamp":1781108679000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Multi-omics Integration of Single-cell and Spatial Transcriptomics with Tissue and Urine Proteomics Identifies TRIM28 as a Translationally Relevant Candidate Regulator in Acute Kidney Injury"],"prefix":"10.1007","volume":"49","author":[{"given":"Kangyu","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yalong","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zijian","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changhong","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaxuan","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiangwei","family":"Man","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,10]]},"reference":[{"key":"2521_CR1","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1016\/S0140-6736(24)02385-7","volume":"405","author":"M Ostermann","year":"2025","unstructured":"Ostermann, M. et al. 2025. Acute kidney injury. The Lancet 405:241\u2013256.","journal-title":"The Lancet"},{"key":"2521_CR2","first-page":"1097","volume":"10","author":"S Fresilli","year":"2026","unstructured":"Fresilli, S. et al. 2026. Long-Term Outcomes After Acute Kidney Injury During Hospitalization: A Systematic Review and Meta-Analysis of Matched Controls Studies. Critical Care Medicine 10:1097.","journal-title":"Critical Care Medicine"},{"key":"2521_CR3","doi-asserted-by":"publisher","first-page":"4892","DOI":"10.1038\/s41467-022-32634-0","volume":"13","author":"L Xu","year":"2022","unstructured":"Xu, L., J. Guo, D. G. Moledina, and L. G. Cantley. 2022. Immune-mediated tubule atrophy promotes acute kidney injury to chronic kidney disease transition. Nature communications 13:4892.","journal-title":"Nature communications"},{"key":"2521_CR4","doi-asserted-by":"crossref","unstructured":"Baker, M. L., and L. G. Cantley. 2025. Adding insult to injury: the spectrum of tubulointerstitial responses in acute kidney injury. The Journal of Clinical Investigation 135(6):e188358.","DOI":"10.1172\/JCI188358"},{"key":"2521_CR5","doi-asserted-by":"publisher","first-page":"e74211","DOI":"10.7554\/eLife.74211","volume":"11","author":"F Freitas","year":"2022","unstructured":"Freitas, F., and D. Attwell. 2022. Pericyte-mediated constriction of renal capillaries evokes no-reflow and kidney injury following ischaemia. Elife 11:e74211.","journal-title":"Elife"},{"key":"2521_CR6","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/j.ejim.2024.05.007","volume":"127","author":"EA Schmidt","year":"2024","unstructured":"Schmidt, E. A. et al. 2024. Acute kidney injury predicts mortality in very elderly critically-ill patients. European Journal of Internal Medicine 127:119\u2013125.","journal-title":"European Journal of Internal Medicine"},{"key":"2521_CR7","doi-asserted-by":"publisher","first-page":"e2351710","DOI":"10.1001\/jamanetworkopen.2023.51710","volume":"7","author":"T Li","year":"2024","unstructured":"Li, T. et al. 2024. Automated electronic alert for the care and outcomes of adults with acute kidney injury: a randomized clinical trial. JAMA network open 7:e2351710\u2013e2351710.","journal-title":"JAMA network open"},{"key":"2521_CR8","doi-asserted-by":"publisher","first-page":"6156","DOI":"10.7150\/ijbs.117838","volume":"21","author":"X Wu","year":"2025","unstructured":"Wu, X. et al. 2025. Dysregulation of SRSF3\/circSAMD4\/CIRBP Axis Promotes Iodinated Contrast-induced Acute Kidney Injury. International Journal of Biological Sciences 21:6156.","journal-title":"International Journal of Biological Sciences"},{"key":"2521_CR9","doi-asserted-by":"publisher","first-page":"e1063","DOI":"10.1097\/CCM.0000000000005337","volume":"49","author":"L Evans","year":"2021","unstructured":"Evans, L. et al. 2021. Surviving sepsis campaign: international guidelines for management of sepsis and septic shock 2021. Critical care medicine 49:e1063\u2013e1143.","journal-title":"Critical care medicine"},{"key":"2521_CR10","doi-asserted-by":"crossref","unstructured":"Teixeira, J. P., S. Hiremath, A. O. Kabli, O. G. Rewa, and E. G. Clark. 2025. Continuous Kidney Replacement Therapies: Core Curriculum 2025. American Journal of Kidney Diseases 85(6):767\u2013786.","DOI":"10.1053\/j.ajkd.2024.09.015"},{"key":"2521_CR11","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.1016\/S0140-6736(21)00350-0","volume":"397","author":"S Gaudry","year":"2021","unstructured":"Gaudry, S. et al. 2021. Comparison of two delayed strategies for renal replacement therapy initiation for severe acute kidney injury (AKIKI 2): a multicentre, open-label, randomised, controlled trial. The Lancet 397:1293\u20131300.","journal-title":"The Lancet"},{"key":"2521_CR12","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1038\/s41586-023-05769-3","volume":"619","author":"BB Lake","year":"2023","unstructured":"Lake, B. B. et al. 2023. An atlas of healthy and injured cell states and niches in the human kidney. Nature 619:585\u2013594.","journal-title":"Nature"},{"key":"2521_CR13","doi-asserted-by":"publisher","first-page":"4018","DOI":"10.1038\/s41467-022-31772-9","volume":"13","author":"MS Balzer","year":"2022","unstructured":"Balzer, M. S. et al. 2022. Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration. Nature communications 13:4018.","journal-title":"Nature communications"},{"key":"2521_CR14","doi-asserted-by":"crossref","unstructured":"Melo Ferreira, R. et al. 2021. Integration of spatial and single-cell transcriptomics localizes epithelial cell-immune cross-talk in kidney injury. JCI Insight, 6 (12). Crossref, Medline.","DOI":"10.1172\/jci.insight.147703"},{"key":"2521_CR15","doi-asserted-by":"publisher","first-page":"bbae095","DOI":"10.1093\/bib\/bbae095","volume":"25","author":"C Xiao","year":"2024","unstructured":"Xiao, C., Y. Chen, Q. Meng, L. Wei, and X. Zhang. 2024. Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data. Briefings in Bioinformatics 25:bbae095.","journal-title":"Briefings in Bioinformatics"},{"key":"2521_CR16","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","volume":"42","author":"Y Hao","year":"2024","unstructured":"Hao, Y. et al. 2024. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nature biotechnology 42:293\u2013304.","journal-title":"Nature biotechnology"},{"key":"2521_CR17","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1038\/s41576-023-00586-w","volume":"24","author":"L Heumos","year":"2023","unstructured":"Heumos, L. et al. 2023. Best practices for single-cell analysis across modalities. Nature Reviews Genetics 24:550\u2013572.","journal-title":"Nature Reviews Genetics"},{"key":"2521_CR18","doi-asserted-by":"publisher","first-page":"D870","DOI":"10.1093\/nar\/gkac947","volume":"51","author":"C Hu","year":"2023","unstructured":"Hu, C. et al. 2023. CellMarker 2.0: an updated database of manually curated cell markers in human\/mouse and web tools based on scRNA-seq data. Nucleic acids research 51:D870\u2013D876.","journal-title":"Nucleic acids research"},{"key":"2521_CR19","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1126\/science.aax0249","volume":"367","author":"GS Gulati","year":"2020","unstructured":"Gulati, G. S. et al. 2020. Single-cell transcriptional diversity is a hallmark of developmental potential. Science 367:405\u2013411.","journal-title":"Science"},{"key":"2521_CR20","doi-asserted-by":"publisher","first-page":"e17","DOI":"10.1093\/nar\/gkad1187","volume":"52","author":"L-Y Chang","year":"2024","unstructured":"Chang, L.-Y. et al. 2024. Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles. Nucleic acids research 52:e17\u2013e17.","journal-title":"Nucleic acids research"},{"key":"2521_CR21","doi-asserted-by":"publisher","first-page":"1122","DOI":"10.1038\/s41592-021-01205-4","volume":"18","author":"I Walsh","year":"2021","unstructured":"Walsh, I. et al. 2021. DOME: recommendations for supervised machine learning validation in biology. Nature methods 18:1122\u20131127.","journal-title":"Nature methods"},{"key":"2521_CR22","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1038\/nmeth.3337","volume":"12","author":"AM Newman","year":"2015","unstructured":"Newman, A. M. et al. 2015. Robust enumeration of cell subsets from tissue expression profiles. Nature methods 12:453\u2013457.","journal-title":"Nature methods"},{"key":"2521_CR23","doi-asserted-by":"crossref","unstructured":"Subramanian, A. et al. 2005. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences 102:15545\u201315550.","DOI":"10.1073\/pnas.0506580102"},{"key":"2521_CR24","doi-asserted-by":"crossref","unstructured":"Dixon, E. E., H. Wu, Y. Muto, P. C. Wilson, and B. D. Humphreys. 2022. Spatially resolved transcriptomic analysis of acute kidney injury in a female murine model. Journal of the American Society of Nephrology 33(2):279\u2013289.","DOI":"10.1681\/ASN.2021081150"},{"key":"2521_CR25","doi-asserted-by":"publisher","first-page":"20888","DOI":"10.1038\/s41598-023-48213-2","volume":"13","author":"S Gharaie","year":"2023","unstructured":"Gharaie, S. et al. 2023. Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys. Scientific reports 13:20888.","journal-title":"Scientific reports"},{"key":"2521_CR26","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1038\/s41587-021-00830-w","volume":"40","author":"DM Cable","year":"2022","unstructured":"Cable, D. M. et al. 2022. Robust decomposition of cell type mixtures in spatial transcriptomics. Nature biotechnology 40:517\u2013526.","journal-title":"Nature biotechnology"},{"key":"2521_CR27","doi-asserted-by":"crossref","unstructured":"Wen, B. et al. 2025. Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment. Nature Methods 22(7):1454\u20131463.","DOI":"10.1038\/s41592-025-02719-x"},{"key":"2521_CR28","doi-asserted-by":"publisher","first-page":"1857","DOI":"10.1021\/acs.jproteome.9b00772","volume":"19","author":"H Ding","year":"2020","unstructured":"Ding, H. et al. 2020. Urine proteomics: evaluation of different sample preparation workflows for quantitative, reproducible, and improved depth of analysis. Journal of Proteome Research 19:1857\u20131862.","journal-title":"Journal of Proteome Research"},{"key":"2521_CR29","doi-asserted-by":"publisher","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","volume":"51","author":"D Szklarczyk","year":"2023","unstructured":"Szklarczyk, D. et al. 2023. The STRING database in 2023: protein\u2013protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic acids research 51:D638\u2013D646.","journal-title":"Nucleic acids research"},{"key":"2521_CR30","doi-asserted-by":"crossref","unstructured":"Wang, K. et al. 2026. Puerarin protects against renal ischemia-reperfusion injury by restoring mitochondrial function and modulating the PI3K\/AKT\/NF-\u03baB pathway and suppressing inflammatory responses. Cellular Signalling 139:112350.","DOI":"10.1016\/j.cellsig.2025.112350"},{"key":"2521_CR31","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1016\/j.ekir.2024.01.034","volume":"9","author":"SK Jensen","year":"2024","unstructured":"Jensen, S. K., U. Heide-J\u00f8rgensen, H. Gammelager, H. Birn, and C. F. Christiansen. 2024. Acute kidney injury duration and 20-year risks of CKD and cardiovascular disease. Kidney international reports 9:817\u2013829.","journal-title":"Kidney international reports"},{"key":"2521_CR32","doi-asserted-by":"crossref","unstructured":"Veltkamp, D. M. et al. 2025. Long-term risks of adverse kidney outcomes after acute kidney injury: a systematic review and meta-analysis. Nephrology Dialysis Transplantation 40(11):2143\u20132158.","DOI":"10.1093\/ndt\/gfaf093"},{"key":"2521_CR33","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1186\/s13073-022-01108-9","volume":"14","author":"C Hinze","year":"2022","unstructured":"Hinze, C. et al. 2022. Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury. Genome Medicine 14:103.","journal-title":"Genome Medicine"},{"key":"2521_CR34","doi-asserted-by":"publisher","first-page":"7010","DOI":"10.1038\/s41467-024-51186-z","volume":"15","author":"M Polonsky","year":"2024","unstructured":"Polonsky, M. et al. 2024. Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease. Nature Communications 15:7010.","journal-title":"Nature Communications"},{"key":"2521_CR35","doi-asserted-by":"publisher","first-page":"e147703","DOI":"10.1172\/jci.insight.147703","volume":"6","author":"RM Ferreira","year":"2021","unstructured":"Ferreira, R. M. et al. 2021. Integration of spatial and single-cell transcriptomics localizes epithelial cell\u2013immune cross-talk in kidney injury. JCI insight 6:e147703.","journal-title":"JCI insight"},{"key":"2521_CR36","doi-asserted-by":"crossref","unstructured":"Rossitto, M. et al. 2021. TRIM28-dependent SUMOylation protects the adult ovary from the male pathway. bioRxiv, 2003. 2024.436749 (2021).","DOI":"10.1101\/2021.03.24.436749"},{"key":"2521_CR37","doi-asserted-by":"publisher","first-page":"750","DOI":"10.1038\/s41467-025-56029-z","volume":"16","author":"K Wei","year":"2025","unstructured":"Wei, K. et al. 2025. TRIM28 is an essential regulator of three-dimensional chromatin state underpinning CD8\u2009+\u2009T cell activation. Nature Communications 16:750.","journal-title":"Nature Communications"},{"key":"2521_CR38","doi-asserted-by":"publisher","first-page":"F107","DOI":"10.1152\/ajprenal.00037.2022","volume":"323","author":"P Jia","year":"2022","unstructured":"Jia, P. et al. 2022. Chemokine CCL2 from proximal tubular epithelial cells contributes to sepsis-induced acute kidney injury. American Journal of Physiology-Renal Physiology 323:F107\u2013F119.","journal-title":"American Journal of Physiology-Renal Physiology"},{"key":"2521_CR39","doi-asserted-by":"crossref","unstructured":"Balzer, M. et al. 2022. Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration. Nat. Commun. 13, 4018. J Am Soc Nephrol 25, 292\u2013304.","DOI":"10.1038\/s41467-022-31772-9"},{"key":"2521_CR40","doi-asserted-by":"publisher","first-page":"1271","DOI":"10.1016\/j.kint.2022.02.033","volume":"101","author":"S Sawhney","year":"2022","unstructured":"Sawhney, S. et al. 2022. Harmonization of epidemiology of acute kidney injury and acute kidney disease produces comparable findings across four geographic populations. Kidney International 101:1271\u20131281.","journal-title":"Kidney International"},{"key":"2521_CR41","doi-asserted-by":"publisher","first-page":"1548","DOI":"10.1038\/s41467-023-37168-7","volume":"14","author":"H Li","year":"2023","unstructured":"Li, H. et al. 2023. A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics. Nature Communications 14:1548.","journal-title":"Nature Communications"}],"container-title":["Inflammation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10753-026-02521-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10753-026-02521-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10753-026-02521-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T03:09:10Z","timestamp":1786936150000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10753-026-02521-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,10]]},"references-count":41,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["2521"],"URL":"https:\/\/doi.org\/10.1007\/s10753-026-02521-7","relation":{},"ISSN":["1573-2576"],"issn-type":[{"value":"1573-2576","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,10]]},"assertion":[{"value":"25 February 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 April 2026","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 May 2026","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 June 2026","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The studies involving human participants were reviewed and approved by the Ethics Committee of Lanzhou University Second Hospital (Approval No. 2024 A-445). Written informed consent was obtained from all participants before inclusion, and the study was conducted in accordance with the Declaration of Helsinki.The animal study was reviewed and approved by the Ethics Committee of Lanzhou University Second Hospital (Approval No. D2026-003). All animal procedures were conducted in accordance with relevant institutional guidelines and regulations, and the study is reported in compliance with the ARRIVE reporting recommendations.","order":1,"name":"Ethics","label":"<b>Ethics Committee Approval<\/b>","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"<b>Clinical Trial Number<\/b>","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"176"}}