{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T13:14:48Z","timestamp":1773926088606,"version":"3.50.1"},"reference-count":36,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,11,17]],"date-time":"2022-11-17T00:00:00Z","timestamp":1668643200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100017577","name":"Basic Public Welfare Research Program of Zhejiang Province","doi-asserted-by":"publisher","award":["LGD20H070002"],"award-info":[{"award-number":["LGD20H070002"]}],"id":[{"id":"10.13039\/501100017577","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014996","name":"Health Commission of Zhejiang Province","doi-asserted-by":"publisher","award":["2022KY523, 2020KY022, 2021KY060"],"award-info":[{"award-number":["2022KY523, 2020KY022, 2021KY060"]}],"id":[{"id":"10.13039\/501100014996","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81970714"],"award-info":[{"award-number":["81970714"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Endocrinol."],"abstract":"<jats:sec><jats:title>Aim<\/jats:title><jats:p>The aims of this study were to analyze the proteomic differences in renal tissues from patients with diabetes mellitus (DM) and diabetic kidney disease (DKD) and to select sensitive biomarkers for early identification of DKD progression.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Pressure cycling technology\u2013pulse data-independent acquisition mass spectrometry was employed to investigate protein alterations in 36 formalin-fixed paraffin-embedded specimens. Then, bioinformatics analysis was performed to identify important signaling pathways and key molecules. Finally, the target proteins were validated in 60 blood and 30 urine samples.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A total of 52 up- and 311 down-regulated differential proteins were identified as differing among the advanced DKD samples, early DKD samples, and DM controls (adjusted p&amp;lt;0.05). These differentially expressed proteins were mainly involved in ion transport, apoptosis regulation, and the inflammatory response. UniProt database analysis showed that these proteins were mostly enriched in signaling pathways related to metabolism, apoptosis, and inflammation. NBR1 was significantly up-regulated in both early and advanced DKD, with fold changes (FCs) of 175 and 184, respectively (both p&amp;lt;0.01). In addition, VPS37A and ATG4B were significantly down-regulated with DKD progression, with FCs of 0.140 and 0.088, respectively, in advanced DKD and 0.533 and 0.192, respectively, in early DKD compared with the DM control group (both p&amp;lt;0.01). Bioinformatics analysis showed that NBR1, VPS37A, and ATG4B are closely related to autophagy. We also found that serum levels of the three proteins and urine levels of NBR1 decreased with disease progression. Moreover, there was a significant difference in serum VPS37A and ATG4B levels between patients with early and advanced DKD (both p&amp;lt;0.05). The immunohistochemistry assaay exhibited that the three proteins were expressed in renal tubular cells, and NBR1 was also expressed in the cystic wall of renal glomeruli.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The increase in NBR1 expression and the decrease in ATG4B and VPS37 expression in renal tissue are closely related to inhibition of the autophagy pathway, which may contribute to DKD development or progression. These three proteins may serve as sensitive serum biomarkers for early identification of DKD progression.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fendo.2022.995362","type":"journal-article","created":{"date-parts":[[2022,11,17]],"date-time":"2022-11-17T10:36:16Z","timestamp":1668681376000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Stratification of diabetic kidney diseases via data-independent acquisition proteomics\u2013based analysis of human kidney tissue specimens"],"prefix":"10.3389","volume":"13","author":[{"given":"Qinghua","family":"Huang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xianming","family":"Fei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhaoxian","family":"Zhong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jieru","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianguang","family":"Gong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuan","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yiwen","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaohong","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2022,11,17]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ekir.2021.10.023","article-title":"Diabetic kidney disease: The \"Silent\" majority","volume":"6","author":"Yau","year":"2021","journal-title":"Kidney Int Rep"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2022.736006","article-title":"Protein methylation in\u2002Diabetic\u2002Kidney\u2002Disease","volume":"9","author":"Cheng","year":"2022","journal-title":"Front Med (Lausanne)"},{"key":"B3","doi-asserted-by":"publisher","first-page":"1205","DOI":"10.3390\/diagnostics12051205","article-title":"Novel markers in\u2002Diabetic\u2002Kidney\u2002Disease-current state and perspectives","volume":"12","author":"Piwkowska","year":"2022","journal-title":"Diagnost (Basel)"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1681\/ASN.2010010010","article-title":"Renal pathology society","volume":"21","author":"Tervaert","year":"2010","journal-title":"Pathol Classification Diabetic Nephropathy J Am Soc Nephrol"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.4239\/wjd.v4.i6.245","article-title":"Diabetic nephropathy: Is it time yet for routine kidney biopsy","volume":"15","author":"Gonzalez Suarez","year":"2013","journal-title":"World J Diabetes"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1001\/archinternmed.2011.16","article-title":"Long-term renal outcomes of patients with type1 diabetes mellitus and microalbuminuria: an analysis of the diabetes control and complications trial\/epidemiology of diabetes interventions and complications cohort","volume":"171","author":"de Boe","year":"2011","journal-title":"Arch Intern Med"},{"key":"B7","doi-asserted-by":"publisher","first-page":"13","DOI":"10.6065\/apem.2015.20.1.13","article-title":"Regression and progression of microalbuminuria in adolescents with childhood onset diabetes mellitus[J]","volume":"20","author":"Son","year":"2015","journal-title":"Ann Pediatr Endocrinol Metab"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1007\/s00125-016-4001-9","article-title":"Proteomics for prediction of disease progression and response to therapy in diabetic kidney disease","volume":"59","author":"Pena","year":"2016","journal-title":"Diabetologia"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1007\/s40620-014-0044-5","article-title":"Proteomics and diabetic nephropathy: what have we learned from a decade of clinical proteomics studies","volume":"27","author":"Papale","year":"2014","journal-title":"J Nephrol"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.4093\/dmj.2021.0329","article-title":"Pathophysiologic mechanisms and potential biomarkers in Diabetic\u2002Kidney\u2002Disease","volume":"46","author":"Jung","year":"2022","journal-title":"Diabetes Metab J"},{"key":"B11","doi-asserted-by":"publisher","first-page":"20420188211049612","DOI":"10.1177\/20420188211049612","article-title":"Current updates on protein as biomarkers for diabetic\u2002kidney\u2002disease: A systematic review","volume":"12","author":"Sauriasari","year":"2021","journal-title":"Ther Adv Endocrinol Metab"},{"key":"B12","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1477-5956-8-4","article-title":"Plasma proteome analysis of patien ts with type 1 diabetes with diabetic nephropathy","volume":"8","author":"Overgaard","year":"2010","journal-title":"Proteome Sci"},{"key":"B13","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1002\/prca.200900169","article-title":"Finding diabetic nephropathy biomar kers in the plasma peptidome by highthroughput magnetic bead processing and MALDI-TOF- MSanalysis","volume":"4","author":"Hansen","year":"2010","journal-title":"Proteomics Clin Appl"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.2337\/db12-0348","article-title":"Urinary pmteomics forearIy diagnosis in diabetic nephropathy","volume":"61","author":"Znrbig","year":"2012","journal-title":"Diabetes"},{"key":"B15","doi-asserted-by":"publisher","first-page":"1042","DOI":"10.1016\/j.cmet.2021.04.004","article-title":"KIM-1 mediates fatty acid uptake by renal tubular cells to promote progressive diabetic kidney disease","volume":"33","author":"Mori","year":"2021","journal-title":"Cell Metab"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1007\/7651_2017_87","article-title":"High-throughput proteomic analysis of fresh-frozen biopsy tissue samples using pressure cycling technology coupled with SWATH mass spectrometry","volume":"1788","author":"Zhu","year":"2018","journal-title":"Methods Mol Biol"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.0c00381","article-title":"PulseDIA: Data-independent acquisition mass spectrometry using multi-injection pulsed gas-phase fractionation","volume":"20","author":"Cai","year":"2021","journal-title":"J Proteome Res"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.9b00790","article-title":"Accelerated lysis and p roteolytic digestion of biopsy-level fresh-frozen and FFPE tissue samples using pressure cycling technology","volume":"19","author":"Gao","year":"2020","journal-title":"J Proteome Res"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1002\/1878-0261.12570","article-title":"High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification","volume":"13","author":"Zhu","year":"2019","journal-title":"Mol Oncol"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1002\/1878-0261.13198","article-title":"Stratification of follicular thyroid tumours using data-independent acquisition proteomics and a comprehensive thyroid tissue spectral library","volume":"16","author":"Sun","year":"2022","journal-title":"Mol Oncol"},{"key":"B21","doi-asserted-by":"publisher","first-page":"5","DOI":"10.6026\/97320630002005","article-title":"Mfuzz: a software package for soft clustering of microarray data","volume":"2","author":"Kumar","year":"2007","journal-title":"Bioinformation"},{"key":"B22","doi-asserted-by":"publisher","first-page":"1523","DOI":"10.1038\/s41467-019-09234-6","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Zhou","year":"2019","journal-title":"Nat Commun"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1131","article-title":"STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets","volume":"47","author":"Szklarczyk","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkj109","article-title":"BioGRID: a general repository for interaction datasets","volume":"34","author":"Stark","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4083","article-title":"OmniPath: guidelines and gateway for literature-curated signaling pathway resources","volume":"13","author":"Turei","year":"2016","journal-title":"Nat Methods"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4083","article-title":"A scored human protein-protein interaction network to catalyze genomic interpretation","volume":"14","author":"Li","year":"2017","journal-title":"Nat Methods"},{"key":"B27","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1186\/1471-2105-4-2","article-title":"An automated method for finding molecular complexes in large protein interaction networks","volume":"4","author":"Bader","year":"2003","journal-title":"BMC Bioinf"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1369\/0022155412465073","article-title":"Diabetic nephropathy and extracellular matrix","volume":"60","author":"Kolset","year":"2012","journal-title":"J Histochem Cytochem"},{"key":"B29","doi-asserted-by":"publisher","first-page":"11857","DOI":"10.3390\/ijms222111857","article-title":"Recent advances in diabetic kidney diseases: From kidney injury to kidney fibrosis","volume":"22","author":"Hung","year":"2021","journal-title":". Int J Mol Sci"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1007\/s10719-021-09989-5","article-title":"Organelle stress and glycation in kidney disease","volume":"38","author":"Inagi","year":"2021","journal-title":"Glycoconj J"},{"key":"B31","doi-asserted-by":"publisher","first-page":"106153","DOI":"10.1016\/j.biocel.2021.106153","article-title":"A comprehensive insight into autophagy and its potential signaling pathways as a therapeutic target in podocyte injury","volume":"143","author":"Teh","year":"2022","journal-title":"Int J Biochem Cell Biol"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1172\/JCI135536","article-title":"p53\/microRNA-214\/ULK1 axis impairs renal tubular autophagy in diabetic kidney disease","volume":"130","author":"Ma","year":"2020","journal-title":"J Clin Invest"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.21999","article-title":"Low neighbor of Brca1 gene expression predicts poor clinical outcome and resistance of sunitinib in clear cell renal cell carcinoma","volume":"8","author":"Xiao","year":"2017","journal-title":"Oncotarget"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1159\/000439185","article-title":"MicroRNA-34a suppresses autophagy in tubular epithelial cells in acute kidney injury","volume":"42","author":"Liu","year":"2015","journal-title":"Am J Nephro"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.23026","article-title":"MicroRNA-19a acts as a prognostic marker and promotes prostate cancer progression via inhibiting\u2002VPS37A\u2002expression","volume":"9","author":"Fu","year":"2017","journal-title":"Oncotarget"},{"key":"B36","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/j.bbrc.2017.05.102","article-title":"Autophagy upregulation ameliorates cell injury in sequestosome 1 knockout podocytes in vitro","volume":"490","author":"Li","year":"2017","journal-title":"Biochem Biophys Res Commun"}],"container-title":["Frontiers in Endocrinology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fendo.2022.995362\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,17]],"date-time":"2022-11-17T10:36:21Z","timestamp":1668681381000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fendo.2022.995362\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,17]]},"references-count":36,"alternative-id":["10.3389\/fendo.2022.995362"],"URL":"https:\/\/doi.org\/10.3389\/fendo.2022.995362","relation":{},"ISSN":["1664-2392"],"issn-type":[{"value":"1664-2392","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,17]]},"article-number":"995362"}}