{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T05:05:01Z","timestamp":1789880701705,"version":"4.0.1"},"posted":{"date-parts":[[2026,9,16]]},"group-title":"Developmental Biology","reference-count":50,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"National Institutes of Health","award":["DK125577"],"award-info":[{"award-number":["DK125577"]}]},{"name":"National Institutes of Health","award":["DK131052"],"award-info":[{"award-number":["DK131052"]}]},{"name":"National Institutes of Health","award":["DK127634"],"award-info":[{"award-number":["DK127634"]}]},{"name":"National Institutes of Health","award":["DK120847"],"award-info":[{"award-number":["DK120847"]}]},{"name":"National Institutes of Health","award":["DK120842"],"award-info":[{"award-number":["DK120842"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Introduction<\/jats:title>\n                  <jats:p>\n                    HNF4A is required for proximal tubule maturation during kidney development, but its role in maintaining proximal tubule identity in the adult kidney has not been defined. Following acute kidney injury,\n                    <jats:italic>Hnf4a<\/jats:italic>\n                    expression is rapidly suppressed in proximal tubule cells, coinciding with loss of mature epithelial features and activation of injury-associated transcriptional programs. It remains unknown whether HNF4A loss is sufficient to drive injury-associated transcriptional changes.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>\n                    We conditionally deleted\n                    <jats:italic>Hnf4a<\/jats:italic>\n                    in mature proximal tubules using\n                    <jats:italic>Slc34a1Cre<\/jats:italic>\n                    in mice and analyzed the consequences of\n                    <jats:italic>Hnf4a<\/jats:italic>\n                    loss in adult kidneys. To identify genes directly regulated by HNF4A, we performed proximal tubule-specific transcriptional profiling together with genome-wide mapping of HNF4A binding sites using CUT&amp;RUN.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    In\n                    <jats:italic>Hnf4a<\/jats:italic>\n                    mutant kidneys, HNF4A protein initially persisted in proximal tubules but was progressively lost from convoluted proximal tubule cells. Loss of\n                    <jats:italic>Hnf4a<\/jats:italic>\n                    resulted in downregulation of proximal tubule-specific transport and metabolic genes, accompanied by reactivation of developmental and injury-associated genes. CUT&amp;RUN analysis revealed that HNF4A directly regulates genes predominantly involved in solute transport and metabolic processes.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>\n                    These findings identify HNF4A as a key regulator of proximal tubule identity and homeostasis in the adult mouse kidney. Genetic loss of\n                    <jats:italic>Hnf4a<\/jats:italic>\n                    in mature proximal tubules leads to loss of mature proximal tubule gene expression and activation of injury-associated transcriptional programs, implicating\n                    <jats:italic>Hnf4a<\/jats:italic>\n                    suppression as a potential contributor to maladaptive repair after kidney injury.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Translational Statement<\/jats:title>\n                  <jats:p>Proximal tubule dysfunction is a major contributor to acute kidney injury and progression to chronic kidney disease. Here, we show that HNF4A is required to maintain mature proximal tubule identity in the adult kidney. Loss of HNF4A suppresses transport and metabolic programs and induces transcriptional features associated with injured, failed-repair, and immature proximal tubule states, even in the absence of exogenous kidney injury. These findings suggest that suppression of HNF4A-dependent transcriptional programs may contribute to maladaptive proximal tubule remodeling after injury and identify HNF4A-regulated pathways as potential mechanisms for preserving differentiated proximal tubule function.<\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.09.10.750757","type":"posted-content","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T14:10:20Z","timestamp":1789567820000},"source":"Crossref","is-referenced-by-count":0,"title":["HNF4A maintains proximal tubule identity and limits injury-associated cell states in the adult mouse kidney"],"prefix":"10.64898","author":[{"given":"Fariba","family":"Nosrati","sequence":"first","affiliation":[{"name":"Feinberg Cardiovascular & Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA"},{"name":"Division of Nephrology and Hypertension, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zeinab","family":"Dehghani-Ghobadi","sequence":"additional","affiliation":[{"name":"Feinberg Cardiovascular & Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA"},{"name":"Division of Nephrology and Hypertension, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eunah","family":"Chung","sequence":"additional","affiliation":[{"name":"Feinberg Cardiovascular & Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA"},{"name":"Division of Nephrology and Hypertension, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Ahn","sequence":"additional","affiliation":[{"name":"Division of Biomedical Informatics, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, OH, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8599-1808","authenticated-orcid":false,"given":"Hee-Woong","family":"Lim","sequence":"additional","affiliation":[{"name":"Division of Biomedical Informatics, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, OH, USA"},{"name":"Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4190-4386","authenticated-orcid":false,"given":"Joo-Seop","family":"Park","sequence":"additional","affiliation":[{"name":"Feinberg Cardiovascular & Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA"},{"name":"Division of Nephrology and Hypertension, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026091921351405000_2026.09.10.750757v1.1","doi-asserted-by":"publisher","DOI":"10.1007\/s00467-013-2581-x"},{"key":"2026091921351405000_2026.09.10.750757v1.2","doi-asserted-by":"crossref","unstructured":"Lee JW , Chou CL , Knepper MA . Deep Sequencing in Microdissected Renal Tubules Identifies Nephron Segment-Specific Transcriptomes. J Am Soc Nephrol 2015.","DOI":"10.1681\/ASN.2014111067"},{"key":"2026091921351405000_2026.09.10.750757v1.3","doi-asserted-by":"publisher","DOI":"10.1681\/ASN.2020101406"},{"key":"2026091921351405000_2026.09.10.750757v1.4","doi-asserted-by":"publisher","DOI":"10.1152\/ajprenal.00164.2016"},{"key":"2026091921351405000_2026.09.10.750757v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/bs.ctdb.2015.10.010"},{"key":"2026091921351405000_2026.09.10.750757v1.6","doi-asserted-by":"publisher","DOI":"10.1681\/ASN.2019020163"},{"key":"2026091921351405000_2026.09.10.750757v1.7","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2005477117"},{"key":"2026091921351405000_2026.09.10.750757v1.8","doi-asserted-by":"crossref","unstructured":"Gerhardt LMS , Liu J , Koppitch K , et al. Single-nuclear transcriptomics reveals diversity of proximal tubule cell states in a dynamic response to acute kidney injury. Proceedings of the National Academy of Sciences 2021; 118.","DOI":"10.1073\/pnas.2026684118"},{"key":"2026091921351405000_2026.09.10.750757v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-05769-3"},{"key":"2026091921351405000_2026.09.10.750757v1.10","doi-asserted-by":"publisher","DOI":"10.1172\/JCI45161"},{"key":"2026091921351405000_2026.09.10.750757v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/nm.2144"},{"key":"2026091921351405000_2026.09.10.750757v1.12","doi-asserted-by":"publisher","DOI":"10.1038\/nrneph.2015.3"},{"key":"2026091921351405000_2026.09.10.750757v1.13","doi-asserted-by":"publisher","DOI":"10.1681\/ASN.2015060647"},{"key":"2026091921351405000_2026.09.10.750757v1.14","doi-asserted-by":"crossref","unstructured":"Chen L , Luo S , Dupre A , et al. The nuclear receptor HNF4 drives a brush border gene program conserved across murine intestine, kidney, and embryonic yolk sac. Nat Commun 2021; 12: 2886.","DOI":"10.1038\/s41467-021-22761-5"},{"key":"2026091921351405000_2026.09.10.750757v1.15","doi-asserted-by":"crossref","unstructured":"Marable SS , Chung E , Adam M , et al. Hnf4a deletion in the mouse kidney phenocopies Fanconi renotubular syndrome. JCI Insight 2018; 3.","DOI":"10.1172\/jci.insight.97497"},{"key":"2026091921351405000_2026.09.10.750757v1.16","doi-asserted-by":"crossref","unstructured":"Marable SS , Chung E , Park JS . Hnf4a is required for the development of Cdh6-expressing progenitors into proximal tubules in the mouse kidney. J Am Soc Nephrol 2020.","DOI":"10.1101\/2020.02.16.951731"},{"key":"2026091921351405000_2026.09.10.750757v1.17","doi-asserted-by":"crossref","first-page":"1672","DOI":"10.1681\/ASN.0000000000000197","article-title":"Elucidating the Proximal Tubule HNF4A Gene Regulatory Network in Human Kidney Organoids","volume":"34","year":"2023","journal-title":"J Am Soc Nephrol"},{"key":"2026091921351405000_2026.09.10.750757v1.18","doi-asserted-by":"crossref","unstructured":"Chung E , Nosrati F , Adam M , et al. Proximal Tubule Cells Contribute to the Thin Descending Limb of the Loop of Henle during Mouse Kidney Development. J Am Soc Nephrol 2025.","DOI":"10.1101\/2025.01.14.633065"},{"key":"2026091921351405000_2026.09.10.750757v1.19","doi-asserted-by":"publisher","DOI":"10.1242\/dev.006155"},{"key":"2026091921351405000_2026.09.10.750757v1.20","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2008.05.020"},{"key":"2026091921351405000_2026.09.10.750757v1.21","doi-asserted-by":"publisher","DOI":"10.1002\/dvg.20334"},{"key":"2026091921351405000_2026.09.10.750757v1.22","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1016\/j.kint.2023.09.013","article-title":"Hepatocyte nuclear factor 4alpha mediated quinolinate phosphoribosylltransferase (QPRT) expression in the kidney facilitates resilience against acute kidney injury","volume":"104","year":"2023","journal-title":"Kidney Int"},{"key":"2026091921351405000_2026.09.10.750757v1.23","doi-asserted-by":"publisher","DOI":"10.1172\/JCI125519"},{"key":"2026091921351405000_2026.09.10.750757v1.24","doi-asserted-by":"crossref","unstructured":"Balzer MS , Doke T , Yang YW , et al. Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration. Nat Commun 2022; 13: 4018.","DOI":"10.1038\/s41467-022-31772-9"},{"key":"2026091921351405000_2026.09.10.750757v1.25","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1016\/j.ajpath.2025.01.011","article-title":"Injured Proximal Tubular Epithelial Cells Lose Hepatocyte Nuclear Factor 4alpha Expression Crucial for Brush Border Formation and Transport","volume":"195","year":"2025","journal-title":"Am J Pathol"},{"key":"2026091921351405000_2026.09.10.750757v1.26","doi-asserted-by":"publisher","DOI":"10.1681\/ASN.2020010052"},{"key":"2026091921351405000_2026.09.10.750757v1.27","doi-asserted-by":"crossref","unstructured":"Telang AC , Ference-Salo JT , McElliott MC , et al. Sustained alterations in proximal tubule gene expression in primary culture associate with HNF4A loss. Sci Rep 2024; 14: 22927.","DOI":"10.1038\/s41598-024-73861-3"},{"key":"2026091921351405000_2026.09.10.750757v1.28","doi-asserted-by":"crossref","unstructured":"Jiang G , Lu X , Cao R , et al. HNF4A P2 isoform alleviates kidney fibrosis by inhibiting dedifferentiation of proximal tubular cells through JAG1\/NOTCH signaling. Cell Mol Biol Lett 2026; 31.","DOI":"10.1186\/s11658-025-00845-0"},{"key":"2026091921351405000_2026.09.10.750757v1.29","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.1016\/j.celrep.2016.12.087","article-title":"Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo","volume":"18","year":"2017","journal-title":"Cell reports"},{"key":"2026091921351405000_2026.09.10.750757v1.30","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.21.4.1393-1403.2001"},{"key":"2026091921351405000_2026.09.10.750757v1.31","doi-asserted-by":"crossref","unstructured":"Dehghani-Ghobadi Z , Chung E , Sayed M , et al. Constitutive YAP activation in distal nephron segments disrupts epithelial identity and nephron patterning. JCI Insight 2026.","DOI":"10.64898\/2025.12.10.693519"},{"key":"2026091921351405000_2026.09.10.750757v1.32","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2018.015"},{"key":"2026091921351405000_2026.09.10.750757v1.33","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"2026091921351405000_2026.09.10.750757v1.34","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt656"},{"key":"2026091921351405000_2026.09.10.750757v1.35","doi-asserted-by":"crossref","unstructured":"Love MI , Huber W , Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014; 15: 550.","DOI":"10.1186\/s13059-014-0550-8"},{"key":"2026091921351405000_2026.09.10.750757v1.36","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw377"},{"key":"2026091921351405000_2026.09.10.750757v1.37","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2010.05.004"},{"key":"2026091921351405000_2026.09.10.750757v1.38","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1310653110"},{"key":"2026091921351405000_2026.09.10.750757v1.39","doi-asserted-by":"crossref","unstructured":"Skene PJ , Henikoff S . An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 2017; 6.","DOI":"10.7554\/eLife.21856"},{"key":"2026091921351405000_2026.09.10.750757v1.40","doi-asserted-by":"publisher","DOI":"10.1681\/ASN.0000000000000057"},{"key":"2026091921351405000_2026.09.10.750757v1.41","doi-asserted-by":"crossref","unstructured":"Muto Y , Wilson PC , Ledru N , et al. Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney. Nat Commun 2021; 12: 2190.","DOI":"10.1038\/s41467-021-22368-w"},{"key":"2026091921351405000_2026.09.10.750757v1.42","doi-asserted-by":"crossref","unstructured":"Rudman-Melnick V , Adam M , Stowers K , et al. Single-cell sequencing dissects the transcriptional identity of activated fibroblasts and identifies novel persistent distal tubular injury patterns in kidney fibrosis. Sci Rep 2024; 14: 439.","DOI":"10.1038\/s41598-023-50195-0"},{"key":"2026091921351405000_2026.09.10.750757v1.43","doi-asserted-by":"crossref","unstructured":"Deacon P , Concodora CW , Chung E , et al. \u03b2-catenin regulates the formation of multiple nephron segments in the mouse kidney. Scientific Reports 2019; 9: 15915.","DOI":"10.1038\/s41598-019-52255-w"},{"key":"2026091921351405000_2026.09.10.750757v1.44","doi-asserted-by":"publisher","DOI":"10.1038\/nm.3762"},{"key":"2026091921351405000_2026.09.10.750757v1.45","doi-asserted-by":"crossref","unstructured":"Ledru N , Wilson PC , Muto Y , et al. Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing. Nat Commun 2024; 15: 1291.","DOI":"10.1038\/s41467-024-45706-0"},{"key":"2026091921351405000_2026.09.10.750757v1.46","doi-asserted-by":"publisher","DOI":"10.1152\/ajprenal.00076.2024"},{"key":"2026091921351405000_2026.09.10.750757v1.47","doi-asserted-by":"crossref","unstructured":"Wen Y , Su E , Xu L , et al. Analysis of the human kidney transcriptome and plasma proteome identifies markers of proximal tubule maladaptation to injury. Sci Transl Med 2023; 15: eade7287.","DOI":"10.1126\/scitranslmed.ade7287"},{"key":"2026091921351405000_2026.09.10.750757v1.48","doi-asserted-by":"crossref","unstructured":"Aggarwal S , Wang Z , Rincon Fernandez Pacheco D , et al. SOX9 switch links regeneration to fibrosis at the single-cell level in mammalian kidneys. Science 2024; 383: eadd6371.","DOI":"10.1126\/science.add6371"},{"key":"2026091921351405000_2026.09.10.750757v1.49","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/j.celrep.2015.12.071","article-title":"Sox9-Positive Progenitor Cells Play a Key Role in Renal Tubule Epithelial Regeneration in Mice","volume":"14","year":"2016","journal-title":"Cell reports"},{"key":"2026091921351405000_2026.09.10.750757v1.50","doi-asserted-by":"crossref","unstructured":"Kumar S , Liu J , Pang P , et al. Sox9 Activation Highlights a Cellular Pathway of Renal Repair in the Acutely Injured Mammalian Kidney. Cell reports 2015.","DOI":"10.1016\/j.celrep.2015.07.034"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.09.10.750757","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T04:35:55Z","timestamp":1789878955000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.09.10.750757"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,16]]},"references-count":50,"URL":"https:\/\/doi.org\/10.64898\/2026.09.10.750757","relation":{},"subject":[],"published":{"date-parts":[[2026,9,16]]},"subtype":"preprint"}}