{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T20:48:20Z","timestamp":1786135700883,"version":"build-2736575974"},"reference-count":108,"publisher":"Ovid Technologies (Wolters Kluwer Health)","issue":"3","content-domain":{"domain":["lww.com","ovid.com"],"crossmark-restriction":true},"short-container-title":["JASN"],"published-print":{"date-parts":[[2023,3]]},"abstract":"<jats:sec>\n                    <jats:title>Significance Statement<\/jats:title>\n                    <jats:p>\n                      Mutations in hepatocyte nuclear factor-1 \u03b2 (\n                      <jats:italic toggle=\"yes\">HNF1B<\/jats:italic>\n                      ) are the most common monogenic causes of congenital renal malformations. HNF1B is necessary to directly reprogram fibroblasts to induced renal tubule epithelial cells (iRECs) and, as we demonstrate, can induce ectopic pronephric tissue in\n                      <jats:italic toggle=\"yes\">Xenopus<\/jats:italic>\n                      ectodermal organoids. Using these two systems, we analyzed the effect of\n                      <jats:italic toggle=\"yes\">HNF1B<\/jats:italic>\n                      mutations found in patients with cystic dysplastic kidney disease. We found cross-species conserved targets of HNF1B, identified transcripts that are differentially regulated by the patient-specific mutant protein, and functionally validated novel HNF1B targets\n                      <jats:italic toggle=\"yes\">in vivo<\/jats:italic>\n                      . These results highlight evolutionarily conserved transcriptional mechanisms and provide insights into the genetic circuitry of nephrogenesis.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Hepatocyte nuclear factor-1 \u03b2 (HNF1B) is an essential transcription factor during embryogenesis. Mutations in\n                      <jats:italic toggle=\"yes\">HNF1B<\/jats:italic>\n                      are the most common monogenic causes of congenital cystic dysplastic renal malformations. The direct functional consequences of mutations in\n                      <jats:italic toggle=\"yes\">HNF1B<\/jats:italic>\n                      on its transcriptional activity are unknown.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Direct reprogramming of mouse fibroblasts to induced renal tubular epithelial cells was conducted both with wild-type\n                      <jats:italic toggle=\"yes\">HNF1B<\/jats:italic>\n                      and with patient mutations.\n                      <jats:italic toggle=\"yes\">HNF1B<\/jats:italic>\n                      was expressed in\n                      <jats:italic toggle=\"yes\">Xenopus<\/jats:italic>\n                      ectodermal explants. Transcriptomic analysis by bulk RNA-Seq identified conserved targets with differentially regulated expression by the wild-type or R295C mutant. CRISPR\/Cas9 genome editing in\n                      <jats:italic toggle=\"yes\">Xenopus<\/jats:italic>\n                      embryos evaluated transcriptional targets\n                      <jats:italic toggle=\"yes\">in vivo<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      HNF1B is essential for reprogramming mouse fibroblasts to induced renal tubular epithelial cells and induces development of ectopic renal organoids from pluripotent\n                      <jats:italic toggle=\"yes\">Xenopus<\/jats:italic>\n                      cells. The mutation R295C retains reprogramming and inductive capacity but alters the expression of specific sets of downstream target genes instead of diminishing overall transcriptional activity of HNF1B. Surprisingly, targets associated with polycystic kidney disease were less affected than genes affected in congenital renal anomalies. Cross-species\u2013conserved transcriptional targets were dysregulated in\n                      <jats:italic toggle=\"yes\">hnf1b<\/jats:italic>\n                      CRISPR-depleted\n                      <jats:italic toggle=\"yes\">Xenopus<\/jats:italic>\n                      embryos, confirming their dependence on\n                      <jats:italic toggle=\"yes\">hnf1b<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>HNF1B activates an evolutionarily conserved program of target genes that disease-causing mutations selectively disrupt. These findings provide insights into the renal transcriptional network that controls nephrogenesis.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1681\/asn.2022010076","type":"journal-article","created":{"date-parts":[[2022,12,15]],"date-time":"2022-12-15T15:55:10Z","timestamp":1671119710000},"page":"412-432","update-policy":"https:\/\/doi.org\/10.1097\/lww.0000000000001000","source":"Crossref","is-referenced-by-count":19,"title":["HNF1B Alters an Evolutionarily Conserved Nephrogenic Program of Target Genes"],"prefix":"10.1681","volume":"34","author":[{"given":"Kelli","family":"Grand","sequence":"first","affiliation":[{"name":"Institute of Anatomy, University of Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martine","family":"Stoltz","sequence":"additional","affiliation":[{"name":"The University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ludovica","family":"Rizzo","sequence":"additional","affiliation":[{"name":"Institute of Anatomy, University of Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth","family":"R\u00f6ck","sequence":"additional","affiliation":[{"name":"Institute of Anatomy, University of Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael M.","family":"Kaminski","sequence":"additional","affiliation":[{"name":"Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany"},{"name":"Department of Nephrology and Medical Intensive Care, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany"},{"name":"Berlin Institute of Health, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela","family":"Salinas","sequence":"additional","affiliation":[{"name":"Berlin Institute of Health, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maike","family":"Getwan","sequence":"additional","affiliation":[{"name":"Institute of Anatomy, University of Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Naert","sequence":"additional","affiliation":[{"name":"Institute of Anatomy, University of Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roman","family":"Pichler","sequence":"additional","affiliation":[{"name":"The University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soeren S.","family":"Lienkamp","sequence":"additional","affiliation":[{"name":"Institute of Anatomy, University of Zurich, Zurich, Switzerland"},{"name":"The University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"276","published-online":{"date-parts":[[2022,12,15]]},"reference":[{"issue":"1","key":"B1-20250823","doi-asserted-by":"crossref","first-page":"29","DOI":"10.3339\/jkspn.2016.20.1.29","article-title":"The prenatal and postnatal incidence of congenital anomalies of the kidneys and urinary tract (CAKUT) detected by ultrasound","volume":"20","author":"Choi","year":"2016","journal-title":"Child Kidney Dis."},{"issue":"9","key":"B2-20250823","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1136\/archdischild-2015-309784","article-title":"The outcome of antenatal ultrasound diagnosed anomalies of the kidney and urinary tract in a large Danish birth cohort","volume":"101","author":"Andr\u00e9s-Jensen","year":"2016","journal-title":"Arch Dis Child."},{"issue":"15","key":"B3-20250823","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1002\/bdr2.1065","article-title":"Congenital unilateral renal agenesis: prevalence, prenatal diagnosis, associated anomalies. Data from two birth-defect registries","volume":"109","author":"Laurichesse Delmas","year":"2017","journal-title":"Birth Defects Res."},{"issue":"8","key":"B4-20250823","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1007\/s00467-003-1158-5","article-title":"Chronic renal insufficiency in children: The 2001 Annual Report of the NAPRTCS","volume":"18","author":"Seikaly","year":"2003","journal-title":"Pediatr Nephrol."},{"issue":"9","key":"B5-20250823","doi-asserted-by":"crossref","first-page":"2348","DOI":"10.1681\/ASN.2017121265","article-title":"Whole-exome sequencing identifies causative mutations in families with congenital anomalies of the kidney and urinary tract","volume":"29","author":"van der Ven","year":"2018","journal-title":"J Am Soc Nephrol."},{"issue":"6","key":"B6-20250823","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.2215\/CJN.06810909","article-title":"Spectrum of HNF1B mutations in a large cohort of patients who harbor renal diseases","volume":"5","author":"Heidet","year":"2010","journal-title":"Clin J Am Soc Nephrol."},{"issue":"6","key":"B7-20250823","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1007\/s00467-010-1454-9","article-title":"HNF1B alterations associated with congenital anomalies of the kidney and urinary tract","volume":"25","author":"Nakayama","year":"2010","journal-title":"Pediatr Nephrol."},{"issue":"2","key":"B8-20250823","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1681\/ASN.2005101040","article-title":"Renal phenotypes related to hepatocyte nuclear factor-1\u03b2 (TCF2) mutations in a pediatric cohort","volume":"17","author":"Ulinski","year":"2006","journal-title":"J Am Soc Nephrol."},{"issue":"7","key":"B9-20250823","doi-asserted-by":"crossref","first-page":"e469","DOI":"10.1097\/MD.0000000000000469","article-title":"A novel mutation of the HNF1B gene associated with hypoplastic glomerulocystic kidney disease and neonatal renal failure: a case report and mutation update","volume":"94","author":"Alvelos","year":"2015","journal-title":"Medicine (Baltimore)."},{"issue":"1","key":"B10-20250823","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1186\/s13148-018-0530-z","article-title":"Genome-wide methylomic analysis in individuals with HNF1B intragenic mutation and 17q12 microdeletion","volume":"1097","author":"Clissold","year":"2018","journal-title":"Clin Epigenetics."},{"issue":"1","key":"B11-20250823","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1086\/316945","article-title":"Mutations in the hepatocyte nuclear factor-1\u03b2 gene are associated with familial hypoplastic glomerulocystic kidney disease","volume":"68","author":"Bingham","year":"2001","journal-title":"Am J Hum Genet."},{"issue":"6","key":"B12-20250823","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1007\/s00467-011-1826-9","article-title":"HNF1B and PAX2 mutations are a common cause of renal hypodysplasia in the CKiD cohort","volume":"26","author":"Thomas","year":"2011","journal-title":"Pediatr Nephrol."},{"issue":"10","key":"B13-20250823","doi-asserted-by":"crossref","first-page":"2864","DOI":"10.1681\/ASN.2006030277","article-title":"Prevalence of mutations in renal developmental genes in children with renal hypodysplasia: Results of the ESCAPE study","volume":"17","author":"Weber","year":"2006","journal-title":"J Am Soc Nephrol."},{"issue":"8","key":"B14-20250823","doi-asserted-by":"crossref","first-page":"3941","DOI":"10.1210\/en.2004-0281","article-title":"Selective deletion of the Hnf1\u03b2 (MODY5) gene in \u03b2-cells leads to altered gene expression and defective insulin release","volume":"145","author":"Wang","year":"2004","journal-title":"Endocrinology."},{"issue":"4","key":"B15-20250823","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1038\/ng1297-384","article-title":"Mutation in hepatocyte nuclear factor-1 beta gene (TCF2) associated with MODY","volume":"17","author":"Horikawa","year":"1997","journal-title":"Nat Genet."},{"issue":"5","key":"B16-20250823","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1016\/j.jhep.2011.09.022","article-title":"Development of the bile ducts: essentials for the clinical hepatologist","volume":"56","author":"Strazzabosco","year":"2012","journal-title":"J Hepatol."},{"issue":"8","key":"B17-20250823","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1038\/labinvest.2008.56","article-title":"Expression of specific hepatocyte and cholangiocyte transcription factors in human liver disease and embryonic development","volume":"88","author":"Limaye","year":"2008","journal-title":"Lab Invest."},{"issue":"2","key":"B18-20250823","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1038\/nrneph.2014.232","article-title":"HNF1B-associated renal and extra-renal disease\u2014an expanding clinical spectrum","volume":"11","author":"Clissold","year":"2015","journal-title":"Nat Rev Nephrol."},{"issue":"12","key":"B19-20250823","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1056\/NEJMoa1908753","article-title":"Causal genetic variants in stillbirth","volume":"383","author":"Stanley","year":"2020","journal-title":"N Engl J Med."},{"issue":"7809","key":"B20-20250823","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/s41586-020-2308-7","article-title":"The mutational constraint spectrum quantified from variation in 141,456 humans","volume":"581","author":"Karczewski","year":"2020","journal-title":"Nature."},{"issue":"11","key":"B21-20250823","doi-asserted-by":"crossref","first-page":"10578","DOI":"10.1074\/jbc.M414121200","article-title":"Role of the hepatocyte nuclear factor-1\u03b2 (HNF-1\u03b2) C-terminal domain in Pkhd1 (ARPKD) gene transcription and renal cystogenesis","volume":"280","author":"Hiesberger","year":"2005","journal-title":"J Biol Chem."},{"issue":"24","key":"B22-20250823","doi-asserted-by":"crossref","first-page":"3139","DOI":"10.1093\/hmg\/ddh338","article-title":"HNF1 \u03b2\/TCF2 mutations impair transactivation potential through altered co-regulator recruitment","volume":"13","author":"Barbacci","year":"2004","journal-title":"Hum Mol Genet."},{"issue":"2","key":"B23-20250823","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1096\/fasebj.10.2.8641560","article-title":"Liver-enriched transcription factors and hepatocyte differentiation","volume":"10","author":"Cereghini","year":"1996","journal-title":"FASEB J."},{"issue":"3","key":"B24-20250823","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1681\/ASN.2013040337","article-title":"Mutations in PCBD1 cause hypomagnesemia and renal magnesium wasting","volume":"25","author":"Ferr\u00e8","year":"2014","journal-title":"J Am Soc Nephrol."},{"issue":"3","key":"B25-20250823","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/j.stemcr.2016.01.007","article-title":"Early developmental perturbations in a human stem cell model of MODY5\/HNF1B pancreatic hypoplasia","volume":"6","author":"Teo","year":"2016","journal-title":"Stem Cell Rep."},{"issue":"6","key":"B26-20250823","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1038\/s41388-019-1065-2","article-title":"HNF1B-mediated repression of SLUG is suppressed by EZH2 in aggressive prostate cancer","volume":"39","author":"Wang","year":"2020","journal-title":"Oncogene."},{"key":"B27-20250823","doi-asserted-by":"crossref","first-page":"14539","DOI":"10.1111\/jcmm.16081","article-title":"HNF1B inhibits cell proliferation via repression of SMAD6 expression in prostate cancer","volume":"24","author":"Lu","year":"2020","journal-title":"J Cell Mol Med."},{"issue":"1","key":"B28-20250823","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1016\/j.bbrc.2010.11.108","article-title":"HNF-1B specifically regulates the transcription of the \u03b3a-subunit of the Na+\/K+-ATPase","volume":"404","author":"Ferr\u00e8","year":"2011","journal-title":"Biochem Biophysical Res Commun."},{"issue":"43","key":"B29-20250823","doi-asserted-by":"crossref","first-page":"12071","DOI":"10.1021\/bi7010527","article-title":"Structural basis of disease-causing mutations in hepatocyte nuclear factor 1\u03b2","volume":"46","author":"Lu","year":"2007","journal-title":"Biochemistry."},{"issue":"5","key":"B30-20250823","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1002\/j.1460-2075.1993.tb05828.x","article-title":"The X-ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1\/HNF1 and implications for DNA binding","volume":"12","author":"Ceska","year":"1993","journal-title":"EMBO J."},{"issue":"8","key":"B31-20250823","doi-asserted-by":"crossref","first-page":"2033","DOI":"10.1097\/01.ASN.0000078808.70309.C4","article-title":"Distinct molecular and morphogenetic properties of mutations in the human HNF1\u03b2 gene that lead to defective kidney development","volume":"14","author":"Bohn","year":"2003","journal-title":"J Am Soc Nephrol."},{"issue":"5134","key":"B32-20250823","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1126\/science.8235591","article-title":"Neural induction by the secreted polypeptide noggin","volume":"262","author":"Lamb","year":"1993","journal-title":"Science."},{"issue":"5","key":"B33-20250823","doi-asserted-by":"crossref","first-page":"dmm047498","DOI":"10.1242\/dmm.047498","article-title":"Hnf1b haploinsufficiency differentially affects developmental target genes in a new renal cysts and diabetes mouse model","volume":"14","author":"Niborski","year":"2021","journal-title":"Dis Models Mech."},{"issue":"2","key":"B34-20250823","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1242\/dev.042226","article-title":"vHNF1 functions in distinct regulatory circuits to control ureteric bud branching and early nephrogenesis","volume":"137","author":"Lokmane","year":"2010","journal-title":"Development."},{"issue":"21","key":"B35-20250823","doi-asserted-by":"crossref","first-page":"4795","DOI":"10.1242\/dev.126.21.4795","article-title":"Variant hepatocyte nuclear factor 1 is required for visceral endoderm specification","volume":"126","author":"Barbacci","year":"1999","journal-title":"Development."},{"issue":"7","key":"B36-20250823","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1038\/ki.2011.225","article-title":"Diagnosis, management, and prognosis of HNF1B nephropathy in adulthood","volume":"80","author":"Faguer","year":"2011","journal-title":"Kidney Int."},{"issue":"4","key":"B37-20250823","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/ki.2015.28","article-title":"Autosomal dominant tubulointerstitial kidney disease: diagnosis, classification, and management\u2014a KDIGO consensus report","volume":"88","author":"Eckardt","year":"2015","journal-title":"Kidney Int."},{"issue":"5","key":"B38-20250823","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1681\/ASN.2008060633","article-title":"HNF1B mutations associate with hypomagnesemia and renal magnesium wasting","volume":"20","author":"Adalat","journal-title":"J Am Soc Nephrol."},{"issue":"12","key":"B39-20250823","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1038\/ncb3437","article-title":"Direct reprogramming of fibroblasts into renal tubular epithelial cells by defined transcription factors","volume":"18","author":"Kaminski","year":"2016","journal-title":"Nat Cell Biol."},{"issue":"13","key":"B40-20250823","doi-asserted-by":"crossref","first-page":"4407","DOI":"10.1016\/j.celrep.2019.11.066","article-title":"Molecular basis for autosomal-dominant renal fanconi syndrome caused by HNF4A","volume":"29","author":"Marchesin","year":"2019","journal-title":"Cell Rep."},{"issue":"2","key":"B41-20250823","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1111\/j.1440-169X.1993.00123.x","article-title":"Induction of pronephric tubules by activin and retinoic acid in presumptive ectoderm of Xenopus laevis. (RA\/kidney\/mesoderm induction\/Xenopus laevis)","volume":"35","author":"Moriya","year":"1993","journal-title":"Dev Growth Differ."},{"issue":"1","key":"B42-20250823","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1007\/s00441-017-2611-2","article-title":"Toolbox in a tadpole: Xenopus for kidney research","volume":"369","author":"Getwan","year":"2017","journal-title":"Cell Tissue Res."},{"key":"B43-20250823","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.semcdb.2016.02.002","article-title":"Using Xenopus to study genetic kidney diseases","volume":"51","author":"Lienkamp","year":"2016","journal-title":"Semin Cell Develop Biol."},{"issue":"12","key":"B44-20250823","doi-asserted-by":"crossref","first-page":"1382","DOI":"10.1038\/ng.2452","article-title":"Vertebrate kidney tubules elongate using a planar cell polarity-dependent, rosette-based mechanism of convergent extension","volume":"44","author":"Lienkamp","year":"2012","journal-title":"Nat Genet."},{"issue":"5","key":"B45-20250823","doi-asserted-by":"crossref","first-page":"R84","DOI":"10.1186\/gb-2008-9-5-r84","article-title":"Organization of the pronephric kidney revealed by large-scale gene expression mapping","volume":"9","author":"Raciti","year":"2008","journal-title":"Genome Biol."},{"issue":"2","key":"B46-20250823","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1016\/j.ydbio.2004.03.036","article-title":"Proximo-distal specialization of epithelial transport processes within the Xenopus pronephric kidney tubules","volume":"271","author":"Zhou","year":"2004","journal-title":"Develop Biol."},{"issue":"8","key":"B47-20250823","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1038\/ng.2681","article-title":"ANKS6 is a central component of a nephronophthisis module linking NEK8 to INVS and NPHP3","volume":"45","author":"Hoff","year":"2013","journal-title":"Nat Genet."},{"issue":"47","key":"B48-20250823","doi-asserted-by":"crossref","first-page":"20388","DOI":"10.1073\/pnas.1013070107","article-title":"Inversin relays Frizzled-8 signals to promote proximal pronephros development","volume":"107","author":"Lienkamp","year":"2010","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"12","key":"B50-20250823","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1002\/dvg.22720","article-title":"Simple and efficient CRISPR\/Cas9-mediated targeted mutagenesis in Xenopus tropicalis","volume":"51","author":"Nakayama","year":"2013","journal-title":"Genesis."},{"issue":"7","key":"B51-20250823","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat Methods."},{"issue":"1","key":"B52-20250823","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/s41592-018-0261-2","article-title":"U-Net: deep learning for cell counting, detection, and morphometry","volume":"16","author":"Falk","year":"2019","journal-title":"Nat Methods."},{"issue":"21","key":"B53-20250823","doi-asserted-by":"crossref","first-page":"dev199664","DOI":"10.1242\/dev.199664","article-title":"Deep learning is widely applicable to phenotyping embryonic development and disease","volume":"148","author":"Naert","year":"2021","journal-title":"Development."},{"issue":"11","key":"B54-20250823","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1038\/s41592-019-0554-0","article-title":"The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue","volume":"16","author":"Voigt","year":"2019","journal-title":"Nat Methods."},{"issue":"1","key":"B56-20250823","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.ydbio.2007.04.030","article-title":"Xenopus Bicaudal-C is required for the differentiation of the amphibian pronephros","volume":"307","author":"Tran","year":"2007","journal-title":"Develop Biol."},{"issue":"6","key":"B57-20250823","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1038\/nprot.2008.73","article-title":"Analyzing real-time PCR data by the comparative CT method","volume":"3","author":"Schmittgen","year":"2008","journal-title":"Nat Protoc."},{"issue":"W1","key":"B58-20250823","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"B59-20250823","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics."},{"issue":"7","key":"B60-20250823","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics."},{"issue":"12","key":"B61-20250823","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"issue":"1","key":"B63-20250823","doi-asserted-by":"crossref","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."},{"issue":"10","key":"B64-20250823","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"issue":"2","key":"B65-20250823","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/nmeth.3252","article-title":"Orchestrating high-throughput genomic analysis with Bioconductor","volume":"12","author":"Huber","year":"2015","journal-title":"Nat Methods."},{"issue":"5","key":"B66-20250823","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R Package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS."},{"issue":"18","key":"B69-20250823","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","article-title":"Complex heatmaps reveal patterns and correlations in multidimensional genomic data","volume":"32","author":"Gu","year":"2016","journal-title":"Bioinformatics."},{"issue":"1","key":"B70-20250823","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/1471-2105-12-35","article-title":"VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R","volume":"12","author":"Chen","year":"2011","journal-title":"BMC Bioinformatics."},{"issue":"43","key":"B73-20250823","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the Tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"J Open Source Softw."},{"issue":"12","key":"B74-20250823","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v021.i12","article-title":"Reshaping data with the reshape package","volume":"21","author":"Wickham","year":"2007","journal-title":"J Stat Softw."},{"issue":"8","key":"B75-20250823","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1093\/bioinformatics\/btw821","article-title":"Biomartr: genomic data retrieval with R","volume":"33","author":"Drost","year":"2017","journal-title":"Bioinformatics."},{"issue":"D1","key":"B76-20250823","doi-asserted-by":"crossref","first-page":"D861","DOI":"10.1093\/nar\/gkx936","article-title":"Xenbase: a genomic, epigenomic and transcriptomic model organism database","volume":"46","author":"Karimi","year":"2018","journal-title":"Nucleic Acids Res."},{"issue":"6","key":"B77-20250823","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/ng.2653","article-title":"The Genotype-Tissue Expression (GTEx) project","volume":"45","year":"2013","journal-title":"Nat Genet."},{"key":"B78-20250823","doi-asserted-by":"crossref","first-page":"e46255","DOI":"10.15252\/embr.201846255","article-title":"ChIP\u2010Atlas: a data\u2010mining suite powered by full integration of public ChIP\u2010seq data","volume":"19","author":"Oki","year":"2018","journal-title":"EMBO Rep."},{"issue":"4","key":"B79-20250823","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1002\/path.2440","article-title":"The Human Protein Atlas\u2014a tool for pathology","volume":"216","author":"Pont\u00e9n","year":"2008","journal-title":"J Pathol."},{"issue":"7","key":"B80-20250823","doi-asserted-by":"crossref","first-page":"510","DOI":"10.7326\/0003-4819-140-7-200404060-00009","article-title":"Clinical spectrum associated with hepatocyte nuclear factor-1\u03b2 mutations","volume":"140","author":"Bellann\u00e9-Chantelot","year":"2004","journal-title":"Ann Intern Med."},{"issue":"11","key":"B81-20250823","doi-asserted-by":"crossref","first-page":"3126","DOI":"10.2337\/diabetes.54.11.3126","article-title":"Large genomic rearrangements in the hepatocyte nuclear factor-1\u03b2 (TCF2) gene are the most frequent cause of maturity-onset diabetes of the young type 5","volume":"54","author":"Bellann\u00e9-Chantelot","year":"2005","journal-title":"Diabetes."},{"issue":"6","key":"B82-20250823","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1111\/febs.15088","article-title":"Identification and classification of epithelial cells in nephron segments by actin cytoskeleton patterns","volume":"287","author":"Kumaran","year":"2019","journal-title":"FEBS J."},{"issue":"4","key":"B83-20250823","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1242\/dev.086538","article-title":"HNF1B controls proximal-intermediate nephron segment identity in vertebrates by regulating Notch signalling components and Irx1\/2","volume":"140","author":"Heliot","year":"2013","journal-title":"Development."},{"issue":"2","key":"B84-20250823","doi-asserted-by":"crossref","first-page":"F478","DOI":"10.1152\/ajprenal.00174.2019","article-title":"Transcriptional profiling of the zebrafish proximal tubule","volume":"317","author":"Sander","year":"2019","journal-title":"Am J Physiol Renal Physiol."},{"issue":"24","key":"B85-20250823","doi-asserted-by":"crossref","first-page":"4704","DOI":"10.1242\/dev.154336","article-title":"HNF1B controls epithelial organization and cell polarity during ureteric bud branching and collecting duct morphogenesis","volume":"144","author":"Desgrange","year":"2017","journal-title":"Development."},{"issue":"3","key":"B86-20250823","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1002\/hep.25876","article-title":"HNF1B deficiency causes ciliary defects in human cholangiocytes","volume":"56","author":"Roelandt","year":"2012","journal-title":"Hepatology."},{"issue":"9","key":"B87-20250823","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1007\/s00431-011-1553-z","article-title":"Educational paper: ciliopathies","volume":"171","author":"Bergmann","year":"2012","journal-title":"Eur J Pediatr."},{"issue":"16","key":"B88-20250823","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1056\/NEJMra1010172","article-title":"Ciliopathies","volume":"364","author":"Hildebrandt","year":"2011","journal-title":"N Engl J Med."},{"issue":"7","key":"B89-20250823","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1038\/ng.3871","article-title":"Mutations in DZIP1L, which encodes a ciliary-transition-zone protein, cause autosomal recessive polycystic kidney disease","volume":"49","author":"Lu","year":"2017","journal-title":"Nat Genet."},{"key":"B90-20250823","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.semcdb.2018.08.013","article-title":"Impact of next generation sequencing on our understanding of CAKUT","volume":"91","author":"Nigam","year":"2019","journal-title":"Semin Cell Dev Biol."},{"issue":"6","key":"B91-20250823","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1016\/0092-8674(94)90137-6","article-title":"The polycystic kidney disease 1 gene encodes a 14 kb transcript and lies within a duplicated region on chromosome 16","volume":"77","year":"1994","journal-title":"Cell."},{"issue":"5266","key":"B92-20250823","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1126\/science.272.5266.1339","article-title":"PKD2, a gene for polycystic kidney disease that encodes an integral membrane protein","volume":"272","author":"Mochizuki","year":"1996","journal-title":"Science."},{"issue":"7409","key":"B93-20250823","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/nature11243","article-title":"A map of the cis-regulatory sequences in the mouse genome","volume":"488","author":"Shen","year":"2012","journal-title":"Nature."},{"issue":"3","key":"B94-20250823","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1681\/ASN.2006091057","article-title":"Anomalies of the TCF2 gene are the main cause of fetal bilateral hyperechogenic kidneys","volume":"18","author":"Decramer","year":"2007","journal-title":"J Am Soc Nephrol."},{"issue":"8","key":"B95-20250823","doi-asserted-by":"crossref","first-page":"2408","DOI":"10.1681\/ASN.2015060607","article-title":"Transcription factor hepatocyte nuclear factor-1\u03b2 regulates renal cholesterol metabolism","volume":"27","author":"Aboudehen","year":"2016","journal-title":"J Am Soc Nephrol."},{"issue":"5","key":"B96-20250823","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1016\/j.kint.2017.03.034","article-title":"Loss of transcriptional activation of the potassium channel Kir5.1 by HNF1\u03b2 drives autosomal dominant tubulointerstitial kidney disease","volume":"92","author":"Kompatscher","year":"2017","journal-title":"Kidney Int."},{"key":"B97-20250823","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1471-213X-11-5","article-title":"The nephrogenic potential of the transcription factors osr1, osr2, hnf1b, lhx1 and pax8 assessed in Xenopus animal caps","volume":"11","author":"Drews","year":"2011","journal-title":"BMC Dev Biol."},{"issue":"8","key":"B98-20250823","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1007\/s00467-018-3990-7","article-title":"New insights into the role of HNF-1\u03b2 in kidney (patho)physiology","volume":"34","author":"Ferr\u00e8","year":"2019","journal-title":"Pediatr Nephrol."},{"issue":"7","key":"B99-20250823","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1038\/sj.emboj.7600160","article-title":"A transcriptional network in polycystic kidney disease","volume":"23","author":"Gresh","year":"2004","journal-title":"EMBO J."},{"issue":"6","key":"B100-20250823","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1172\/JCI200420083","article-title":"Mutation of hepatocyte nuclear factor\u20131\u03b2 inhibits Pkhd1 gene expression and produces renal cysts in mice","volume":"113","author":"Hiesberger","year":"2004","journal-title":"J Clin Invest."},{"key":"B101-20250823","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1681\/ASN.2008050456","article-title":"Nephronophthisis: disease mechanisms of a ciliopathy","volume":"20","author":"Hildebrandt","journal-title":"J Am Soc Nephrol."},{"issue":"8","key":"B102-20250823","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1038\/ng2072","article-title":"Loss of GLIS2 causes nephronophthisis in humans and mice by increased apoptosis and fibrosis","volume":"39","author":"Attanasio","year":"2007","journal-title":"Nat Genet."},{"issue":"10","key":"B103-20250823","doi-asserted-by":"crossref","first-page":"1985","DOI":"10.1093\/hmg\/ddq077","article-title":"Uromodulin is expressed in renal primary cilia and UMOD mutations result in decreased ciliary uromodulin expression","volume":"19","author":"Zaucke","year":"2010","journal-title":"Hum Mol Genet."},{"issue":"10","key":"B104-20250823","doi-asserted-by":"crossref","first-page":"2508","DOI":"10.1097\/01.ASN.0000029587.47950.25","article-title":"The polycystic kidney disease proteins, polycystin-1, polycystin-2, polaris, and cystin, are co-localized in renal cilia","volume":"13","author":"Yoder","year":"2002","journal-title":"J Am Soc Nephrol."},{"issue":"5","key":"B105-20250823","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1016\/j.kint.2017.05.026","article-title":"A new epitope-tagged Pkhd1 allele sheds light on fibrocystin signaling","volume":"92","author":"Lea","year":"2017","journal-title":"Kidney Int."},{"issue":"10","key":"B106-20250823","doi-asserted-by":"crossref","first-page":"2887","DOI":"10.1681\/ASN.2016101095","article-title":"Hepatocyte nuclear factor-1\u03b2 regulates urinary concentration and response to hypertonicity","volume":"28","author":"Aboudehen","year":"2017","journal-title":"J Am Soc Nephrol."},{"issue":"11","key":"B107-20250823","doi-asserted-by":"crossref","first-page":"2306","DOI":"10.1158\/1541-7786.MCR-19-0461","article-title":"A hypoxia-inducible HIF1\u2013GAL3ST1-sulfatide Axis enhances ccRCC immune evasion via increased tumor cell\u2013platelet binding","volume":"17","author":"Robinson","year":"2019","journal-title":"Mol Cancer Res."},{"issue":"24","key":"B108-20250823","doi-asserted-by":"crossref","first-page":"9998","DOI":"10.1073\/pnas.1217775110","article-title":"Sulfatides are required for renal adaptation to chronic metabolic acidosis","volume":"110","author":"Stettner","year":"2013","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"6","key":"B109-20250823","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.1016\/S0002-9440(10)63249-X","article-title":"Hypoxia in renal disease with proteinuria and\/or glomerular hypertension","volume":"165","author":"Tanaka","year":"2004","journal-title":"Am J Pathol."},{"issue":"3","key":"B110-20250823","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1681\/ASN.2013030209","article-title":"Hypoxia-inducible factor-1\u03b1 causes renal cyst expansion through calcium-activated chloride secretion","volume":"25","author":"Buchholz","year":"2014","journal-title":"J Am Soc Nephrol."},{"issue":"4","key":"B111-20250823","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/j.ccr.2007.02.005","article-title":"Targeted inactivation of fh1 causes proliferative renal cyst development and activation of the hypoxia pathway","volume":"11","author":"Pollard","year":"2007","journal-title":"Cancer Cell."},{"issue":"5","key":"B112-20250823","doi-asserted-by":"crossref","first-page":"e63585","DOI":"10.1371\/journal.pone.0063585","article-title":"Hnf-1\u03b2 transcription factor is an early hif-1\u03b1-independent marker of epithelial hypoxia and controls renal repair","volume":"8","author":"Faguer","year":"2013","journal-title":"PLoS One."},{"issue":"9","key":"B113-20250823","doi-asserted-by":"crossref","first-page":"e23926","DOI":"10.1371\/journal.pone.0023926","article-title":"Transgenic expression of human LAMA5 suppresses murine Lama5 mRNA and laminin \u03b15 protein deposition","volume":"6","author":"Steenhard","year":"2011","journal-title":"PLoS One."},{"issue":"2","key":"B114-20250823","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1006\/dbio.1999.9546","article-title":"Defective glomerulogenesis in the absence of laminin \u03b15 demonstrates a developmental role for the kidney glomerular basement membrane","volume":"217","author":"Miner","year":"2000","journal-title":"Develop Biol."},{"issue":"10","key":"B115-20250823","doi-asserted-by":"crossref","first-page":"2493","DOI":"10.1681\/ASN.2018040437","article-title":"Mechanism of fibrosis in HNF1B-related autosomal dominant tubulointerstitial kidney disease","volume":"29","author":"Chan","year":"2018","journal-title":"J Am Soc Nephrol."}],"updated-by":[{"DOI":"10.1681\/asn.0000000000000472","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000}}],"container-title":["Journal of the American Society of Nephrology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.ovid.com\/10.1681\/ASN.2022010076","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T19:48:10Z","timestamp":1786132090000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.ovid.com\/10.1681\/ASN.2022010076"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,15]]},"references-count":108,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023]]}},"URL":"https:\/\/doi.org\/10.1681\/asn.2022010076","relation":{},"ISSN":["1046-6673","1533-3450"],"issn-type":[{"value":"1046-6673","type":"print"},{"value":"1533-3450","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,12,15]]},"assertion":[{"value":"2022-01-18","name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-11-09","name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}}]}}