Additional Titles

• Professor, Pathology and Immunology
• Professor, Pediatrics
• Director, Kidney Translational Research Center

Related Links

• Jain Lab

Mailing Address

In the News

• 2020 Translational Innovation Grant Awarded to Drs. Sanjay Jain and Tingting Li
• Sanjay Jain, with New Publication in Nature Communications, Awarded NIH HuBMAP Grant for 3D Molecular Atlas of Urinary System
• Sanjay Jain and Joseph Gaut, Co-authors of Newly Released Diagnostic Pathology: Kidney Diseases Book

Education

• Postdoctoral Fellow, Cancer, Neurodevelopment: Washington University School of Medicine, St. Louis, MO (2004)
• Residency, Anatomic Pathology: Washington University School of Medicine, St. Louis, MO (2001)
• MD: Northwestern University, Chicago, IL (1999)
• PhD, Integrated Biology: Northwestern University, Chicago, IL (1999)
• AB, Genetics: University of California-Berkeley, Berkeley, CA (1990)

Recognition

2018-2020
Steering Committee, Human Biomolecular Atlas Project (HuBMAP) (NIH – common fund)

2017-Present
Executive Committee, Kidney Precision Medicine Project (KPMP, NIH/NIDDK)
– Chair, Quality control Tissue Interrogation Sites (KPMP)
– Co-Chair, Pathology and Molecular Integration Committee (KPMP)

2017-2019
Chair, NIDDK/KMBD study section, Center for Scientific Review, NIH

2017-2019
Steering Committee, Kidney Precision Medicine Project (NIH/NIDDK)

2017-2018
American Society of Nephrology, Program Committee

2017
First Prize, British Medical Association book award in the Pathology category for Diagnostic Pathology: Kidney Diseases, 2nd edition, Editor Robert Colvin and Anthony Chang, Publisher- Elsevier Inc. 2015. ISBN 978-0-323-37707-2; contributed 9 chapters

2016-present
Steering Committee, ReBuilding a Kidney (RBK) project (NIH/NIDDK)

2014-2019
Standing member, KMBD study section, Center for Scientific Review, NIH

2014
Study Section Member, Center for Scientific Review, KMBD, NIH

2013-2016
Steering and Executive Committee, Genitourinary Development Molecular Anatomy Project (GUDMAP) (NIDDK)

2013
ASCI Inductee, American Society of Clinical Investigators
Steering and Executive Committee, GUDMAP, NIH-NIDDK

2012
Editorial Board Member, Journal of Biological Chemistry

2009
CDI Investigator Award, Children’s Discovery Institute

2008-2010
Board of Directors, Chair Communications and Website Committee, Renal Pathology Society

2008
Board of Directors, Chair, communications and publications committee, Renal Pathology Society

2007
Pirani Award, Renal Pathology Society
KUFA-RPS research award, Kidney and Urology Foundation

2004
K08 Award, NIH-NICHD

2003
NIH-LRP award (3 competitive renewals), NIH

2001
NRSA training grant fellowship (T32), Washington University School of Medicine, St. Louis

1995
Graduate Student Fellowship Award, International Society of Toxicology

1995
Molecular Biology Specialty Section Award, First Prize, International Society of Toxicology

1991
MSTP Fellowship, Northwestern University

1990
Graduation with Distinction in General Scholarship
High Honors for Undergraduate Thesis
Departmental Citation for Outstanding Accomplishment in Genetics, University of California, Berkeley, CA

1984
Open Merit Scholarship, Indian Ministry of Education, India

Research

Research Interests:  Single cell and spatial biology, molecular cartography, multiorgan interactions, AKI-CKD transition, aging, kidney development, ureter development, congenital anomalies of the kidney and urinary tract (CAKUT), genomics, neurodevelopment, GDNF, RET, branching morphogenesis, genetics, biobanking, translational research, biomarkers, regeneration, stem cells, bladder innervation. Kidney organoids and iPSC.

Funding: NIH/NIDDK, BJH Foundation

Research Description
My research is basic and translational in nature.  The fundamental premise is to better understand how kidneys and the lower urinary tract are organized at a cellular resolution and maintain homeostasis during aging and in kidney disease.  Understanding this will help design better strategies for early diagnosis, prognosis and intervention.  We employ the latest cutting-edge technologies to answer our research questions or build new technologies that will lead to discovery.  There are four guiding pillars or themes that have been the cornerstone of my lab’s accomplishments and contribution with an international impact over the last 20 years.

The first pillar is related to fundamental mechanisms of early kidney and nervous system development.  Here we used conceptual and technical innovations to engineer more than 15 different genetically engineered mice to elucidate how a single gene, the RET tyrosine kinase receptor, can cause both gain and loss of function phenotypes ranging from birth defects and cancer.  These in vivo mechanistic experiments led to the discovery that the differential phenotypes are due to differentially activated downstream signaling cascades through distinct phosphorylation sites in RET.  Interestingly, there were distinct phenotypes in the peripheral nervous system and the urinary system, many reminiscent of congenital nervous system and kidney diseases (published in Genes & Development, Development, JCI, J of Neuroscience, and JASN). Using sophisticated microscopy and mouse genetics we discovered the mechanism that ensures only one kidney emerges from each side and that the kidney and the bladder are connected with a single ureter at precise entry and exit points through a highly regulated interactive events of cell death between the migrating front of the nephric duct and the primitive bladder and result in abnormalities reminiscent of CAKUT in children (published in Development, JASN, Mach of Dev, Dev. Cell).

The second pillar of my research is to adopt and develop new technologies to aid in scientific discovery and translational research.  In the field of genomics, my lab was one of the first at WashU to use whole exome sequencing (before GTAC was established) translating our mouse studies to find pathogenic variants in children with CAKUT and FSGS.  We found an oligo genic model contributing to CAKUT in addition to traditional view of monogenic cause of renal defects. We implemented multiplexed PCR to individual FACS-sorted progenitors during branching morphogenesis and showed gene expression heterogeneity and transitions during collecting duct progenitor renewal and differentiation.  My lab developed single cell RNA-seq protocols that work on biopsy size tissue, an approach now of key importance in interrogating clinical samples at a single cell resolution.  We refined methods to apply dual snRNA-seq and chromatin accessibility studies on the same cell in clinical samples, protocols that are now in the workflow of KPMP recruitment sites.  Realizing that we need multiple modalities to understand a cells basic structure and biology, we developed methods that measure gene, RNA, protein and metabolite profiles on the same tissue block.  Recently, we are benchmarking various spatial transcriptomic technologies in human kidney biopsies and their reuse.  We developed methods to perform 3D light sheet fluorescence microscopy in human kidney and analytical methods that are practically nonexistent, to delineate relationships between nerves and key functional tissue units in the human kidney and across the life span in aging and disease.  These above contributions have international readership and have published in journals including Human Genetics, Kidney International, Pediatric Nephrology, Nature Communications (several) and Nature. 

The third pillar of my research is to inculcate team science into our research mission.  This was a risky change of direction for my lab in ~2016 from the traditional individual R01 type research.  Motivation here was to fill the critical gap in knowledge about molecular identities of the human kidney at a single cell and spatial resolution in healthy and disease states that is necessary to glean insights into mechanisms of how cellular program changes in injury and repair.  We wished to define cellular identities from multiple perspectives that incorporate morphology, multiple omics technologies and micro to macroscopic scales.  There were limited resources locally to carry these ambitious goal and we fostered collaborations nationally to gain diverse perspectives and expertise and were able to secure >20 million dollars of funding in cross institutional collaborative projects with industry and research institutions under three NIH initiatives – HuBMAP, KPMP and Pediatric Centers of Excellence in Nephrology (only 3 in the US).  These projects have been one of my best collaborations with multiple shared authorship papers, several of which I had the opportunity to lead, guiding trainees, junior and senior faculty under “one lab umbrella.”  Several high impact papers have resulted with many exceeding 150 citations already (Nature, Nature Comm, Nat Methods, Nat Cell Biol, Sci Trans Adv, JASN, Kid Int…).

The fourth pillar of my research is establishing the Kidney Translational Research Center (KTRC), partly supported by the Division of Nephrology.  My team serves the international community by providing them biospecimens and data on a wide variety of tissue and fluid samples without the need for them to consent or obtain regulatory approvals and thereby accelerates their research and minimizes burden to patients in participating in research studies.  Here my training as a pathologist and in basic research was critical.  The KTRC also helps researchers and trainees at all stages in designing experiments that are most optimal for generating data for grant or publications and continuously bringing in cutting edge technologies to human sample interrogations for investigators.  This infrastructure has led us to conduct critical R&D for several consortia and helped attain international recognition (HuBMAP, KPMP, RBK, GUDMAP, PCEN).  We also supply iPSC cell lines to researchers worldwide (the only organized resource for kidney cell lines in the world).  To date these efforts have supported more than 150 researchers worldwide and more than 100 publications including helping every research faculty in nephrology. 

Publications
(Research Articles and Book Chapters)

Research Articles

Debora L. Gisch, Michelle Brennan, Blue B. Lake, Jeannine Basta, … Sanjay Jain*, Michael Rauchman*, Michael T. Eadon*. The chromatin landscape of healthy and injured cell types in the human kidney. Nat Commun. 2024 Jan 10;15(1):433. * Co-corresponding authors

Zhang W, Li Y, Fung AA, Li Z, Jang H, Zha H, Chen X, Gao F, Wu JY, Sheng H, Yao J, Skowronska-Krawczyk D, Jain S, Shi L. Multi-molecular hyperspectral PRM-SRS microscopy. Nat Commun. 2024 Feb 21;15(1):1599.

Kalhor, K., Chen, C. J., Lee, H. S., Cai, M., Nafisi, M., Que, R., Palmer, C. R., Yuan, Y., Zhang, Y., Li, X., Song, J., Knoten, A., Lake, B. B., Gaut, J. P., Keene, C. D., Lein, E., Kharchenko, P. V., Chun, J., Jain, S., Fan, JB., Zhang, K. Mapping human tissues with highly multiplexed RNA in situ hybridization.  Nature communications, 2024,15(1), Article 2511. 

Border S, Ferreira RM, Lucarelli N, Manthey D, Kumar S, Paul A, Mimar S, Naglah A, Cheng YH, Barisoni L, Ray J, Strekalova Y, Rosenberg AZ, Tomaszewski JE, Hodgin JB; HuBMAP consortium; El-Achkar TM, Jain S*, Eadon MT, Sarder P. FUSION: A web-based application for in-depth exploration of multi-omics data with brightfield histology. Accepted in Principle in Nature Communications 2025. (*Co-corresponding author)

McLaughlin L, Zhang B, Sharma S, Knoten AL, Kaushal M, Purkerson JM, Huyck HL, Pryhuber GS, Gaut JP, Jain S. Three dimensional multiscalar neurovascular nephron connectivity map of the human kidney across the lifespan. Nat Commun. 2025Jun 3;16(1):5161.

Fung AA, Li Z, Boote C, Markov P, Jain S*, Shi L*. Label-Free Optical Biopsy Reveals Biomolecular and Morphological Features of Diabetic Kidney Tissue in 2D and 3D. Nat Commun. 2025 May 15;16(1):4509.   * Co-corresponding author

Blue B. Lake, Song Chen Masato Hoshi, Nongluk Plongthongkum, Diane Salamon, Amanda Knoten, Anitha Vijayan, Ramakrishna Venkatesh, Eric H. Kim, Derek Gao, Joseph Gaut, Kun Zhang, Sanjay Jain. A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys Nature Communications 2019 Jun 27;10(1):2832. PMID: 31249312 PMCID: PMC6597610

Hongtao Zhang, Mazdak Bagherie-Lachidan, Caroline Badouel, Leonie Enderle, Philippos Peidis, Rod Bremner, Sanjay Jain, Helen McNeill. FAT4 fine-tunes kidney development by regulating RET signaling. Dev Cell, 2019 Mar 25;48(6):780-792. PMID: 30853441

Brendon Lutnick, Brandon Ginley, Darshana Govind, Sean D. McGarry, Peter S.       LaViolette, Rabi Yacoub, Sanjay Jain, John E. Tomaszewski, Kuang-Yu Jen and Pinaki Sarder. An integrated iterative annotation technique for easing neural network training in medical image Analysis. Nature Machine Intelligence, 2019. (1):112-119.  PMID: 31187088.  PMCID: PMC6557463

Seifert ME, Gaut JP, Guo B, Jain S, Malone AF, Geraghty F, Della Manna D, Yang ES, Yi N, Brennan DC, Mannon RB.  WNT pathway signaling is associated with microvascular injury and predicts kidney transplant failure. Am J Transplant. 2019 Mar 27. PMID: 30916889 

S. Jain and Chen, F. Developmental pathology of congenital kidney and urinary tract anomalies. Clin Kidney J, 2018. 12(3):382-399. PMID: 31198539 PMCID: PMC6543978 

Lai Kuan Dionne, Kyuhwan Shim, Masato Hoshi, Tao Cheng, Jinzhi Wang, Veronique Marthiens, Amanda Knoten, Renata Basto, Sanjay Jain, and Moe R. Mahjoub.  Centrosome Amplification Disrupts Renal Development and Causes Cystic Dysplasia. Journal of Cell Biology 2018 217(7):2485-2501. PMID:29895697. PMCID:PMC6028550

Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ; Cancer Genome Atlas Research Network., Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039. PMID: 29625052.

Kudose S, Hoshi M, Jain S, Gaut JP. Renal Histopathologic Findings Associated With Severity of Clinical Acute Kidney Injury. Am J Surg Pathol. 2018 Mar 13. [Epub ahead of print] PubMed PMID: 29537990.

Hoshi M, Reginensi A, Joens M, Fitzpatrick J, McNeill H, Jain S.  Distinct RET and YAP signals regulate the fusion of Wolffian duct and cloaca through a novel reciprocal spatiotemporally controlled apoptosis. JASN, 2018. 29(3):775-783. PMID: 29326158. PMCID: PMC5827592.

Simon O, Yacoub R, Jain S, Tomaszewski JE, Sarder P. Multi-radial LBP Features as a Tool for Rapid Glomerular Detection and Assessment in Whole Slide Histopathology Images. Sci Rep. 2018 Feb 1;8(1):2032. PubMed PMID: 29391542; PubMed Central PMCID: PMC5795004.

Kim AH, Chung JJ, Akilesh S, Koziell A, Jain S, Hodgin JB, Miller MJ, Stappenbeck TS, Miner JH, Shaw AS. B cell derived IL-4 acts on podocytes to induce proteinuria and podocyte foot process effacement. JCI Insight. 2017;2(21). Kim AH, Chung JJ, Akilesh S, Koziell A, Jain S, Hodgin JB, Miller MJ, Stappenbeck TS, Miner JH, Shaw AS. B cell derived IL-4 acts on podocytes to induce proteinuria and podocyte foot process effacement. JCI Insight. 2017;2(21). PMID: 29093269 PMCID: PMC5752294.

Suleiman HY, Roth R, Jain S, Heuser JE, Shaw AS, Miner JH. Injury-induced actin cytoskeleton reorganization in podocytes revealed by super-resolution microscopy. JCI Insight. 2017;2(16). . PMID:28814668.

Jeremy K. Moore, Junjie Chen, Hua Pan, Joseph P. Gaut,  Sanjay Jain,  Samuel A. Wickline.  Quantification of vascular damage in acute kidney injury with fluorine magnetic resonance imaging and spectroscopy.  Magnetic Resonance in Medicine. 2017. 79;3144-3153. PMID: 29148253.

Andrew J. Shepherd, Aaron D. Mickle, Bryan A. Copits, Páll Karlsson, Suraj Kadunganattil, Judith P. Golden, Satya M. Tadinada, Madison Mack, Simon Haroutounian,  Annette D. de Kloet, Vijay K. Samineni, Manouela V. Valtcheva, Sanjay Jain, Pradipta R. Ray, Yuriy M. Usachev, Gregory Dussor, Justin L. Grobe, Brian S. Kim, Eric G. Krause, Theodore J. Price, Robert W. Gereau IV, and Durga P. Mohapatra.  Angiotensin II triggers peripheral macrophage-to-sensory neuron redox crosstalk to elicit pain. J. Neurosci. 2018 38 (32) 7032-7057. PMID: 29976627.

Gaut JP, Jain S, Pfeifer JD, Vigh-Conrad KA, Corliss M, Sharma MK, Heusel JW, Cottrell CE.  Routine Use of Clinical Exome-Based Next Generation Sequencing for Evaluation of Patients with Thrombotic Microangiopathies. Modern Pathology. 2017 Jul 28. doi: 10.1038/modpathol.2017.90. [Epub ahead of print]. PMID:28752844.

Oxburgh L, Carroll TJ, Cleaver O, Gossett DR, Hoshizaki DK, Hubbell JA, Humphreys BD, Jain S, Jensen J, Kaplan DL, Kesselman C, Ketchum CJ, Little MH, McMahon AP, Shankland SJ, Spence JR, Valerius MT, Wertheim JA, Wessely O, Zheng Y, Drummond IA. (Re)Building a Kidney. J J Am Soc Nephrol. 2017. PMID:28096308. PMCID: “In Process”

Wilfert, A. B., K. R. Chao, M. Kaushal, S. Jain, S. Zollner, D. R. Adams and D. F. Conrad. Genome-wide significance testing of variation from single case exomes. Nat Genet advance online publication. 2016. Dec; 48(12):1455-1461. PMID:27776118. 

Kramann R, Goettsch C, Wongboonsin J, Iwata H, Schneider RK, Kuppe C, Kaesler N, Chang-Panesso M, Machado FG, Gratwohl S, Madhurima K, Hutcheson JD, Jain S, Aikawa E, Humphreys BD. Adventitial MSC-like cells are progenitors of vascular smooth muscle cells and drive vascular calcification in chronic kidney disease. Cell Stem Cell. 2016. Nov 3;19(5):628-642.  PMID: 27618218 

Emily Ma, Joel Vetter, Laura Bliss, H. Henry Lai, Indira U. Mysorekar, Sanjay Jain.  A multiplexed analysis approach identifies new association of inflammatory proteins in patients with overactive bladder.  Am J Physiol Gastrointest Renal Physiol. 2016:Jul 1;311(1):F28-34. PMID: 27029431.

Lai HH, Vetter J, Jain S, Andriole GL. Systemic Non-Urologic Symptoms in Patients with Overactive Bladder. J Urol. 2016 Mar 17. 2016. Jul 1;311(1):F28-34. PMID: 26997309. PMCID: “In Process”

Yu, Haiyang, Artomov, Mykyta, Brähler, Sebastian, Stander, M. Christine, 

Shamsan, Ghaidan, Sampson, Matthew G., White, J. Michael, Kretzler, Matthias,

Miner, Jeffrey H., Jain, Sanjay, Winkler, Cheryl A., Mitra, Robi D., Kopp, Jeffrey B., Daly, Mark J. and Shaw, Andrey S.  A role for genetic susceptibility in sporadic focal segmental glomerulosclerosis. The Journal of Clinical Investigation 2016.126:1067-1078. PMID: 26927868.

Mwangi SM, Peng S, Nezami BG, Thorn N, Farris AB 3rd, Jain S, Laroui H, Merlin D, Anania FA, Srinivasan S.Glial Cell Line-Derived Neurotrophic Factor Protects Against High Fat Diet-Induced Hepatic Steatosis by Suppressing Hepatic PPAR-gamma Expression. Am J Physiol Gastrointest Liver Physiol. 2016. Jan 15;310(2):G103-16. PMID:26564715.

Hoshi M, Wang J, Jain S and Mahjoub MR.  Imaging centrosomes and cilia in the mouse kidney.  Methods Cell Biol. 2015;127:1-17

Antoine Reginensi, Masato Hoshi, Sami Kamel Boualia, Maxime Bouchard, Sanjay Jain, and Helen McNeill.  Yap and Taz are Required for Ret-Dependent Urinary Tract Morphogenesis.  Development, 2015.142(15):2696-2703.  PMID: 26243870. PMCID: PMC4529030

Vijayan A, Li T, Dusso A, Jain S and Coyne D. Relationship of 1,25 dihydroxy Vitamin D Levels to Clinical Outcomes in Critically Ill Patients with Acute Kidney Injury. Nephrology & Therapeutics, 2015, 5(1):1000190 (open access).

Book Chapters

Jain S. (2014) Kidney Development and Related Anomalies. In: Linda M. McManus, Richard N. Mitchell, editors. Pathobiology of Human Disease. San Diego: Elsevier; 2014. p. 2701-2715. 

Following 9 chapters in Diagnostic Pathology: Kidney Diseases, 3rd edition, Editor Robert Colvin and Anthony Chang, Publisher- Elsevier Inc. 2019. IISBN 978-0-323-66108-9

*First Prize, British Medical Association book award in the Pathology category (2015 2nd edition)

1.Jain S. Normal Kidney Development, 36-45.

2.Jain S. Overview and Classification of Genetic Diseases of the Glomerulus, 350-351

3.Jain S. Overview of Congenital Anomalies of the Kidney and Urinary Tract, 828-831

4.Jain S. Dysplasia, Hypoplasia and Agenesis, 832-837

5.Jain S. Ectopia, Malrotation, Duplication, Fusion, Supernumerary Kidney, 840-843

6.Jain S. Introduction to Impediments to Urine Flow, 914-917

7.Jain S. Reflux Nephropathy, 918-921 

8.Jain S. Obstructive Nephropathy, 922-925 

9.Jain S. Diagnostic Genetics of Kidney Diseases, 1098-1101

PhD Thesis (1999): Characterization of a subset of bHLH-PAS superfamily of transcription factors.  (Ph.D., Northwestern University).