1
|
Haug S, Muthusamy S, Li Y, Stewart G, Li X, Treppner M, Köttgen A, Akilesh S. Multi-omic analysis of human kidney tissue identified medulla-specific gene expression patterns. Kidney Int 2024; 105:293-311. [PMID: 37995909 PMCID: PMC10843743 DOI: 10.1016/j.kint.2023.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 09/21/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
Abstract
The kidney medulla is a specialized region with important homeostatic functions. It has been implicated in genetic and developmental disorders along with ischemic and drug-induced injuries. Despite its role in kidney function and disease, the medulla's baseline gene expression and epigenomic signatures have not been well described in the adult human kidney. Here we generated and analyzed gene expression (RNA-seq), chromatin accessibility (ATAC-seq), chromatin conformation (Hi-C) and spatial transcriptomic data from the adult human kidney cortex and medulla. Tissue samples were obtained from macroscopically dissected cortex and medulla of tumor-adjacent normal material in nephrectomy specimens from five male patients. We used these carefully annotated specimens to reassign incorrectly labeled samples in the larger public Genotype-Tissue Expression (GTEx) Project, and to extract meaningful medullary gene expression signatures. Using integrated analysis of gene expression, chromatin accessibility and conformation profiles, we found insights into medulla development and function and then validated this by spatial transcriptomics and immunohistochemistry. Thus, our datasets provide a valuable resource for functional annotation of variants from genome-wide association studies and are freely accessible through an epigenome browser portal.
Collapse
Affiliation(s)
- Stefan Haug
- Institute of Genetic Epidemiology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Selvaraj Muthusamy
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Yong Li
- Institute of Genetic Epidemiology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Galen Stewart
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Xianwu Li
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Martin Treppner
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Medical Center-University of Freiburg, Freiburg, Germany.
| | - Shreeram Akilesh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA.
| |
Collapse
|
2
|
Yeung C, Jones-Isaac K, Lindberg K, Yang J, Bain J, Ruiz M, Koenig G, Koenig P, Countryman S, Himmelfarb J, Kelly E. Development of a Kidney Microphysiological System Hardware Platform for Microgravity Studies. Res Sq 2023:rs.3.rs-3750478. [PMID: 38196654 PMCID: PMC10775353 DOI: 10.21203/rs.3.rs-3750478/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Study of the physiological effects of microgravity on humans is limited to non-invasive testing of astronauts. Microphysiological models of human organs recapitulate many functions and disease states. Here we describe the development of an advanced, semi-autonomous hardware platform to support kidney microphysiological model experiments in microgravity.
Collapse
|
3
|
Kelly E, Lindberg K, Jones-Isaac K, Yang J, Bain J, Wang L, MacDonald J, Bammler T, Calamia J, Thummel K, Yeung C, Countryman S, Koenig P, Himmelfarb J. Impact of microgravity on a three-dimensional microphysiologic culture of the human kidney proximal tubule epithelium: cell response to serum and vitamin D. Res Sq 2023:rs.3.rs-3778779. [PMID: 38196580 PMCID: PMC10775397 DOI: 10.21203/rs.3.rs-3778779/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The microgravity environment aboard the International Space Station (ISS) provides a unique stressor that can help understand underlying cellular and molecular drivers of pathological changes observed in astronauts with the ultimate goals of developing strategies to enable long-term spaceflight and better treatment of diseases on Earth. We used this unique environment to evaluate the effects of microgravity on kidney proximal tubule epithelial cell (PTEC) response to serum exposure and vitamin D biotransformation capacity. To test if microgravity alters the pathologic response of the proximal tubule to serum exposure, we treated PTECs cultured in a microphysiological system (PT-MPS) with human serum and measured biomarkers of toxicity and inflammation (KIM-1 and IL-6) and conducted global transcriptomics via RNAseq on cells undergoing flight (microgravity) and respective controls (ground). We also treated 3D cultured PTECs with 25(OH)D3 (vitamin D) and monitored vitamin D metabolite formation, conducted global transcriptomics via RNAseq, and evaluated transcript expression of CYP27B1, CYP24A1, or CYP3A5 in PTECs undergoing flight (microgravity) and respective ground controls. We demonstrated that microgravity neither altered PTEC metabolism of vitamin D nor did it induce a unique response of PTECs to human serum, suggesting that these fundamental biochemical pathways in the kidney proximal tubule are not significantly altered by short-term exposure to microgravity. Given the prospect of extended spaceflight, more study is needed to determine if these responses are consistent with extended (> 6 month) exposure to microgravity.
Collapse
|
4
|
Azushima K, Kovalik JP, Yamaji T, Ching J, Chng TW, Guo J, Liu JJ, Nguyen M, Sakban RB, George SE, Tan PH, Lim SC, Gurley SB, Coffman TM. Abnormal lactate metabolism is linked to albuminuria and kidney injury in diabetic nephropathy. Kidney Int 2023; 104:1135-1149. [PMID: 37843477 DOI: 10.1016/j.kint.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 10/17/2023]
Abstract
Diabetic nephropathy (DN) is characterized by abnormal kidney energy metabolism, but its causes and contributions to DN pathogenesis are not clear. To examine this issue, we carried out targeted metabolomics profiling in a mouse model of DN that develops kidney disease resembling the human disorder. We found a distinct profile of increased lactate levels and impaired energy metabolism in kidneys of mice with DN, and treatment with an angiotensin-receptor blocker (ARB) reduced albuminuria, attenuated kidney pathology and corrected many metabolic abnormalities, restoring levels of lactate toward normal while increasing kidney ATP content. We also found enhanced expression of lactate dehydrogenase isoforms in DN. Expression of both the LdhA and LdhB isoforms were significantly increased in kidneys of mice, and treatment with ARB significantly reduced their expression. Single-cell sequencing studies showed specific up-regulation of LdhA in the proximal tubule, along with enhanced expression of oxidative stress pathways. There was a significant correlation between albuminuria and lactate in mice, and also in a Southeast Asian patient cohort consisting of individuals with type 2 diabetes and impaired kidney function. In the individuals with diabetes, this association was independent of ARB and angiotensin-converting enzyme inhibitor use. Furthermore, urinary lactate levels predicted the clinical outcomes of doubling of serum creatinine or development of kidney failure, and there was a significant correlation between urinary lactate levels and biomarkers of tubular injury and epithelial stress. Thus, we suggest that kidney metabolic disruptions leading to enhanced generation of lactate contribute to the pathogenesis of DN and increased urinary lactate levels may be a potential biomarker for risk of kidney disease progression.
Collapse
Affiliation(s)
- Kengo Azushima
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore; Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Japan Society for the Promotion of Science, Tokyo, Japan
| | - Jean-Paul Kovalik
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore
| | - Takahiro Yamaji
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore; Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Jianhong Ching
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore
| | - Tze Wei Chng
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Jing Guo
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore
| | - Jian-Jun Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore
| | - Mien Nguyen
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore
| | - Rashidah Binte Sakban
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore
| | - Simi E George
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore
| | - Puay Hoon Tan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Su Chi Lim
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore; Diabetes Centre, Khoo Teck Puat Hospital, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Lee Kong Chian School of Medicine, Singapore; Nanyang Technological University, Singapore
| | - Susan B Gurley
- Department of Medicine, Division of Nephrology and Hypertension, Keck School of Medicine of USC, Los Angeles, California, USA
| | - Thomas M Coffman
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore; Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.
| |
Collapse
|
5
|
Chen M, Gu X. Emerging roles of proximal tubular endocytosis in renal fibrosis. Front Cell Dev Biol 2023; 11:1235716. [PMID: 37799275 PMCID: PMC10547866 DOI: 10.3389/fcell.2023.1235716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023] Open
Abstract
Endocytosis is a crucial component of many pathological conditions. The proximal tubules are responsible for reabsorbing the majority of filtered water and glucose, as well as all the proteins filtered through the glomerular barrier via endocytosis, indicating an essential role in kidney diseases. Genetic mutations or acquired insults could affect the proximal tubule endocytosis processes, by disturbing or overstressing the endolysosomal system and subsequently activating different pathways, orchestrating renal fibrosis. This paper will review recent studies on proximal tubular endocytosis affected by other diseases and factors. Endocytosis plays a vital role in the development of renal fibrosis, and renal fibrosis could also, in turn, affect tubular endocytosis.
Collapse
Affiliation(s)
- Min Chen
- Department of Nephrology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiangchen Gu
- Department of Nephrology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Medicine, Shanghai Hospital of Civil Aviation Administration of China, Shanghai, China
| |
Collapse
|
6
|
Molitoris BA, Wagner MC. Is Albumin Toxic to the Kidney?: It Depends. Clin J Am Soc Nephrol 2023; 18:1222-1224. [PMID: 36942999 PMCID: PMC10564333 DOI: 10.2215/cjn.0000000000000153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023]
Affiliation(s)
- Bruce A Molitoris
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana
| | | |
Collapse
|
7
|
Cao X, Wang J, Zhang T, Liu Z, Liu L, Chen Y, Li Z, Zhao Y, Yu Q, Liu T, Nie J, Niu Y, Chen Y, Yang L, Zhang L. Chromatin accessibility dynamics dictate renal tubular epithelial cell response to injury. Nat Commun 2022; 13:7322. [PMID: 36443310 DOI: 10.1038/s41467-022-34854-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
Renal tubular epithelial cells (TECs) can initiate an adaptive response to completely recover from mild acute kidney injury (AKI), whereas severe injury often leads to persistence of maladaptive repair and progression to kidney fibrosis. Through profiling of active DNA regulatory elements by ATAC-seq, we reveal widespread, dynamic changes in the chromatin accessibility of TECs after ischemia-reperfusion injury. We show that injury-specific domains of regulatory chromatin become accessible prior to gene activation, creating poised chromatin states to activate the consequent gene expression program and injury response. We further identify RXRα as a key transcription factor in promoting adaptive repair. Activation of RXRα by bexarotene, an FDA-approved RXRα agonist, restores the chromatin state and gene expression program to protect TECs against severe kidney injury. Together, our findings elucidate a chromatin-mediated mechanism underlying differential responses of TECs to varying injuries and identify RXRα as a therapeutic target of acute kidney injury.
Collapse
|
8
|
O'Neill WC. Serum Protein-Induced Tubular Injury. J Am Soc Nephrol 2022; 33:1627. [PMID: 35906090 PMCID: PMC9342633 DOI: 10.1681/asn.2022050568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
|
9
|
Lidberg K, Himmelfarb J, Kelly E, Akilesh S. Authors' Reply: Serum Protein-induced Tubular Injury. J Am Soc Nephrol 2022; 33:1627-1628. [PMID: 35906085 PMCID: PMC9342649 DOI: 10.1681/asn.2022060657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Kevin Lidberg
- University of Washington Ringgold Standard Institution—Pharmaceutics, Seattle, Washington
| | - Jonathan Himmelfarb
- Division of Nephrology, University of Washington—Medicine, Seattle, Washington
| | - Edward Kelly
- University of Washington Ringgold Standard Institution—Pharmaceutics, Seattle, Washington
| | - Shreeram Akilesh
- University of Washington—Laboratory Medicine and Pathology, Seattle, Washington
| |
Collapse
|