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Hong Z, Xu Y, Wu J. Bisphenol a: Epigenetic effects on the male reproductive system and male offspring. Reprod Toxicol 2024:108656. [PMID: 39004383 DOI: 10.1016/j.reprotox.2024.108656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 06/23/2024] [Accepted: 07/03/2024] [Indexed: 07/16/2024]
Abstract
Bisphenol A (BPA) is a commonly used organic compound. Over the past decades, many studies have examined the mechanisms of BPA toxicity, with BPA-induced alterations in epigenetic modifications receiving considerable attention. Particularly in the male reproductive system, abnormal alterations in epigenetic markers can adversely affect reproductive function. Furthermore, these changes in epigenetic markers can be transmitted to offspring through the father. Here, we review the effects of BPA exposure on various epigenetic markers in the male reproductive system, including DNA methylation, histone modifications, and noncoding RNA, as well as associated changes in the male reproductive function. We also reviewed the effects of father's exposure to BPA on offspring epigenetic modification patterns.
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Affiliation(s)
- Zhilin Hong
- The center of clinical laboratory, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, PR China
| | - Yingpei Xu
- Department of Reproductive Medicine, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, Fujian, 364000, PR China
| | - Jinxiang Wu
- Department of reproductive medicine, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, PR China
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Yao S, Prates K, Freydenzon A, Assante G, McRae AF, Morris MJ, Youngson NA. Liver-specific deletion of de novo DNA methyltransferases protects against glucose intolerance in high-fat diet-fed male mice. FASEB J 2024; 38:e23690. [PMID: 38795327 DOI: 10.1096/fj.202301546rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 04/25/2024] [Accepted: 05/10/2024] [Indexed: 05/27/2024]
Abstract
Alterations to gene transcription and DNA methylation are a feature of many liver diseases including fatty liver disease and liver cancer. However, it is unclear whether the DNA methylation changes are a cause or a consequence of the transcriptional changes. It is even possible that the methylation changes are not required for the transcriptional changes. If DNA methylation is just a minor player in, or a consequence of liver transcriptional change, then future studies in this area should focus on other systems such as histone tail modifications. To interrogate the importance of de novo DNA methylation, we generated mice that are homozygous mutants for both Dnmt3a and Dnmt3b in post-natal liver. These mice are viable and fertile with normal sized livers. Males, but not females, showed increased adipose depots, yet paradoxically, improved glucose tolerance on both control diet and high-fat diets (HFD). Comparison of the transcriptome and methylome with RNA sequencing and whole-genome bisulfite sequencing in adult hepatocytes revealed that widespread loss of methylation in CpG-rich regions in the mutant did not induce loss of homeostatic transcriptional regulation. Similarly, extensive transcriptional changes induced by HFD did not require de novo DNA methylation. The improved metabolic phenotype of the Dnmt3a/3b mutant mice may be mediated through the dysregulation of a subset of glucose and fat metabolism genes which increase both glucose uptake and lipid export by the liver. However, further work is needed to confirm this.
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Affiliation(s)
- S Yao
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - K Prates
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Department of Biotechnology, Genetics, and Cellular Biology, State University of Maringá, Maringá, Brazil
| | - A Freydenzon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - G Assante
- Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - A F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - M J Morris
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - N A Youngson
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
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Fóthi Á, Liu H, Susztak K, Aranyi T. Improve-RRBS: a novel tool to correct the 3' trimming of reduced representation sequencing reads. BIOINFORMATICS ADVANCES 2024; 4:vbae076. [PMID: 38846137 PMCID: PMC11154647 DOI: 10.1093/bioadv/vbae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/18/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024]
Abstract
Motivation Reduced Representation Bisulfite Sequencing (RRBS) is a popular approach to determine DNA methylation of the CpG-rich regions of the genome. However, we observed that false positive differentially methylated sites (DMS) are also identified using the standard computational analysis. Results During RRBS library preparation the MspI digested DNA undergo end-repair by a cytosine at the 3' end of the fragments. After sequencing, Trim Galore cuts these end-repaired nucleotides. However, Trim Galore fails to detect end-repair when it overlaps with the 3' end of the sequencing reads. We found that these non-trimmed cytosines bias methylation calling, thus, can identify DMS erroneously. To circumvent this problem, we developed improve-RRBS, which efficiently identifies and hides these cytosines from methylation calling with a false positive rate of maximum 0.5%. To test improve-RRBS, we investigated four datasets from four laboratories and two different species. We found non-trimmed 3' cytosines in all datasets analyzed and as much as >50% of false positive DMS under certain conditions. By applying improve-RRBS, these DMS completely disappeared from all comparisons. Availability and implementation Improve-RRBS is a freely available python package https://pypi.org/project/iRRBS/ or https://github.com/fothia/improve-RRBS to be implemented in RRBS pipelines.
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Affiliation(s)
- Ábel Fóthi
- Institute of Molecular Life Sciences, Research Center for Natural Sciences, HUN-REN, Budapest 1117, Hungary
- Department of Molecular Biology, Semmelweis University, Budapest 1094, Hungary
| | - Hongbo Liu
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Tamas Aranyi
- Institute of Molecular Life Sciences, Research Center for Natural Sciences, HUN-REN, Budapest 1117, Hungary
- Department of Molecular Biology, Semmelweis University, Budapest 1094, Hungary
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Perwad F, Akwo EA, Vartanian N, Suva LJ, Friedman PA, Robinson-Cohen C. Multi-trait Analysis of GWAS for circulating FGF23 Identifies Novel Network Interactions Between HRG-HMGB1 and Cardiac Disease in CKD. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.04.24303051. [PMID: 38496593 PMCID: PMC10942519 DOI: 10.1101/2024.03.04.24303051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Background Genome-wide association studies (GWAS) have identified numerous genetic loci associated with mineral metabolism (MM) markers but have exclusively focused on single-trait analysis. In this study, we performed a multi-trait analysis of GWAS (MTAG) of MM, exploring overlapping genetic architecture between traits, to identify novel genetic associations for fibroblast growth factor 23 (FGF23). Methods We applied MTAG to genetic variants common to GWAS of 5 genetically correlated MM markers (calcium, phosphorus, FGF23, 25-hydroxyvitamin D (25(OH)D) and parathyroid hormone (PTH)) in European-ancestry subjects. We integrated information from UKBioBank GWAS for blood levels for phosphate, 25(OH)D and calcium (n=366,484), and CHARGE GWAS for PTH (n=29,155) and FGF23 (n=16,624). We then used functional genomics to model interactive and dynamic networks to identify novel associations between genetic traits and circulating FGF23. Results MTAG increased the effective sample size for all MM markers to n=50,325 for FGF23. After clumping, MTAG identified independent genome-wide significant SNPs for all traits, including 62 loci for FGF23. Many of these loci have not been previously reported in single-trait analyses. Through functional genomics we identified Histidine-rich glycoprotein (HRG) and high mobility group box 1(HMGB1) genes as master regulators of downstream canonical pathways associated with FGF23. HRG-HMGB1 network interactions were also highly enriched in left ventricular heart tissue of a cohort of deceased hemodialysis patients. Conclusion Our findings highlight the importance of MTAG analysis of MM markers to boost the number of genome-wide significant loci for FGF23 to identify novel genetic traits. Functional genomics revealed novel networks that inform unique cellular functions and identified HRG-HMGB1 as key master regulators of FGF23 and cardiovascular disease in CKD. Future studies will provide a deeper understanding of genetic signatures associated with FGF23 and its role in health and disease.
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Affiliation(s)
- Farzana Perwad
- University of California San Francisco, San Francisco, CA
| | - Elvis A Akwo
- Vanderbilt University Medical Center, Nashville, TN
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Pérez-Coria M, Vázquez-Rivera GE, Gómez-García EF, Mendoza-Carrera F. Sex differences in fetal kidney reprogramming: the case in the renin-angiotensin system. Pediatr Nephrol 2024; 39:645-653. [PMID: 37572115 DOI: 10.1007/s00467-023-06112-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/14/2023]
Abstract
During the early stages of the development of the living multiorgan systems, genome modifications other than sequence variation occur that guide cell differentiation and organogenesis. These modifications are known to operate as a fetal programming code during this period, and recent research indicates that there are some tissue-specific codes in organogenesis whose effects may persist after birth until adulthood. Consequently, the events that disrupt the pre-established epigenetic pattern could induce shifts in organ physiology, with implications on health from birth or later in adult life. Chronic kidney disease (CKD) is one of the main causes of mortality worldwide; its etiology is multifactorial, but diabetes, obesity, and hypertension are the main causes of CKD in adults, although there are other risk factors that are mainly associated with an individual's lifestyle. Recent studies suggest that fetal reprogramming in the developing kidney could be implicated in the susceptibility to kidney disease in both childhood and adulthood. Some epigenetic modifications, such as genome methylation status, dysregulation of miRNA, and histone coding alterations in genes related to the regulation of the renin-angiotensin axis, a common denominator in CKD, may have originated during fetal development. This review focuses on epigenetic changes during nephrogenesis and their repercussions on kidney health and disease. In addition, the focus is on the influence of environmental factors during pregnancy, such as maternal metabolic diseases and dietary and metabolic conditions, as well as some sex differences in fetal kidney reprogramming during which dysregulation of the renin-angiotensin system is involved.
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Affiliation(s)
- Mariana Pérez-Coria
- Molecular Medicine Division, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social, Sierra Mojada # 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Gloria Elizabeth Vázquez-Rivera
- Molecular Medicine Division, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social, Sierra Mojada # 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Erika Fabiola Gómez-García
- Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Tijuana, Baja California, Mexico
| | - Francisco Mendoza-Carrera
- Molecular Medicine Division, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social, Sierra Mojada # 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico.
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Liang X, Liu H, Hu H, Zhou J, Abedini A, Navarro AS, Klötzer KA, Susztak K. Genetic Studies Highlight the Role of TET2 and INO80 in DNA Damage Response and Kidney Disease Pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578718. [PMID: 38370682 PMCID: PMC10871294 DOI: 10.1101/2024.02.02.578718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Genome-wide association studies (GWAS) have identified over 800 loci associated with kidney function, yet the specific genes, variants, and pathways involved remain elusive. By integrating kidney function GWAS, human kidney expression and methylation quantitative trait analyses, we identified Ten-Eleven Translocation (TET) DNA demethylase 2: TET2 as a novel kidney disease risk gene. Utilizing single-cell chromatin accessibility and CRISPR-based genome editing, we highlight GWAS variants that influence TET2 expression in kidney proximal tubule cells. Experiments using kidney-tubule-specific Tet2 knockout mice indicated its protective role in cisplatin-induced acute kidney injury, as well as chronic kidney disease and fibrosis, induced by unilateral ureteral obstruction or adenine diet. Single-cell gene profiling of kidneys from Tet2 knockout mice and TET2- knock-down tubule cells revealed the altered expression of DNA damage repair and chromosome segregation genes, notably including INO80 , another kidney function GWAS target gene itself. Remarkably both TET2- null and INO80- null cells exhibited an increased accumulation of micronuclei after injury, leading to the activation of cytosolic nucleotide sensor cGAS-STING. Genetic deletion of cGAS or STING in kidney tubules or pharmacological inhibition of STING protected TET2 null mice from disease development. In conclusion, our findings highlight TET2 and INO80 as key genes in the pathogenesis of kidney diseases, indicating the importance of DNA damage repair mechanisms.
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Ogura Y, Mimura I. Epigenetic roles in clonal hematopoiesis and aging kidney-related chronic kidney disease. Front Cell Dev Biol 2023; 11:1281850. [PMID: 37928907 PMCID: PMC10623128 DOI: 10.3389/fcell.2023.1281850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023] Open
Abstract
Accumulation of somatic hematopoietic stem cell mutations with aging has been revealed by the recent genome-wide analysis. Clonal expansion, known as clonal hematopoiesis of indeterminate potential (CHIP), is a premalignant condition of hematological cancers. It is defined as the absence of definitive morphological evidence of a hematological neoplasm and occurrence of ≥2% of mutant allele fraction in the peripheral blood. In CHIP, the most frequently mutated genes are epigenetic regulators such as DNMT3A, TET2, and ASXL1. CHIP induces inflammation. CHIP is shown to be associated with not only hematological malignancy but also non-malignant disorders such as atherosclerosis, cardiovascular diseases and chronic liver disease. In addition, recent several large clinical trials have shown that CHIP is also the risk factor for developing chronic kidney disease (CKD). In this review article, we proposed novel findings about CHIP and CHIP related kidney disease based on the recent basic and clinical research. The possible mechanism of the kidney injury in CHIP is supposed to be due to the clonal expansion in both myeloid and lymphoid cell lines. In myeloid cell lines, the mutated macrophages increase the inflammatory cytokine level and induce chronic inflammation. It leads to epigenetic downregulation of kidney and macrophage klotho level. In lymphoid cell lines, CHIP might be related to monoclonal gammopathy of renal significance (MGRS). It describes any B cell or plasma cell clonal disorder that does not fulfill the criteria for cancer yet produces a nephrotoxic monoclonal immunoglobulin that leads to kidney injury or disease. MGRS causes M-protein related nephropathy frequently observed among aged CKD patients. It is important to consider the CHIP-related complications such as hematological malignancy, cardiovascular diseases and metabolic disorders in managing the elderly CKD patients. There are no established therapies for CHIP and CHIP-related CKD yet. However, recent studies have supported the development of effective CHIP therapies, such as blocking the expansion of aberrant HSCs and inhibiting chronic inflammation. In addition, drugs targeting the epigenetic regulation of Klotho in the kidney and macrophages might be therapeutic targets of CHIP in the kidney.
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Affiliation(s)
| | - Imari Mimura
- Division of Nephrology and Endocrinology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
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Zhang Z, Cao C, Zhou CL, Li X, Miao C, Shen L, Singla RK, Lu X. Identification of a novel 5-methylcytosine-related signature for prognostic prediction of kidney renal papillary cell carcinoma and a Putative target for drug repurposing. Transl Oncol 2023; 36:101741. [PMID: 37523897 PMCID: PMC10400932 DOI: 10.1016/j.tranon.2023.101741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 03/14/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Many studies have demonstrated the crucial roles of 5-methylcytosine (m5C) RNA methylation in cancer pathogenesis. METHODS Two datasets, including TCGA-KIRP and ICGC, and related clinical information were downloaded, where the expression of 13 m5C regulators was examined. We applied LASSO regression to construct a multi-m5C-regulator-based signature in the TCGA cohort, which was further validated using the ICGC cohort. Univariate and multivariate Cox regressions were applied to evaluate the independent prognostic value of our model. The differences in biological functions and immune characterizations between high and low-risk groups divided based on the risk scores were also investigated via multiple approaches, such as enrichment analyses, mutation mining, and immune scoring. Finally, the sensitivities of commonly used targeted drugs were tested, and the connectivity MAP (cMAP) was utilized to screen potentially effective molecules for patients in the high-risk group. Experimental validation was done following qPCR tests in Caki-2 and HK-2 cell lines. RESULTS 3 m5C regulators, including ALYREF, DNMT3B and YBX1, were involved in our model. Survival analysis revealed a worse prognosis for patients in the high-risk group. Cox regression results indicated our model's superior predictive performance compared to single-factor prognostic evaluation. Functional enrichment analyses indicated a higher mutation frequency and poorer tumor microenvironment of patients in the high-risk group. qPCR-based results revealed that ALYREF, DNMT3B, and YBX1 were significantly up-regulated in Caki-2 cell lines compared with HK-2 cell lines. Molecules like BRD-K72451865, Levosimendan, and BRD-K03515135 were advised by cMAP for patients in the high-risk group. CONCLUSION Our study presented a novel predictive model for KIRP prognosis. Furthermore, the results of our analysis provide new insights for investigating m5C events in KIRP pathogenesis.
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Affiliation(s)
- Zhen Zhang
- Department of Anesthesiology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China.
| | - Chunhua Cao
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang 441021, China; Institute of Oncology, Hubei University of Arts and Science, Xiangyang 441021, China
| | - Chun-Li Zhou
- Department of Anesthesiology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang 441021, China
| | - Xilong Li
- Department of Anesthesiology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China
| | - Changhong Miao
- Department of Anesthesiology, Cancer Hospital of Fudan University, Shanghai 200032, China
| | - Li Shen
- Department of Biomedical Engineering, Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Rajeev K Singla
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab-144411, India.
| | - Xihua Lu
- Department of Anesthesiology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China.
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Xiao X, Huo E, Guo C, Zhou X, Hu X, Dong C, Shi H, Dong Z, Wei Q. Hypermethylation suppresses microRNA-219a-2 to activate the ALDH1L2/GSH/PAI-1 pathway for fibronectin degradation in renal fibrosis. RESEARCH SQUARE 2023:rs.3.rs-2986934. [PMID: 37333081 PMCID: PMC10275039 DOI: 10.21203/rs.3.rs-2986934/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Epigenetic regulations, such as DNA methylation and microRNAs, play an important role in renal fibrosis. Here, we report the regulation of microRNA-219a-2 (mir-219a-2) by DNA methylation in fibrotic kidneys, unveiling the crosstalk between these epigenetic mechanisms. Through genome-wide DNA methylation analysis and pyro-sequencing, we detected the hypermethylation of mir-219a-2 in renal fibrosis induced by unilateral ureter obstruction (UUO) or renal ischemia/reperfusion, which was accompanied by a significant decrease in mir-219a-5p expression. Functionally, overexpression of mir-219a-2 enhanced fibronectin induction during hypoxia or TGF-β1 treatment of cultured renal cells. In mice, inhibition of mir-219a-5p suppressed fibronectin accumulation in UUO kidneys. ALDH1L2 was identified to be the direct target gene of mir-219a-5p in renal fibrosis. Mir-219a-5p suppressed ALDH1L2 expression in cultured renal cells, while inhibition of mir-219a-5p prevented the decrease of ALDH1L2 in UUO kidneys. Knockdown of ALDH1L2 enhanced PAI-1 induction during TGF-β1 treatment of renal cells, which was associated with fibronectin expression. In conclusion, the hypermethylation of mir-219a-2 in response to fibrotic stress attenuates mir-219a-5p expression and induces the up-regulation of its target gene ALDH1L2, which may reduce fibronectin deposition by suppressing PAI-1.
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Affiliation(s)
- Xiao Xiao
- Zhongnan Hospital of Wuhan University
| | | | - Chunyuan Guo
- Shanghai Skin Disease Hospital, Tongji University School of Medicine
| | | | - Xiaoru Hu
- The Second Xiangya Hospital at Central South University
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Liang X, Aranyi T, Zhou J, Guan Y, Hu H, Liu H, Susztak K. Tet2- and Tet3- Mediated Cytosine Hydroxymethylation in Six2 Progenitor Cells in Mice Is Critical for Nephron Progenitor Differentiation and Nephron Endowment. J Am Soc Nephrol 2023; 34:572-589. [PMID: 36522157 PMCID: PMC10103262 DOI: 10.1681/asn.2022040460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/10/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
SIGNIFICANCE STATEMENT Epigenetic changes have been proposed to mediate nephron endowment during development, a critical determinant of future renal disease development. Hydroxymethyl cytosine, an epigenetic modification important for gene regulation, is abundant in the human kidney, but its physiologic role and the role of DNA demethylase enzymes encoded by the Tet1 , Tet2 , or Tet3 , which mediate cytosine hydroxymethylation, are unclear. By genetically deleting Tet1 , Tet2 , or Tet3 in nephron progenitors in mice, the authors showed that combined Tet2 and Tet3 loss in nephron progenitors cause defective kidney development, leading to kidney failure and perinatal death. Tet2 and Tet3 deletion also caused an alteration in demethylation and expression of genes critical for nephron formation. These findings establish that Tet2- and Tet3 -mediated cytosine hydroxymethylation in nephron progenitors plays a critical role in nephron endowment. BACKGROUND Nephron endowment is a key determinant of hypertension and renal disease in later life. Epigenetic changes have been proposed to mediate fetal programming and nephron number. DNA cytosine methylation, which plays a critical role in gene regulation, is affected by proteins encoded by the ten-eleven translocation (TET) DNA demethylase gene family ( Tet1 , Tet2 , and Tet3 ), but the roles of TET proteins in kidney development and nephron endowment have not been characterized . METHODS To study whether epigenetic changes-specifically, active DNA hydroxymethylation mediated by Tet1 , Tet2 , and Tet3- are necessary for nephron progenitor differentiation and nephron endowment, we generated mice with deletion of Tet1 , Tet2 , or Tet3 in Six2-positive nephron progenitors cells (NPCs). We then performed unbiased omics profiling, including whole-genome bisulfite sequencing on isolated Six2-positive NPCs and single-cell RNA sequencing on kidneys from newborn mice. RESULTS We did not observe changes in kidney development or function in mice with NPC-specific deletion of Tet1 , Tet2 , Tet3 or Tet1 / Tet2 , or Tet1 / Tet3 . On the other hand, mice with combined Tet2 and Tet3 loss in Six2-positive NPCs failed to form nephrons, leading to kidney failure and perinatal death. Tet2 and Tet3 loss in Six2 -positive NPCs resulted in defective mesenchymal to epithelial transition and renal vesicle differentiation. Whole-genome bisulfite sequencing, single-cell RNA sequencing, and gene and protein expression analysis identified a defect in expression in multiple genes, including the WNT- β -catenin signaling pathway, due to a failure in demethylation of these loci in the absence of Tet2 and Tet3 . CONCLUSIONS These findings suggest that Tet2- and Tet3 -mediated active cytosine hydroxymethylation in NPCs play a key role in kidney development and nephron endowment.
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Affiliation(s)
- Xiujie Liang
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Tamas Aranyi
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Jianfu Zhou
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Yuting Guan
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Hailong Hu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
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Lingaas F, Tengvall K, Jansen JH, Pelander L, Hurst MH, Meuwissen T, Karlsson Å, Meadows JRS, Sundström E, Thoresen SI, Arnet EF, Guttersrud OA, Kierczak M, Hytönen MK, Lohi H, Hedhammar Å, Lindblad-Toh K, Wang C. Bayesian mixed model analysis uncovered 21 risk loci for chronic kidney disease in boxer dogs. PLoS Genet 2023; 19:e1010599. [PMID: 36693108 PMCID: PMC9897549 DOI: 10.1371/journal.pgen.1010599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 02/03/2023] [Accepted: 01/04/2023] [Indexed: 01/25/2023] Open
Abstract
Chronic kidney disease (CKD) affects 10% of the human population, with only a small fraction genetically defined. CKD is also common in dogs and has been diagnosed in nearly all breeds, but its genetic basis remains unclear. Here, we performed a Bayesian mixed model genome-wide association analysis for canine CKD in a boxer population of 117 canine cases and 137 controls, and identified 21 genetic regions associated with the disease. At the top markers from each CKD region, the cases carried an average of 20.2 risk alleles, significantly higher than controls (15.6 risk alleles). An ANOVA test showed that the 21 CKD regions together explained 57% of CKD phenotypic variation in the population. Based on whole genome sequencing data of 20 boxers, we identified 5,206 variants in LD with the top 50 BayesR markers. Following comparative analysis with human regulatory data, 17 putative regulatory variants were identified and tested with electrophoretic mobility shift assays. In total four variants, three intronic variants from the MAGI2 and GALNT18 genes, and one variant in an intergenic region on chr28, showed alternative binding ability for the risk and protective alleles in kidney cell lines. Many genes from the 21 CKD regions, RELN, MAGI2, FGFR2 and others, have been implicated in human kidney development or disease. The results from this study provide new information that may enlighten the etiology of CKD in both dogs and humans.
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Affiliation(s)
- Frode Lingaas
- Faculty of Veterinary Medicine, Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, Ås, Norway
| | - Katarina Tengvall
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Johan Høgset Jansen
- Faculty of Veterinary Medicine, Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, Ås, Norway
| | - Lena Pelander
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Theo Meuwissen
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Åsa Karlsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jennifer R. S. Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Elisabeth Sundström
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Stein Istre Thoresen
- Faculty of Veterinary Medicine, Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, Ås, Norway
| | - Ellen Frøysadal Arnet
- Faculty of Veterinary Medicine, Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, Ås, Norway
| | - Ole Albert Guttersrud
- Faculty of Veterinary Medicine, Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, Ås, Norway
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marjo K. Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (KL-T); (CW)
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail: (KL-T); (CW)
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12
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Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease. Nat Genet 2022; 54:950-962. [PMID: 35710981 DOI: 10.1038/s41588-022-01097-w] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 05/09/2022] [Indexed: 12/29/2022]
Abstract
More than 800 million people suffer from kidney disease, yet the mechanism of kidney dysfunction is poorly understood. In the present study, we define the genetic association with kidney function in 1.5 million individuals and identify 878 (126 new) loci. We map the genotype effect on the methylome in 443 kidneys, transcriptome in 686 samples and single-cell open chromatin in 57,229 kidney cells. Heritability analysis reveals that methylation variation explains a larger fraction of heritability than gene expression. We present a multi-stage prioritization strategy and prioritize target genes for 87% of kidney function loci. We highlight key roles of proximal tubules and metabolism in kidney function regulation. Furthermore, the causal role of SLC47A1 in kidney disease is defined in mice with genetic loss of Slc47a1 and in human individuals carrying loss-of-function variants. Our findings emphasize the key role of bulk and single-cell epigenomic information in translating genome-wide association studies into identifying causal genes, cellular origins and mechanisms of complex traits.
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13
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Lysine-specific demethylase 1 as a corepressor of mineralocorticoid receptor. Hypertens Res 2022; 45:641-649. [PMID: 35177789 DOI: 10.1038/s41440-022-00859-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/26/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022]
Abstract
Mineralocorticoid receptor (MR) and its ligand aldosterone play a central role in controlling blood pressure by promoting sodium reabsorption in the kidney. Coregulators are recruited to regulate the activation of steroid hormone receptors. In our previous study, we identified several new candidates for MR coregulators through liquid chromatography-tandem mass spectrometry analysis using a biochemical approach. Lysine-specific demethylase 1 (LSD1) was identified as a candidate. The relationship between LSD1 and salt-sensitive hypertension has been reported; however, the role of MR in this condition is largely unknown. Here, we investigated the functions of LSD1 as a coregulator of MR. First, a coimmunoprecipitation assay using HEK293F cells showed specific interactions between MR and LSD1. A chromatin immunoprecipitation study demonstrated LSD1 recruitment to the gene promoter of epithelial Na+ channel (ENaC), a target gene of MR. Reduced LSD1 expression by treatment with shRNA potentiated the hormonal activation of ENaC and serum/glucocorticoid-regulated kinase 1, another target gene of MR, indicating that LSD1 is a corepressor of MR. In an animal study, mice with kidney-specific LSD1 knockout (LSD1flox/floxKSP-Cre mice) developed hypertension after a high-salt diet without elevation of aldosterone levels, which was counteracted by cotreatment with spironolactone, an MR antagonist. In conclusion, our in vitro and in vivo studies demonstrated that LSD1 is a newly identified corepressor of MR.
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14
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Guan Y, Liang X, Ma Z, Hu H, Liu H, Miao Z, Linkermann A, Hellwege JN, Voight BF, Susztak K. A single genetic locus controls both expression of DPEP1/CHMP1A and kidney disease development via ferroptosis. Nat Commun 2021; 12:5078. [PMID: 34426578 PMCID: PMC8382756 DOI: 10.1038/s41467-021-25377-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified loci for kidney disease, but the causal variants, genes, and pathways remain unknown. Here we identify two kidney disease genes Dipeptidase 1 (DPEP1) and Charged Multivesicular Body Protein 1 A (CHMP1A) via the triangulation of kidney function GWAS, human kidney expression, and methylation quantitative trait loci. Using single-cell chromatin accessibility and genome editing, we fine map the region that controls the expression of both genes. Mouse genetic models demonstrate the causal roles of both genes in kidney disease. Cellular studies indicate that both Dpep1 and Chmp1a are important regulators of a single pathway, ferroptosis and lead to kidney disease development via altering cellular iron trafficking.
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Affiliation(s)
- Yuting Guan
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xiujie Liang
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ziyuan Ma
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hailong Hu
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hongbo Liu
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zhen Miao
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Graduate group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andreas Linkermann
- Division of Nephrology, Department of Internal Medicine, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
- Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Jacklyn N Hellwege
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Benjamin F Voight
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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15
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Riluzole Administration to Rats with Levodopa-Induced Dyskinesia Leads to Loss of DNA Methylation in Neuronal Genes. Cells 2021; 10:cells10061442. [PMID: 34207710 PMCID: PMC8228416 DOI: 10.3390/cells10061442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/16/2022] Open
Abstract
Dyskinesias are characterized by abnormal repetitive involuntary movements due to dysfunctional neuronal activity. Although levodopa-induced dyskinesia, characterized by tic-like abnormal involuntary movements, has no clinical treatment for Parkinson’s disease patients, animal studies indicate that Riluzole, which interferes with glutamatergic neurotransmission, can improve the phenotype. The rat model of Levodopa-Induced Dyskinesia is a unilateral lesion with 6-hydroxydopamine in the medial forebrain bundle, followed by the repeated administration of levodopa. The molecular pathomechanism of Levodopa-Induced Dyskinesia is still not deciphered; however, the implication of epigenetic mechanisms was suggested. In this study, we investigated the striatum for DNA methylation alterations under chronic levodopa treatment with or without co-treatment with Riluzole. Our data show that the lesioned and contralateral striata have nearly identical DNA methylation profiles. Chronic levodopa and levodopa + Riluzole treatments led to DNA methylation loss, particularly outside of promoters, in gene bodies and CpG poor regions. We observed that several genes involved in the Levodopa-Induced Dyskinesia underwent methylation changes. Furthermore, the Riluzole co-treatment, which improved the phenotype, pinpointed specific methylation targets, with a more than 20% methylation difference relative to levodopa treatment alone. These findings indicate potential new druggable targets for Levodopa-Induced Dyskinesia.
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16
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Miao Z, Balzer MS, Ma Z, Liu H, Wu J, Shrestha R, Aranyi T, Kwan A, Kondo A, Pontoglio M, Kim J, Li M, Kaestner KH, Susztak K. Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. Nat Commun 2021; 12:2277. [PMID: 33859189 PMCID: PMC8050063 DOI: 10.1038/s41467-021-22266-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/28/2021] [Indexed: 12/19/2022] Open
Abstract
Determining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response. Here, we profile open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We reveal key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrates that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells follow a more complex differentiation, where Hfn4a is associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease implicates critical cell types, developmental stages, genes, and regulatory mechanisms. The single cell multi-omics atlas reveals key chromatin remodeling events and gene expression dynamics associated with kidney development.
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Affiliation(s)
- Zhen Miao
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael S Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ziyuan Ma
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Junnan Wu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Rojesh Shrestha
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Tamas Aranyi
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Amy Kwan
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ayano Kondo
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Marco Pontoglio
- Epigenetics and Development Laboratory, Université de Paris Inserm U1151/CNRS UMR 8253, Institut Necker Enfants Malades, Paris, France
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Mingyao Li
- Department of Epidemiology and Biostatistics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Klaus H Kaestner
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
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