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McDonough AA, Harris AN, Xiong LI, Layton AT. Sex differences in renal transporters: assessment and functional consequences. Nat Rev Nephrol 2024; 20:21-36. [PMID: 37684523 PMCID: PMC11090267 DOI: 10.1038/s41581-023-00757-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2023] [Indexed: 09/10/2023]
Abstract
Mammalian kidneys are specialized to maintain fluid and electrolyte homeostasis. The epithelial transport processes along the renal tubule that match output to input have long been the subject of experimental and theoretical study. However, emerging data have identified a new dimension of investigation: sex. Like most tissues, the structure and function of the kidney is regulated by sex hormones and chromosomes. Available data demonstrate sex differences in the abundance of kidney solute and electrolyte transporters, establishing that renal tubular organization and operation are distinctly different in females and males. Newer studies have provided insights into the physiological consequences of these sex differences. Computational simulations predict that sex differences in transporter abundance are likely driven to optimize reproduction, enabling adaptive responses to the nutritional requirements of serial pregnancies and lactation - normal life-cycle changes that challenge the ability of renal transporters to maintain fluid and electrolyte homeostasis. Later in life, females may also undergo menopause, which is associated with changes in disease risk. Although numerous knowledge gaps remain, ongoing studies will provide further insights into the sex-specific mechanisms of sodium, potassium, acid-base and volume physiology throughout the life cycle, which may lead to therapeutic opportunities.
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Affiliation(s)
- Alicia A McDonough
- Department of Physiology and Neuroscience, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Autumn N Harris
- Department of Small Animal Clinical Sciences, University of Florida, College of Veterinary Medicine, Gainesville, FL, USA
| | - Lingyun Ivy Xiong
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Anita T Layton
- Departments of Applied Mathematics and Biology, University of Waterloo, Waterloo, Ontario, Canada
- Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
- School of Pharmacy, University of Waterloo, Waterloo, Ontario, Canada
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2
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Huynh NV, Rehage C, Hyndman KA. Mild dehydration effects on the murine kidney single-nucleus transcriptome and chromatin accessibility. Am J Physiol Renal Physiol 2023; 325:F717-F732. [PMID: 37767569 DOI: 10.1152/ajprenal.00161.2023] [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: 06/12/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Daily, we may experience mild dehydration with a rise in plasma osmolality that triggers the release of vasopressin. Although the effect of dehydration is well characterized in collecting duct principal cells (CDPCs), we hypothesized that mild dehydration (<12 h) results in many kidney cell-specific changes in transcriptomes and chromatin accessibility. Single-nucleus (sn) multiome (RNA-assay for transposase-accessible chromatin) sequencing and bulk RNA sequencing of kidneys from male and female mice that were mildly water deprived or not were compared. Water-deprived mice had a significant increase in plasma osmolality. sn-multiome-seq resulted in 19,837 nuclei that were annotated into 33 clusters. In CDPCs, aquaporin 2 (Aqp2) and aquaporin 3 (Apq3) were greater in dehydrated mice, but there were novel genes like gremlin 2 (Grem2; a cytokine) that were increased compared with ad libitum mice. The transcription factor cAMP-responsive element modulator (Crem) was greater in CDPCs of dehydrated mice, and the Crem DNA motif was more accessible. There were hundreds of sex- and dehydration-specific differentially expressed genes (DEGs) throughout the kidney, especially in the proximal tubules and thin limbs. In male mice, DEGs were enriched in pathways related to lipid metabolism, whereas female DEGs were enriched in organic acid metabolism. Many highly expressed genes had a positive correlation with increased chromatin accessibility, and mild dehydration exerted many transcriptional changes that we detected at the chromatin level. Even with a rise in plasma osmolality, male and female kidneys have distinct transcriptomes suggesting that there may be diverse mechanisms used to remain in fluid balance.NEW & NOTEWORTHY The kidney consists of >30 cell types that work collectively to maintain fluid-electrolyte balance. Kidney single-nucleus transcriptomes and chromatin accessibility profiles from male and female control (ad libitum water and food) or mildly dehydrated mice (ad libitum food, water deprivation) were determined. Mild dehydration caused hundreds of cell- and sex-specific transcriptomic changes, even though the kidney function to conserve water was the same.
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Affiliation(s)
- Nha Van Huynh
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Cassidy Rehage
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Kelly A Hyndman
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
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3
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Xiong L, Liu J, Han SY, Koppitch K, Guo JJ, Rommelfanger M, Miao Z, Gao F, Hallgrimsdottir IB, Pachter L, Kim J, MacLean AL, McMahon AP. Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney. Dev Cell 2023; 58:2338-2358.e5. [PMID: 37673062 PMCID: PMC10873092 DOI: 10.1016/j.devcel.2023.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023]
Abstract
Mammalian organs exhibit distinct physiology, disease susceptibility, and injury responses between the sexes. In the mouse kidney, sexually dimorphic gene activity maps predominantly to proximal tubule (PT) segments. Bulk RNA sequencing (RNA-seq) data demonstrated that sex differences were established from 4 and 8 weeks after birth under gonadal control. Hormone injection studies and genetic removal of androgen and estrogen receptors demonstrated androgen receptor (AR)-mediated regulation of gene activity in PT cells as the regulatory mechanism. Interestingly, caloric restriction feminizes the male kidney. Single-nuclear multiomic analysis identified putative cis-regulatory regions and cooperating factors mediating PT responses to AR activity in the mouse kidney. In the human kidney, a limited set of genes showed conserved sex-linked regulation, whereas analysis of the mouse liver underscored organ-specific differences in the regulation of sexually dimorphic gene expression. These findings raise interesting questions on the evolution, physiological significance, disease, and metabolic linkage of sexually dimorphic gene activity.
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Affiliation(s)
- Lingyun Xiong
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jing Liu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Seung Yub Han
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kari Koppitch
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Jin-Jin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Megan Rommelfanger
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Zhen Miao
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fan Gao
- Caltech Bioinformatics Resource Center at Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ingileif B Hallgrimsdottir
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adam L MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA.
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Abstract
PURPOSE OF REVIEW Women experience unique life events, for example, pregnancy and lactation, that challenge renal regulation of electrolyte homeostasis. Recent analyses of nephron organization in female vs. male rodent kidneys, revealed distinct sexual dimorphisms in electrolyte transporter expression, abundance, and activity. This review aims to provide an overview of electrolyte transporters' organization and operation in female compared with the commonly studied male kidney, and the (patho)physiologic consequences of the differences. RECENT FINDINGS When electrolyte transporters are assessed in kidney protein homogenates from both sexes, relative transporter abundance ratios in females/males are less than one along proximal tubule and greater than one post macula densa, which is indicative of a 'downstream shift' in fractional reabsorption of electrolytes in females. This arrangement improves the excretion of a sodium load, challenges potassium homeostasis, and is consistent with the lower blood pressure and greater pressure natriuresis observed in premenopausal women. SUMMARY We summarize recently reported new knowledge about sex differences in renal transporters: abundance and expression along nephron, implications for regulation by Na + , K + and angiotensin II, and mathematical models of female nephron function.
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Affiliation(s)
- Alicia A. McDonough
- Department of Physiology and Neuroscience, Keck School of Medicine of the University of Southern California, Los Angeles, CA
| | - Anita T. Layton
- Departments of Applied Mathematics and Biology, University of Waterloo, Waterloo, Ontario, Canada; Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada; School of Pharmacy, University of Waterloo, Waterloo, Ontario, Canada
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5
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Xiong L, Liu J, Han SY, Koppitch K, Guo JJ, Rommelfanger M, Gao F, Hallgrimsdottir IB, Pachter L, Kim J, MacLean AL, McMahon AP. Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.06.539585. [PMID: 37205355 PMCID: PMC10187285 DOI: 10.1101/2023.05.06.539585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mammalian organs exhibit distinct physiology, disease susceptibility and injury responses between the sexes. In the mouse kidney, sexually dimorphic gene activity maps predominantly to proximal tubule (PT) segments. Bulk RNA-seq data demonstrated sex differences were established from 4 and 8 weeks after birth under gonadal control. Hormone injection studies and genetic removal of androgen and estrogen receptors demonstrated androgen receptor (AR) mediated regulation of gene activity in PT cells as the regulatory mechanism. Interestingly, caloric restriction feminizes the male kidney. Single-nuclear multiomic analysis identified putative cis-regulatory regions and cooperating factors mediating PT responses to AR activity in the mouse kidney. In the human kidney, a limited set of genes showed conserved sex-linked regulation while analysis of the mouse liver underscored organ-specific differences in the regulation of sexually dimorphic gene expression. These findings raise interesting questions on the evolution, physiological significance, and disease and metabolic linkage, of sexually dimorphic gene activity.
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Affiliation(s)
- Lingyun Xiong
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jing Liu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Seung Yub Han
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kari Koppitch
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Jin-Jin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Megan Rommelfanger
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Fan Gao
- Caltech Bioinformatics Resource Center at Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
- Lead Contact
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6
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Shao S, Mo N, Yang Y, Cui Z, Bao C. Identifying sex-differential gene expression in the antennal gland of the swimming crab by transcriptomic analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101087. [PMID: 37178607 DOI: 10.1016/j.cbd.2023.101087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/25/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023]
Abstract
The antennal glands (AnGs) are recognized as an important organ that functions in ion regulation and excretion in decapods. Previously, many studies had explored this organ at the biochemical, physiological, and ultrastructural levels but had few molecular resources. In this study, the transcriptomes of the male and female AnGs of Portunus trituberculatus were sequenced using RNA sequencing (RNA-Seq) technology. Genes involved in osmoregulation and organic/inorganic solute transport were identified. This suggests that AnGs might be involved in these physiological functions as versatile organs. A total of 469 differentially expressed genes (DEGs) were further identified between male and female transcriptomes and found to be male-biased. Enrichment analysis showed that females were enriched in amino acid metabolism and males were enriched in nucleic acid metabolism. These results suggested differences in possible metabolic patterns between males and females. Furthermore, two transcription factors related to reproduction, namely AF4/FMR2 family members Lilli (Lilli) and Virilizer (Vir), were identified in DEGs. Lilli was found to be specifically expressed in the male AnGs, whereas Vir showed high expression levels in the female AnGs. The expression of up-regulated metabolism and sexual development-related genes in three males and six females was verified by qRT-PCR and the pattern was found to be consistent with the transcriptome expression pattern. Our results suggest that although the AnG is a unified somatic tissue composed of individual cells, it still demonstrates distinct sex-specific expression patterns. These results provide foundational knowledge of the function and differences between male and female AnGs in P. trituberculatus.
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Affiliation(s)
- Shucheng Shao
- School of Marine Sciences, Ningbo University, Ningbo 315020, China
| | - Nan Mo
- School of Marine Sciences, Ningbo University, Ningbo 315020, China
| | - Yanan Yang
- School of Marine Sciences, Ningbo University, Ningbo 315020, China
| | - Zhaoxia Cui
- School of Marine Sciences, Ningbo University, Ningbo 315020, China
| | - Chenchang Bao
- School of Marine Sciences, Ningbo University, Ningbo 315020, China..
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7
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Conte C, Antonelli G, Melica ME, Tarocchi M, Romagnani P, Peired AJ. Role of Sex Hormones in Prevalent Kidney Diseases. Int J Mol Sci 2023; 24:ijms24098244. [PMID: 37175947 PMCID: PMC10179191 DOI: 10.3390/ijms24098244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Chronic kidney disease (CKD) is a constantly growing global health burden, with more than 840 million people affected worldwide. CKD presents sex disparities in the pathophysiology of the disease, as well as in the epidemiology, clinical manifestations, and disease progression. Overall, while CKD is more frequent in females, males have a higher risk to progress to end-stage kidney disease. In recent years, numerous studies have highlighted the role of sex hormones in the health and diseases of several organs, including the kidney. In this review, we present a clinical overview of the sex-differences in CKD and a selection of prominent kidney diseases causing CKD: lupus nephritis, diabetic kidney disease, IgA nephropathy, and autosomal dominant polycystic kidney disease. We report clinical and experimental findings on the role of sex hormones in the development of the disease and its progression to end-stage kidney disease.
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Affiliation(s)
- Carolina Conte
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134 Florence, Italy
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, 50139 Florence, Italy
| | - Giulia Antonelli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134 Florence, Italy
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, 50139 Florence, Italy
| | - Maria Elena Melica
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134 Florence, Italy
| | - Mirko Tarocchi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134 Florence, Italy
| | - Paola Romagnani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134 Florence, Italy
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, 50139 Florence, Italy
| | - Anna Julie Peired
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, 50134 Florence, Italy
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Suman TY, Kim SY, Yeom DH, Jang Y, Jeong TY, Jeon J. Transcriptome and computational approaches highlighting the molecular regulation of Zacco platypus induced by mesocosm exposure to common disinfectant chlorine. CHEMOSPHERE 2023; 319:137989. [PMID: 36736481 DOI: 10.1016/j.chemosphere.2023.137989] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/26/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Chlorine (Cl2) is a disinfectant often used in swimming pools and water treatment facilities. However, it is released into aquatic ecosystems, where it may harm non-targeted organisms. Here, we performed a mesocosm experiment exposing Zacco platypus (Z. platypus) to biocide Cl2 for 30 days (30 d) at two days' time points 15 days (15 d) and 30 d samples were collected. Here, Z. platypus was exposed to a sublethal concentration (0.1 mg/L) of Cl2, and comparative transcriptomics analyses were performed to determine their response mechanisms at the molecular level. According to RNA sequencing of the whole-body transcriptome, 860 and 1189 differentially expressed genes (DEGs) were identified from the 15 d and 30 d responses to Cl2, respectively. After enrichment analysis of GO (Gene Ontology) functions and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, identified DEGs were demonstrated to be associated with a variety of functions, including "ion binding and transmembrane transporters". Cl2 also induced oxidative stress in Z. platypus by increasing the levels of reactive oxygen species (ROS) while decreasing the catalase (CAT) content and the levels of solute carrier family 22 member 11 (slc22a11), Caspase-8 (casp-8), inducible nitric oxide synthase (NOS2), cytosolic phospholipase A2 gamma (PLA2G4). However, Z. platypus still allows recovery during stress suspension by increasing the expression levels of solute carrier family proteins. The GO and KEGG annotation results revealed that the expression of DEGs were related to the detoxification process, immune response, and antioxidant mechanism. Additionally, protein-protein interaction networks (PPI) and cytoHubba analyses identified sixteen hub genes and their interaction. These findings elucidate the regulation of various DEGs and signaling pathways in response to Cl2 exposure, which will improve our knowledge and laid foundation for further investigation of the toxicity of Cl2 to Z. platypus.
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Affiliation(s)
- Thodhal Yoganandham Suman
- Department of Environmental Engineering, Changwon National University, Changwon, Gyeongsangnamdo, 51140, Republic of Korea; School of Smart and Green Engineering, Changwon National University, Changwon, Gyeongsangnamdo, 51140, Republic of Korea
| | - Soo-Yeon Kim
- Gyeongnam Branch Institute, Korea Institute of Toxicology (KIT), Jinju-si, 52834, Republic of Korea
| | - Dong-Hyuk Yeom
- Gyeongnam Branch Institute, Korea Institute of Toxicology (KIT), Jinju-si, 52834, Republic of Korea
| | - Younghoon Jang
- Department of Biology and Chemistry, Changwon National University, Changwon, Republic of Korea
| | - Tae-Yong Jeong
- Department of Environmental Science, Hankuk University of Foreign Studies, 81, Oedae-ro, Mohyeon-eup,Cheoin-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Junho Jeon
- Department of Environmental Engineering, Changwon National University, Changwon, Gyeongsangnamdo, 51140, Republic of Korea; School of Smart and Green Engineering, Changwon National University, Changwon, Gyeongsangnamdo, 51140, Republic of Korea.
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9
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Bishop AC, Spradling‐Reeves KD, Shade RE, Lange KJ, Birnbaum S, Favela K, Dick EJ, Nijland MJ, Li C, Nathanielsz PW, Cox LA. Postnatal persistence of nonhuman primate sex-dependent renal structural and molecular changes programmed by intrauterine growth restriction. J Med Primatol 2022; 51:329-344. [PMID: 35855511 PMCID: PMC9796938 DOI: 10.1111/jmp.12601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 06/09/2022] [Accepted: 06/17/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Poor nutrition during fetal development programs postnatal kidney function. Understanding postnatal consequences in nonhuman primates (NHP) is important for translation to our understanding the impact on human kidney function and disease risk. We hypothesized that intrauterine growth restriction (IUGR) in NHP persists postnatally, with potential molecular mechanisms revealed by Western-type diet challenge. METHODS IUGR juvenile baboons were fed a 7-week Western diet, with kidney biopsies, blood, and urine collected before and after challenge. Transcriptomics and metabolomics were used to analyze biosamples. RESULTS Pre-challenge IUGR kidney transcriptome and urine metabolome differed from controls. Post-challenge, sex and diet-specific responses in urine metabolite and renal signaling pathways were observed. Dysregulated mTOR signaling persisted postnatally in female pre-challenge. Post-challenge IUGR male response showed uncoordinated signaling suggesting proximal tubule injury. CONCLUSION Fetal undernutrition impacts juvenile offspring kidneys at the molecular level suggesting early-onset blood pressure dysregulation.
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Affiliation(s)
- Andrew C. Bishop
- Center for Precision MedicineDepartment of Internal Medicine, Wake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Kimberly D. Spradling‐Reeves
- Center for Precision MedicineDepartment of Internal Medicine, Wake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Robert E. Shade
- Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioTexasUSA
| | - Kenneth J. Lange
- Department of Pharmaceuticals and BioengineeringSouthwest Research InstituteSan AntonioTexasUSA
| | - Shifra Birnbaum
- Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioTexasUSA
| | - Kristin Favela
- Department of Pharmaceuticals and BioengineeringSouthwest Research InstituteSan AntonioTexasUSA
| | - Edward J. Dick
- Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioTexasUSA
| | - Mark J. Nijland
- Department of Obstetrics and GynecologyUniversity of Texas Health Science CenterSan AntonioTexasUSA
| | - Cun Li
- Department of Animal SciencesUniversity of WyomingLaramieWyomingUSA
| | - Peter W. Nathanielsz
- Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioTexasUSA
- Department of Animal SciencesUniversity of WyomingLaramieWyomingUSA
| | - Laura A. Cox
- Center for Precision MedicineDepartment of Internal Medicine, Wake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioTexasUSA
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10
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Hansen J, Sealfon R, Menon R, Eadon MT, Lake BB, Steck B, Anjani K, Parikh S, Sigdel TK, Zhang G, Velickovic D, Barwinska D, Alexandrov T, Dobi D, Rashmi P, Otto EA, Rivera M, Rose MP, Anderton CR, Shapiro JP, Pamreddy A, Winfree S, Xiong Y, He Y, de Boer IH, Hodgin JB, Barisoni L, Naik AS, Sharma K, Sarwal MM, Zhang K, Himmelfarb J, Rovin B, El-Achkar TM, Laszik Z, He JC, Dagher PC, Valerius MT, Jain S, Satlin LM, Troyanskaya OG, Kretzler M, Iyengar R, Azeloglu EU. A reference tissue atlas for the human kidney. SCIENCE ADVANCES 2022; 8:eabn4965. [PMID: 35675394 PMCID: PMC9176741 DOI: 10.1126/sciadv.abn4965] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/20/2022] [Indexed: 05/08/2023]
Abstract
Kidney Precision Medicine Project (KPMP) is building a spatially specified human kidney tissue atlas in health and disease with single-cell resolution. Here, we describe the construction of an integrated reference map of cells, pathways, and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 56 adult subjects. We use single-cell/nucleus transcriptomics, subsegmental laser microdissection transcriptomics and proteomics, near-single-cell proteomics, 3D and CODEX imaging, and spatial metabolomics to hierarchically identify genes, pathways, and cells. Integrated data from these different technologies coherently identify cell types/subtypes within different nephron segments and the interstitium. These profiles describe cell-level functional organization of the kidney following its physiological functions and link cell subtypes to genes, proteins, metabolites, and pathways. They further show that messenger RNA levels along the nephron are congruent with the subsegmental physiological activity. This reference atlas provides a framework for the classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.
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Affiliation(s)
- Jens Hansen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Sealfon
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
| | - Rajasree Menon
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | | | - Blue B. Lake
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Becky Steck
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Kavya Anjani
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Samir Parikh
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Tara K. Sigdel
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Guanshi Zhang
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | | | - Daria Barwinska
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Dejan Dobi
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Priyanka Rashmi
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Edgar A. Otto
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Miguel Rivera
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Michael P. Rose
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Christopher R. Anderton
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - John P. Shapiro
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Annapurna Pamreddy
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | - Seth Winfree
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yuguang Xiong
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yongqun He
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Ian H. de Boer
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
| | | | | | - Abhijit S. Naik
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Kumar Sharma
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | - Minnie M. Sarwal
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jonathan Himmelfarb
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
| | - Brad Rovin
- Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Zoltan Laszik
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | | | | | - M. Todd Valerius
- Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Sanjay Jain
- Washington University in Saint Louis School of Medicine, St. Louis, MS, USA
| | - Lisa M. Satlin
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olga G. Troyanskaya
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
| | | | - Ravi Iyengar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Kidney Precision Medicine Project
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
- University of Michigan School of Medicine, Ann Arbor, MI, USA
- Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- University of California San Francisco School of Medicine, San Francisco, CA, USA
- Ohio State University College of Medicine, Columbus, OH, USA
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
- European Molecular Biology Laboratory, Heidelberg, Germany
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
- Duke University School of Medicine, Durham, NC, USA
- Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
- Washington University in Saint Louis School of Medicine, St. Louis, MS, USA
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11
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Hyndman KA, Crossman DK. Kidney cell type-specific changes in the chromatin and transcriptome landscapes following epithelial Hdac1 and Hdac2 knockdown. Physiol Genomics 2022; 54:45-57. [PMID: 34890513 PMCID: PMC8791845 DOI: 10.1152/physiolgenomics.00102.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/21/2021] [Accepted: 12/08/2021] [Indexed: 02/03/2023] Open
Abstract
Recent studies have identified at least 20 different kidney cell types based upon chromatin structure and gene expression. Histone deacetylases (HDACs) are epigenetic transcriptional repressors via deacetylation of histone lysines resulting in inaccessible chromatin. We reported that kidney epithelial HDAC1 and HDAC2 activity is critical for maintaining a healthy kidney and preventing fluid-electrolyte abnormalities. However, to what extent does Hdac1/Hdac2 knockdown affect chromatin structure and subsequent transcript expression in the kidney? To answer this question, we used single nucleus assay for transposase-accessible chromatin-sequencing (snATAC-seq) and snRNA-seq to profile kidney nuclei from male and female, control, and littermate kidney epithelial Hdac1/Hdac2 knockdown mice. Hdac1/Hdac2 knockdown resulted in significant changes in the chromatin structure predominantly within the promoter region of gene loci involved in fluid-electrolyte balance such as the aquaporins, with both increased and decreased accessibility captured. Moreover, Hdac1/Hdac2 knockdown resulted different gene loci being accessible with a corresponding increased transcript number in the kidney, but among all mice only 24%-30% of chromatin accessibility agreed with transcript expression (e.g., open chromatin and increased transcript). To conclude, although chromatin structure does affect transcription, ∼70% of the differentially expressed genes cannot be explained by changes in chromatin accessibility and HDAC1/HDAC2 had a minimal effect on these global patterns. Yet, the genes that are targets of HDAC1 and HDAC2 are critically important for maintaining kidney function.
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Affiliation(s)
- Kelly A Hyndman
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - David K Crossman
- The UAB Genomics Core Facility, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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12
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Lewis S, Chen L, Raghuram V, Khundmiri SJ, Chou CL, Yang CR, Knepper MA. "SLC-omics" of the kidney: Solute transporters along the nephron. Am J Physiol Cell Physiol 2021; 321:C507-C518. [PMID: 34191628 DOI: 10.1152/ajpcell.00197.2021] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The fluid in the 14 distinct segments of the renal tubule undergoes sequential transport processes that gradually convert the glomerular filtrate into the final urine. The solute carrier (SLC) family of proteins is responsible for much of the transport of ions and organic molecules along the renal tubule. In addition, some SLC family proteins mediate housekeeping functions by transporting substrates for metabolism. Here, we have developed a curated list of SLC family proteins. We used the list to produce resource webpages that map these proteins and their transcripts to specific segments along the renal tubule. The data were used to highlight some interesting features of expression along the renal tubule including sex-specific expression in the proximal tubule and the role of accessory proteins (β-subunit proteins) that are thought to be important for polarized targeting in renal tubule epithelia. Also, as an example of application of the data resource, we describe the patterns of acid-base transporter expression along the renal tubule.
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Affiliation(s)
- Spencer Lewis
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Lihe Chen
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Viswanathan Raghuram
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Syed J Khundmiri
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Chung-Lin Chou
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Chin-Rang Yang
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
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13
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Xia C, Zhang X, Zhang Y, Li J, Xing H. Ammonia exposure causes the disruption of the solute carrier family gene network in pigs. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 210:111870. [PMID: 33440271 DOI: 10.1016/j.ecoenv.2020.111870] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/22/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
Ammonia is the main harmful gas in livestock houses. However, the toxic mechanism of ammonia is still unclear. Therefore, we examined the effects of ammonia exposure on different tissues of fattening pigs by histological analysis and transcriptome techniques in this study. The results showed that there were varying degrees of pathological changes in liver, kidney, hypothalamus, jejunum, lungs, spleen, heart and trachea of fattening pigs under ammonia exposure. Notably, the extent of damage in liver, kidney, jejunum, lungs, hypothalamus and trachea was more severe than that in heart and spleen. Transcriptome results showed that ammonia exposure caused changes in 349, 335, 340, 229, 120, 578, 407 and 115 differentially expressed genes in liver, kidney, spleen, lung, trachea, hypothalamus, jejunum and heart, respectively. Interestingly, the changes in solute vector (SLC) family genes were found in all 8 tissues, and the verified gene results (SLC11A1, SLC17A7, SLC17A6, SLC6A4, SLC22A7, SLC25A3, SLC28A3, SLC7A2, SLC6A6, SLC38A5, SLC22A12, SLC34A1, SLC26A1, SLC26A6, SLC27A5, SLC22A8 and SLC44A4) were consistent with qRT-PCR results. In conclusion, ammonia exposure can cause pathological changes in many tissues and organs of fattening pigs and changes in the SCL family gene network. Importantly, the SCL family is involved in the toxic mechanism of ammonia. Our findings will provide a new insight for better assessing the mechanism of ammonia toxicity.
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Affiliation(s)
- Chunli Xia
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Xinxin Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yu Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China; Heilongjiang Agricultural and Rural Department, 4-1 Wenfu Street, Harbin 150060, People's Republic of China
| | - Jichang Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, People's Republic of China.
| | - Houjuan Xing
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China.
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