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Chen L, Chou CL, Yang CR, Knepper MA. Multiomics Analyses Reveal Sex Differences in Mouse Renal Proximal Subsegments. J Am Soc Nephrol 2023; 34:829-845. [PMID: 36758122 PMCID: PMC10125651 DOI: 10.1681/asn.0000000000000089] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023] Open
Abstract
SIGNIFICANCE STATEMENT Sex-dependent differences in kidney function are recognized but the underlying molecular mechanisms are largely unexplored. Advances in genomics and proteomic technologies now allow extensive characterization of differences between the same cell types of males and females. Multiomics integrating RNA-seq, ATAC-seq, and proteomics data to investigate differences in gene expression, chromatin accessibility, and protein expression in proximal tubules of male and female mice identified many sex-biased genes and proteins associated with kidney functions, including metabolic and transport processes. Sex differences may also arise from variations of the interaction between transcription factors and accessible chromatin regions. A comprehensive web resource is provided to advance understanding of sex differences in cells of the proximal tubule. BACKGROUND Sex differences have been increasingly recognized as important in kidney physiology and pathophysiology, but limited resources are available for comprehensive interrogation of sex differences. METHODS RNA-seq and ATAC-seq of microdissected mouse proximal tubules and protein mass spectrometry of homogenized perfused mouse kidneys reveal differences in proximal tubule cells of males and females. RESULTS The transcriptomic data indicated that the major differences in the proximal tubules between the sexes were in the S2/S3 segments, and most of the sex-biased transcripts mapped to autosomes rather than to the sex chromosomes. Many of the transcripts exhibiting sex-biased expression are involved in monocarboxylic acid metabolic processes, organic anion transport, and organic acid transport. The ATAC-seq method on microdissected tubules captured chromatin accessibility. Many of the more than 7000 differentially accessible DNA regions identified were in distal regions. Motif analyses revealed a lack of direct involvement of estrogen receptors or the androgen receptor (absence of canonical hormone response elements), suggesting an indirect regulatory role of sex hormones. Instead, analyses identified several transcription factors (TFs) ( Tead1 , Nfia/b , and Pou3f3 ) whose interplay with proximal tubule-specific TFs ( e.g. , Hnf1b , Hnf4a ) may contribute to sex differences. Finally, the whole-kidney proteome was correlated with the transcriptome, and many sex-biased proteins ( e.g. , Cyp2e1, Acsm2/3) were identified. CONCLUSIONS Sex-dependent cis-regulatory elements interact with TFs in ways that lead to sex-biased gene expression in proximal tubule cells. These data are provided as a user-friendly web page at https://esbl.nhlbi.nih.gov/MRECA/PT/ .
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Affiliation(s)
- Lihe Chen
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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Shen H, Scialis RJ, Lehman-McKeeman L. Xenobiotic Transporters in the Kidney: Function and Role in Toxicity. Semin Nephrol 2019; 39:159-175. [DOI: 10.1016/j.semnephrol.2018.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Komers R, Xu B, Fu Y, McClelland A, Kantharidis P, Mittal A, Cohen HT, Cohen DM. Transcriptome-based analysis of kidney gene expression changes associated with diabetes in OVE26 mice, in the presence and absence of losartan treatment. PLoS One 2014; 9:e96987. [PMID: 24827579 PMCID: PMC4020814 DOI: 10.1371/journal.pone.0096987] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 04/14/2014] [Indexed: 12/24/2022] Open
Abstract
Diabetes is among the most common causes of end-stage renal disease, although its pathophysiology is incompletely understood. We performed next-generation sequencing-based transcriptome analysis of renal gene expression changes in the OVE26 murine model of diabetes (age 15 weeks), relative to non-diabetic control, in the presence and absence of short-term (seven-day) treatment with the angiotensin receptor blocker, losartan (n = 3-6 biological replicates per condition). We detected 1438 statistically significant changes in gene expression across conditions. Of the 638 genes dysregulated in diabetes relative to the non-diabetic state, >70% were downregulation events. Unbiased functional annotation of genes up- and down-regulated by diabetes strongly associated (p<1 × 10(-8)) with terms for oxidative stress and for endoplasmic reticulum stress/protein folding. Most of the individual gene products up- or down-regulated with diabetes were unaffected by losartan treatment; however, of the gene products dysregulated in diabetes and influenced by losartan treatment, the vast majority of changes were in the direction of amelioration rather than exacerbation of the diabetic dysregulation. This group of losartan-protected genes associated strongly with annotation terms for endoplasmic reticulum stress, heat shock proteins, and chaperone function, but not oxidative stress; therefore, the losartan-unaffected genes suggest avenues for additional therapeutic opportunity in diabetes. Interestingly, the gene product most highly upregulated by diabetes (>52-fold), encoded by the cationic amino acid transporter Slc7a12, and the gene product most highly downregulated by diabetes (>99%)--encoded by the "pseudogene" Gm6300--are adjacent in the murine genome, are members of the SLC7 gene family, and are likely paralogous. Therefore, diabetes activates a near-total genetic switch between these two paralogs. Other individual-level changes in gene expression are potentially relevant to diabetic pathophysiology, and novel pathways are suggested. Genes unaffected by diabetes alone but exhibiting increased renal expression with losartan produced a signature consistent with malignant potential.
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Affiliation(s)
- Radko Komers
- Division of Nephrology and Hypertension, Department of Medicine, Oregon Health & Science University, Portland, Oregon
- Portland V. A. Medical Center, Portland, Oregon, United States of America
| | - Bei Xu
- Division of Nephrology and Hypertension, Department of Medicine, Oregon Health & Science University, Portland, Oregon
- Portland V. A. Medical Center, Portland, Oregon, United States of America
| | - Yi Fu
- Division of Nephrology and Hypertension, Department of Medicine, Oregon Health & Science University, Portland, Oregon
- Portland V. A. Medical Center, Portland, Oregon, United States of America
| | - Aaron McClelland
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Phillip Kantharidis
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Amit Mittal
- Nephrology Section, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Herbert T. Cohen
- Nephrology Section, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - David M. Cohen
- Division of Nephrology and Hypertension, Department of Medicine, Oregon Health & Science University, Portland, Oregon
- Portland V. A. Medical Center, Portland, Oregon, United States of America
- * E-mail:
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Beyer SR, Mallmann RT, Jaenecke I, Habermeier A, Boissel JP, Closs EI. Identification of cysteine residues in human cationic amino acid transporter hCAT-2A that are targets for inhibition by N-ethylmaleimide. J Biol Chem 2013; 288:30411-30419. [PMID: 24019517 DOI: 10.1074/jbc.m113.490698] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In most cells, cationic amino acids such as l-arginine, l-lysine, and l-ornithine are transported by cationic (CAT) and y(+)L (y(+)LAT) amino acid transporters. In human erythrocytes, the cysteine-modifying agent N-ethylmaleimide (NEM) has been shown to inhibit system y(+) (most likely CAT-1), but not system y(+)L (Devés, R., Angelo, S., and Chávez, P. (1993) J. Physiol. 468, 753-766). We thus wondered if sensitivity to NEM distinguishes generally all CAT and y(+)LAT isoforms. Transport assays in Xenopus laevis oocytes established that indeed all human CATs (including the low affinity hCAT-2A), but neither y(+)LAT isoform, are inhibited by NEM. hCAT-2A inhibition was not due to reduced transporter expression in the plasma membrane, indicating that NEM reduces the intrinsic transporter activity. Individual mutation of each of the seven cysteine residues conserved in all CAT isoforms did not lead to NEM insensitivity of hCAT-2A. However, a cysteine-less mutant was no longer inhibited by NEM, suggesting that inhibition occurs through modification of more than one cysteine in hCAT-2A. Indeed, also the double mutant C33A/C273A was insensitive to NEM inhibition, whereas reintroduction of a cysteine at either position 33 or 273 in the cysteine-less mutant led to NEM sensitivity. We thus identified Cys-33 and Cys-273 in hCAT-2A as the targets of NEM inhibition. In addition, all proteins with Cys-33 mutations showed a pronounced reduction in transport activity, suggesting that, surprisingly, this residue, located in the cytoplasmic N terminus, is important for transporter function.
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Affiliation(s)
- Sarah R Beyer
- From the Department of Pharmacology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Robert T Mallmann
- From the Department of Pharmacology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Isabel Jaenecke
- From the Department of Pharmacology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Alice Habermeier
- From the Department of Pharmacology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Jean-Paul Boissel
- From the Department of Pharmacology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Ellen I Closs
- From the Department of Pharmacology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany.
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Bröer S. Amino acid transport across mammalian intestinal and renal epithelia. Physiol Rev 2008; 88:249-86. [PMID: 18195088 DOI: 10.1152/physrev.00018.2006] [Citation(s) in RCA: 614] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The transport of amino acids in kidney and intestine is critical for the supply of amino acids to all tissues and the homeostasis of plasma amino acid levels. This is illustrated by a number of inherited disorders affecting amino acid transport in epithelial cells, such as cystinuria, lysinuric protein intolerance, Hartnup disorder, iminoglycinuria, dicarboxylic aminoaciduria, and some other less well-described disturbances of amino acid transport. The identification of most epithelial amino acid transporters over the past 15 years allows the definition of these disorders at the molecular level and provides a clear picture of the functional cooperation between transporters in the apical and basolateral membranes of mammalian epithelial cells. Transport of amino acids across the apical membrane not only makes use of sodium-dependent symporters, but also uses the proton-motive force and the gradient of other amino acids to efficiently absorb amino acids from the lumen. In the basolateral membrane, antiporters cooperate with facilitators to release amino acids without depleting cells of valuable nutrients. With very few exceptions, individual amino acids are transported by more than one transporter, providing backup capacity for absorption in the case of mutational inactivation of a transport system.
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Affiliation(s)
- Stefan Bröer
- School of Biochemistry and Molecular Biology, Australian National University, Canberra, Australian Capital Territory, Australia.
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Nishimura M, Naito S. Tissue-specific mRNA expression profiles of human ATP-binding cassette and solute carrier transporter superfamilies. Drug Metab Pharmacokinet 2006; 20:452-77. [PMID: 16415531 DOI: 10.2133/dmpk.20.452] [Citation(s) in RCA: 287] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pairs of forward and reverse primers and TaqMan probes specific to each of 46 human ATP-binding cassette (ABC) transporters and 108 human solute carrier (SLC) transporters were prepared. The mRNA expression level of each target transporter was analyzed in total RNA from single and pooled specimens of various human tissues (adrenal gland, bone marrow, brain, colon, heart, kidney, liver, lung, pancreas, peripheral leukocytes, placenta, prostate, salivary gland, skeletal muscle, small intestine, spinal cord, spleen, stomach, testis, thymus, thyroid gland, trachea, and uterus) by real-time reverse transcription PCR using an ABI PRISM 7700 sequence detector system. In contrast to previous methods for analyzing the mRNA expression of single ABC and SLC genes such as Northern blotting, our method allowed us to perform sensitive, semiautomatic, rapid, and complete analysis of ABC and SLC transporters in total RNA samples. Our newly determined expression profiles were then used to study the gene expression in 23 different human tissues, and tissues with high transcriptional activity for human ABC and SLC transporters were identified. These results are expected to be valuable for establishing drug transport-mediated screening systems for new chemical entities in new drug development and for research concerning the clinical diagnosis of disease.
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Affiliation(s)
- Masuhiro Nishimura
- Division of Pharmacology, Drug Safety and Metabolism, Otsuka Pharmaceutical Factory, Inc., Tokushima, Japan.
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Cariappa R, Heath-Monnig E, Smith CH. Isoforms of amino acid transporters in placental syncytiotrophoblast: plasma membrane localization and potential role in maternal/fetal transport. Placenta 2003; 24:713-26. [PMID: 12852862 DOI: 10.1016/s0143-4004(03)00085-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many cell proteins exist as isoforms arising either from gene duplication or alternate RNA splicing. There is growing evidence that isoforms with different, but closely related, functional characteristics are often directed to discrete cellular locations. Thus, specialized functions may be carried out by proteins of similar evolutionary origin in different membrane compartments. In polarized epithelial cells, this mechanism allows the cell to control amino acid transport independently at each of its specialized apical and basolateral plasma membrane domains. Investigations of isoform localization in these membranes have generally been performed in epithelia other than the placental trophoblast.This review of placental amino acid transporter isoforms first provides an overview of their properties and preliminary plasma membrane localization. We then discuss studies suggesting various roles of isoform localization in trophoblast function. To provide insights into the molecular basis of this localization in trophoblast, we present a review of current knowledge of plasma membrane protein localization as derived from investigations with a widely used epithelial model cell line. Finally, we discuss a potential approach using cultured trophoblast-derived cells for studies of transporter isoform localization and function. We hope that this review will stimulate investigation of the properties of trophoblast transporter isoforms, their membrane localization and their contribution to the cellular mechanism of maternal-fetal nutrient transport.
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Affiliation(s)
- R Cariappa
- Department of Pediatrics, Washington University School of Medicine and St Louis Children's Hospital, Box 8116 One Children's Place, St Louis, MO 63110, USA
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