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Riojas AM, Spradling-Reeves KD, Christensen CL, Hall-Ursone S, Cox LA. Cell-type deconvolution of bulk RNA-Seq from kidney using opensource bioinformatic tools. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528258. [PMID: 36824792 PMCID: PMC9949078 DOI: 10.1101/2023.02.13.528258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Traditional bulk RNA-Seq pipelines do not assess cell-type composition within heterogeneous tissues. Therefore, it is difficult to determine whether conflicting findings among samples or datasets are the result of biological differences or technical differences due to variation in sample collections. This report provides a user-friendly, open source method to assess cell-type composition in bulk RNA-Seq datasets for heterogeneous tissues using published single cell (sc)RNA-Seq data as a reference. As an example, we apply the method to analysis of kidney cortex bulk RNA-Seq data from female (N=8) and male (N=9) baboons to assess whether observed transcriptome sex differences are biological or technical, i.e., variation due to ultrasound guided biopsy collections. We found cell-type composition was not statistically different in female versus male transcriptomes based on expression of 274 kidney cell-type specific transcripts, indicating differences in gene expression are not due to sampling differences. This method of cell-type composition analysis is recommended for providing rigor in analysis of bulk RNA-Seq datasets from complex tissues. It is clear that with reduced costs, more analyses will be done using scRNA-Seq; however, the approach described here is relevant for data mining and meta analyses of the thousands of bulk RNA-Seq data archived in the NCBI GEO public database.
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Affiliation(s)
- Angelica M. Riojas
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Kimberly D. Spradling-Reeves
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | | | - Shannan Hall-Ursone
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Laura A. Cox
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
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Riojas AM, Reeves KD, Shade RE, Puppala SR, Christensen CL, Birnbaum S, Glenn JP, Li C, Shaltout H, Hall-Ursone S, Cox LA. Blood pressure and the kidney cortex transcriptome response to high-sodium diet challenge in female nonhuman primates. Physiol Genomics 2022; 54:443-454. [PMID: 36062883 PMCID: PMC9639778 DOI: 10.1152/physiolgenomics.00144.2021] [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: 11/03/2021] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
Blood pressure (BP) is influenced by genetic variation and sodium intake with sex-specific differences; however, studies to identify renal molecular mechanisms underlying the influence of sodium intake on BP in nonhuman primates (NHP) have focused on males. To address the gap in our understanding of molecular mechanisms regulating BP in female primates, we studied sodium-naïve female baboons (n = 7) fed a high-sodium (HS) diet for 6 wk. We hypothesized that in female baboons variation in renal transcriptional networks correlates with variation in BP response to a high-sodium diet. BP was continuously measured for 64-h periods throughout the study by implantable telemetry devices. Sodium intake, blood samples for clinical chemistries, and ultrasound-guided kidney biopsies were collected before and after the HS diet for RNA-Seq and bioinformatic analyses. We found that on the LS diet but not the HS diet, sodium intake and serum 17 β-estradiol concentration correlated with BP. Furthermore, kidney transcriptomes differed by diet-unbiased weighted gene coexpression network analysis revealed modules of genes correlated with BP on the HS diet but not the LS diet. Our results showed variation in BP on the HS diet correlated with variation in novel kidney gene networks regulated by ESR1 and MYC; i.e., these regulators have not been associated with BP regulation in male humans or rodents. Validation of the mechanisms underlying regulation of BP-associated gene networks in female NHP will inform better therapies toward greater precision medicine for women.
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Affiliation(s)
- Angelica M Riojas
- Molecular Medicine and Translational Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Kimberly D Reeves
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Robert E Shade
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | - Sobha R Puppala
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | | | - Shifra Birnbaum
- Molecular Services Core, Texas Biomedical Research Institute, San Antonio, Texas
| | - Jeremy P Glenn
- Molecular Services Core, Texas Biomedical Research Institute, San Antonio, Texas
| | - Cun Li
- Department of Animal Science, University of Wyoming, Laramie, Wyoming
| | - Hossam Shaltout
- Hypertension and Vascular Research Center, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Shannan Hall-Ursone
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | - Laura A Cox
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
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Rogers J, Raveendran M, Harris RA, Mailund T, Leppälä K, Athanasiadis G, Schierup MH, Cheng J, Munch K, Walker JA, Konkel MK, Jordan V, Steely CJ, Beckstrom TO, Bergey C, Burrell A, Schrempf D, Noll A, Kothe M, Kopp GH, Liu Y, Murali S, Billis K, Martin FJ, Muffato M, Cox L, Else J, Disotell T, Muzny DM, Phillips-Conroy J, Aken B, Eichler EE, Marques-Bonet T, Kosiol C, Batzer MA, Hahn MW, Tung J, Zinner D, Roos C, Jolly CJ, Gibbs RA, Worley KC. The comparative genomics and complex population history of Papio baboons. SCIENCE ADVANCES 2019; 5:eaau6947. [PMID: 30854422 PMCID: PMC6401983 DOI: 10.1126/sciadv.aau6947] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/06/2018] [Indexed: 05/26/2023]
Abstract
Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.
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Affiliation(s)
- Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - R. Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark
| | - Kalle Leppälä
- Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark
| | - Georgios Athanasiadis
- Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark
| | - Mikkel Heide Schierup
- Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark
| | - Jade Cheng
- Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark
| | - Jerilyn A. Walker
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Miriam K. Konkel
- Department of Genetics and Biochemistry, 105 Collings Street, Clemson University, Clemson, SC 29634, USA
| | - Vallmer Jordan
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Cody J. Steely
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Thomas O. Beckstrom
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Christina Bergey
- Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA
- Departments of Anthropology and Biology, Pennsylvania State University, 514 Carpenter Building, University Park, PA 16802, USA
| | - Andrew Burrell
- Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA
| | - Dominik Schrempf
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 11210 Vienna, Austria
| | - Angela Noll
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Maximillian Kothe
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Gisela H. Kopp
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
- Department of Biology, University of Konstanz, Universitätsstr. 10, 78467 Konstanz, Germany
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Am Obstberg 1, 78315 Radolfzell, Germany
| | - Yue Liu
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Shwetha Murali
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA
- Howard Hughes Medical Institute, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Fergal J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Laura Cox
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 W. Military Drive, San Antonio, TX 78227, USA
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, 475 Vine Street, Winston-Salem, NC 27101, USA
| | - James Else
- Department of Pathology and Laboratory Medicine and Yerkes Primate Research Center, 954 Gatewood Road, Emory University, Atlanta, GA 30322, USA
| | - Todd Disotell
- Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
- Department of Anthropology, Washington University, McMillan Hall, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA
- Howard Hughes Medical Institute, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader, 88. 08003, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Baldiri Reixac, 4, 08028, Barcelona, Spain
- Institut Catala de Paleontologia Miquel Crusafont, Universitat Autonoma de Barcelona, c/de les Columnes, s/n. Campus de la UAB. 08193–Cerdanyola del Vallès, Barcelona, Spain
| | - Carolin Kosiol
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 11210 Vienna, Austria
- Centre for Biological Diversity, School of Biology, University of St. Andrews, Dyers Brae House, Greenside Place, St Andrews, Fife, KY16 9TH, UK
| | - Mark A. Batzer
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Matthew W. Hahn
- Department of Biology and Department of Computer Science, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA
| | - Jenny Tung
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
- Duke Population Research Institute, Duke University, Box 90989, Durham, NC 27708, USA
- Institute of Primate Research, P.O. Box 24481, Nairobi, Kenya
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Clifford J. Jolly
- Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Kim C. Worley
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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4
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Jordan VE, Walker JA, Beckstrom TO, Steely CJ, McDaniel CL, St Romain CP, Worley KC, Phillips-Conroy J, Jolly CJ, Rogers J, Konkel MK, Batzer MA. A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms. Mob DNA 2018; 9:13. [PMID: 29632618 PMCID: PMC5885306 DOI: 10.1186/s13100-018-0118-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/26/2018] [Indexed: 12/17/2022] Open
Abstract
Background Since the completion of the human genome project, the diversity of genome sequencing data produced for non-human primates has increased exponentially. Papio baboons are well-established biological models for studying human biology and evolution. Despite substantial interest in the evolution of Papio, the systematics of these species has been widely debated, and the evolutionary history of Papio diversity is not fully understood. Alu elements are primate-specific transposable elements with a well-documented mutation/insertion mechanism and the capacity for resolving controversial phylogenetic relationships. In this study, we conducted a whole genome analysis of Alu insertion polymorphisms unique to the Papio lineage. To complete these analyses, we created a computational algorithm to identify novel Alu insertions in next-generation sequencing data. Results We identified 187,379 Alu insertions present in the Papio lineage, yet absent from M. mulatta [Mmul8.0.1]. These elements were characterized using genomic data sequenced from a panel of twelve Papio baboons: two from each of the six extant Papio species. These data were used to construct a whole genome Alu-based phylogeny of Papio baboons. The resulting cladogram fully-resolved relationships within Papio. Conclusions These data represent the most comprehensive Alu-based phylogenetic reconstruction reported to date. In addition, this study produces the first fully resolved Alu-based phylogeny of Papio baboons. Electronic supplementary material The online version of this article (10.1186/s13100-018-0118-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vallmer E Jordan
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
| | - Jerilyn A Walker
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
| | - Thomas O Beckstrom
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
| | - Cody J Steely
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
| | - Cullen L McDaniel
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
| | - Corey P St Romain
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
| | | | - Kim C Worley
- 2Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA.,3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jane Phillips-Conroy
- 4Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Clifford J Jolly
- 5Department of Anthropology, New York University, New York, NY 10003 USA
| | - Jeffrey Rogers
- 2Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA.,3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Miriam K Konkel
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA.,6Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634 USA
| | - Mark A Batzer
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
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Spradling-Reeves KD, Shade RE, Haywood JR, Cox LA. Primate response to angiotensin infusion and high sodium intake differ by sodium lithium countertransport phenotype. ACTA ACUST UNITED AC 2017; 11:178-184. [PMID: 28238630 DOI: 10.1016/j.jash.2017.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/05/2017] [Accepted: 01/24/2017] [Indexed: 11/18/2022]
Abstract
An increased level of sodium-lithium countertransport (SLC) activity has been associated with salt-sensitive hypertension. Previous findings have suggested that dysregulation of the renin-angiotensin-aldosterone system (RAAS) may be involved in the mechanism linking elevated SLC activity and hypertension. Therefore, baboons with different levels of SLC activity were given two diets differing in sodium content, with and without an angiotensin II (ANG II) infusion, to investigate the relationship between SLC activity, the RAAS, and physiological regulation by sodium. Although we anticipated that high SLC activity would be associated with inappropriate function of the RAAS and greater arterial pressure sensitivity to dietary sodium and ANG II and that low SLC activity would be associated with the least BP sensitivity, we found that the low SLC phenotype correlated with BP sensitivity similar to the high SLC phenotype, and the normal SLC phenotype showed the least BP sensitivity to dietary sodium and ANG II.
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Affiliation(s)
| | - Robert E Shade
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Joseph R Haywood
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
| | - Laura A Cox
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA; Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
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NHA2 is expressed in distal nephron and regulated by dietary sodium. J Physiol Biochem 2016; 73:199-205. [PMID: 27909897 DOI: 10.1007/s13105-016-0539-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 11/22/2016] [Indexed: 01/02/2023]
Abstract
Increased renal reabsorption of sodium is a significant risk factor in hypertension. An established clinical marker for essential hypertension is elevated sodium lithium countertransport (SLC) activity. NHA2 is a newly identified Na+(Li+)/H+ antiporter with potential genetic links to hypertension, which has been shown to mediate SLC activity and H+-coupled Na+(Li+) efflux in kidney-derived MDCK cells. To evaluate a putative role in sodium homeostasis, we determined the effect of dietary salt on NHA2. In murine kidney sections, NHA2 localized apically to distal convoluted (both DCT1 and 2) and connecting tubules, partially overlapping in distribution with V-ATPase, AQP2, and NCC1 transporters. Mice fed a diet high in sodium chloride showed elevated transcripts and expression of NHA2 protein. We propose a model in which NHA2 plays a dual role in salt reabsorption or secretion, depending on the coupling ion (sodium or protons). The identified novel regulation of Na+/H+ antiporter in the kidney suggests new roles in salt homeostasis and disease.
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Holmes RS, Spradling-Reeves KD, Cox LA. Evolution of Vertebrate Solute Carrier Family 9B Genes and Proteins ( SLC9B): Evidence for a Marsupial Origin for Testis Specific SLC9B1 from an Ancestral Vertebrate SLC9B2 Gene. ACTA ACUST UNITED AC 2016; 4. [PMID: 28868326 DOI: 10.4172/2329-9002.1000167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
SLC9B genes and proteins are members of the sodium/lithium hydrogen antiporter family which function as solute exchangers within cellular membranes of mammalian tissues. SLC9B2 and SLC9B1 amino acid sequences and structures and SLC9B-like gene locations were examined using bioinformatic data from several vertebrate genome projects. Vertebrate SLC9B2 sequences shared 56-98% identity as compared with ∼50% identities with mammalian SLC9B1 sequences. Sequence alignments, key amino acid residues and conserved predicted transmembrane structures were also studied. Mammalian SLC9B2 and SLC9B1 genes usually contained 11 or 12 coding exons with differential tissue expression patterns: SLC9B2, broad tissue distribution; and SLC9B1, being testis specific. Transcription factor binding sites and CpG islands within the human SLC9B2 and SLC9B1 gene promoters were identified. Phylogenetic analyses suggested that SLC9B1 originated in an ancestral marsupial genome from a SLC9B2 gene duplication event.
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Affiliation(s)
- Roger S Holmes
- Eskitis Institute for Drug Discovery and School of Natural Sciences, Griffith University, Nathan, QLD, Australia.,Department of Genetics and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Kimberly D Spradling-Reeves
- Department of Genetics and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Laura A Cox
- Department of Genetics and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
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Cox LA, Comuzzie AG, Havill LM, Karere GM, Spradling KD, Mahaney MC, Nathanielsz PW, Nicolella DP, Shade RE, Voruganti S, VandeBerg JL. Baboons as a model to study genetics and epigenetics of human disease. ILAR J 2014; 54:106-21. [PMID: 24174436 DOI: 10.1093/ilar/ilt038] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A major challenge for understanding susceptibility to common human diseases is determining genetic and environmental factors that influence mechanisms underlying variation in disease-related traits. The most common diseases afflicting the US population are complex diseases that develop as a result of defects in multiple genetically controlled systems in response to environmental challenges. Unraveling the etiology of these diseases is exceedingly difficult because of the many genetic and environmental factors involved. Studies of complex disease genetics in humans are challenging because it is not possible to control pedigree structure and often not practical to control environmental conditions over an extended period of time. Furthermore, access to tissues relevant to many diseases from healthy individuals is quite limited. The baboon is a well-established research model for the study of a wide array of common complex diseases, including dyslipidemia, hypertension, obesity, and osteoporosis. It is possible to acquire tissues from healthy, genetically characterized baboons that have been exposed to defined environmental stimuli. In this review, we describe the genetic and physiologic similarity of baboons with humans, the ability and usefulness of controlling environment and breeding, and current genetic and genomic resources. We discuss studies on genetics of heart disease, obesity, diabetes, metabolic syndrome, hypertension, osteoporosis, osteoarthritis, and intrauterine growth restriction using the baboon as a model for human disease. We also summarize new studies and resources under development, providing examples of potential translational studies for targeted interventions and therapies for human disease.
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Spradling KD, Glenn JP, Garcia R, Shade RE, Cox LA. The baboon kidney transcriptome: analysis of transcript sequence, splice variants, and abundance. PLoS One 2013; 8:e57563. [PMID: 23637735 PMCID: PMC3634053 DOI: 10.1371/journal.pone.0057563] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 01/24/2013] [Indexed: 12/25/2022] Open
Abstract
The baboon is an invaluable model for the study of human health and disease, including many complex diseases of the kidney. Although scientists have made great progress in developing this animal as a model for numerous areas of biomedical research, genomic resources for the baboon, such as a quality annotated genome, are still lacking. To this end, we characterized the baboon kidney transcriptome using high-throughput cDNA sequencing (RNA-Seq) to identify genes, gene variants, single nucleotide polymorphisms (SNPs), insertion-deletion polymorphisms (InDels), cellular functions, and key pathways in the baboon kidney to provide a genomic resource for the baboon. Analysis of our sequencing data revealed 45,499 high-confidence SNPs and 29,813 InDels comparing baboon cDNA sequences with the human hg18 reference assembly and identified 35,900 cDNAs in the baboon kidney, including 35,150 transcripts representing 15,369 genic genes that are novel for the baboon. Gene ontology analysis of our sequencing dataset also identified numerous biological functions and canonical pathways that were significant in the baboon kidney, including a large number of metabolic pathways that support known functions of the kidney. The results presented in this study catalogues the transcribed mRNAs, noncoding RNAs, and hypothetical proteins in the baboon kidney and establishes a genomic resource for scientists using the baboon as an experimental model.
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Affiliation(s)
- Kimberly D Spradling
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America.
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Kondapalli KC, Kallay LM, Muszelik M, Rao R. Unconventional chemiosmotic coupling of NHA2, a mammalian Na+/H+ antiporter, to a plasma membrane H+ gradient. J Biol Chem 2012; 287:36239-50. [PMID: 22948142 DOI: 10.1074/jbc.m112.403550] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human NHA2, a newly discovered cation proton antiporter, is implicated in essential hypertension by gene linkage analysis. We show that NHA2 mediates phloretin-sensitive Na(+)-Li(+) counter-transport (SLC) activity, an established marker for hypertension. In contrast to bacteria and fungi where H(+) gradients drive uptake of metabolites, secondary transport at the plasma membrane of mammalian cells is coupled to the Na(+) electrochemical gradient. Our findings challenge this paradigm by showing coupling of NHA2 and V-type H(+)-ATPase at the plasma membrane of kidney-derived MDCK cells, resulting in a virtual Na(+) efflux pump. Thus, NHA2 functionally recapitulates an ancient shared evolutionary origin with bacterial NhaA. Although plasma membrane H(+) gradients have been observed in some specialized mammalian cells, the ubiquitous tissue distribution of NHA2 suggests that H(+)-coupled transport is more widespread. The coexistence of Na(+) and H(+)-driven chemiosmotic circuits has implications for salt and pH regulation in the kidney.
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Affiliation(s)
- Kalyan C Kondapalli
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Northcott CA, Glenn JP, Shade RE, Kammerer CM, Hinojosa-Laborde C, Fink GD, Haywood JR, Cox LA. A custom rat and baboon hypertension gene array to compare experimental models. Exp Biol Med (Maywood) 2012; 237:99-110. [PMID: 22228705 DOI: 10.1258/ebm.2011.011188] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
One challenge in understanding the polygenic disease of hypertension is elucidating the genes involved and defining responses to environmental factors. Many studies focus on animal models of hypertension; however, this does not necessarily extrapolate to humans. Current technology and cost limitations are prohibitive in fully evaluating hypertension within humans. Thus, we have designed a single-array platform that allows direct comparison of genes relevant to hypertension in animal models and non-human primates/human hypertension. The custom array is targeted to 328 genes known to be potentially related to blood pressure control. Studies compared gene expression in the kidney from normotensive rats and baboons. We found 74 genes expressed in both the rat and baboon kidney, 41 genes expressed in the rat kidney that were not detected in the baboon kidney and 34 genes expressed in the baboon kidney that were not detected in the rat kidney. To begin the evaluation of the array in a pathological condition, kidney gene expression was compared between the salt-sensitive deoxycorticosterone acetate (DOCA) rat model of hypertension and sham animals. Gene expression in the renal cortex and medulla from hypertensive DOCA compared with sham rats revealed three genes differentially expressed in the renal cortex: annexin A1 (up-regulated; relative intensity: 1.316 ± 0.321 versus 2.312 ± 0.283), glutamate-cysteine ligase (down-regulated; relative intensity: 3.738 ± 0.174 versus 2.645 ± 0.364) and glutathione-S transferase (down-regulated; relative intensity: 5.572 ± 0.246 versus 4.215 ± 0.411) and 21 genes differentially expressed in the renal medulla. Interestingly, few genes were differentially expressed in the kidney in the DOCA-salt model of hypertension; this may suggest that the complexity of hypertension may be the result of only a few gene-by-environment responsive events.
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Affiliation(s)
- Carrie A Northcott
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA.
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Gagliardi C, Falkenstein KP, Franke DE, Kubisch HM. Estimates of heritability for reproductive traits in captive rhesus macaque females. Am J Primatol 2010; 72:811-9. [PMID: 20653007 PMCID: PMC2909610 DOI: 10.1002/ajp.20843] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Records from a colony of captive Indian rhesus macaques (Macaca mulatta) were used to estimate heritability for a number of reproductive traits. Records were based on a total of 7,816 births by 1,901 females from 1979 to 2007. Heritability was estimated with a linear animal model using a multiple trait derivative free REML set of programs. Because no male parents were identified, the numerator relationship matrix contained female kinships established over six generations. Reproductive traits included female age at the birth of the first, second and last infant, age at death, inter-birth intervals, number of infants born per female and infant survival. Heritability for each trait was estimated as the ratio of the additive genetic variance to phenotypic variance adjusted for significant fixed effects. Estimates of heritability for early reproduction ranged from 0.000+/-0.072 for birth interval after the first reproduction to 0.171+/-0.062 for age of female at the first infant. Higher estimates of heritability were found for female longevity [0.325+/-0.143] and for productivity of deceased females born before 1991 [0.221+/-0.138]. Heritability for infant survival ranged from 0.061+/-0.018 for survival from 30 days to 1 year to 0.290+/-0.050 for survival from birth to 30 days when adjusted to an underlying normal distribution. Eight of the 13 estimates of heritability for reproductive traits in this study were different from zero [P<0.05]. Generally, heritability estimates reported in this study for reproductive traits of captive rhesus macaque females are similar to those reported in the literature for free-ranging rhesus macaque females and for similar reproductive traits of other species. These estimates of heritability for reproductive traits appear to be among the first for a relatively large colony of captive rhesus macaque females.
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Affiliation(s)
- Christine Gagliardi
- Division of Gene Therapy, Tulane National Primate Research Center, Covington LA 70433 USA
| | - Kathrine P. Falkenstein
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington LA 70433 USA
| | - Donald E. Franke
- School of Animal Sciences, Louisiana State University AgCenter, Baton Rouge, LA 70803
| | - H. Michael Kubisch
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington LA 70433 USA
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Cox LA, Glenn J, Ascher S, Birnbaum S, VandeBerg JL. Integration of genetic and genomic methods for identification of genes and gene variants encoding QTLs in the nonhuman primate. Methods 2009; 49:63-9. [PMID: 19596448 PMCID: PMC2760456 DOI: 10.1016/j.ymeth.2009.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 06/01/2009] [Accepted: 06/05/2009] [Indexed: 11/20/2022] Open
Abstract
We have developed an integrated approach, using genetic and genomic methods, in conjunction with resources from the Southwest National Primate Research Center (SNPRC) baboon colony, for the identification of genes and their functional variants that encode quantitative trait loci (QTL). In addition, we use comparative genomic methods to overcome the paucity of baboon specific reagents and to augment translation of our findings in a nonhuman primate (NHP) to the human population. We are using the baboon as a model to study the genetics of cardiovascular disease (CVD). A key step for understanding gene-environment interactions in cardiovascular disease is the identification of genes and gene variants that influence CVD phenotypes. We have developed a sequential methodology that takes advantage of the SNPRC pedigreed baboon colony, the annotated human genome, and current genomic and bioinformatic tools. The process of functional polymorphism identification for genes encoding QTLs involves comparison of expression profiles for genes and predicted genes in the genomic region of the QTL for individuals discordant for the phenotypic trait mapping to the QTL. After comparison, genes of interest are prioritized, and functional polymorphisms are identified in candidate genes by genotyping and quantitative trait nucleotide analysis. This approach reduces the time and labor necessary to prioritize and identify genes and their polymorphisms influencing variation in a quantitative trait compared with traditional positional cloning methods.
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Affiliation(s)
- Laura A Cox
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78227, USA.
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Association of SLC34A2 variation and sodium-lithium countertransport activity in humans and baboons. Am J Hypertens 2009; 22:288-93. [PMID: 19119262 DOI: 10.1038/ajh.2008.355] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Sodium-lithium countertransport (SLC) activity, an intermediate phenotype of essential hypertension, has been linked to a region of baboon chromosome 5, homologous to human chromosome 4p. Human SLC34A2, located at chromosome 4p15.1-p15.3, is a positional candidate gene for SLC. The specific aim of this study was to identify genetic variants of the SLC34A2 gene in both baboon and human, and to examine the relationship of these polymorphisms with SLC activity and blood pressure. METHODS Single-nucleotide polymorphism (SNP) was identified by sequencing the SLC34A2 gene in 24 baboon founders and 94 unrelated individuals. All tag SNPs in SLC34A2 were genotyped in 1,856 individuals from 252 pedigrees of mixed European ancestry. Three SNPs in baboon were genotyped in 634 baboons comprising 11 pedigrees. RESULTS In human, one SNP (rs12501856) was found to be significantly associated with SLC individually, though it did not pass multiple testing correction; however, haplotype 2 containing allele C of SNP rs12501856 showed strong evidence of association with SLC (P = 0.0037) after multiple comparison adjustment. This haplotype was also marginally associated with diastolic blood pressure and systolic blood pressure. This finding was confirmed in baboons, where a highly significant association was detected between SLC and baboon SNP Asn136Asn (P = 0.0001). However, the associated SNP did not account for the linkage signal on baboon chromosome 5. CONCLUSIONS Consistent results in two different species imply that SLC34A2 is associated with SLC activity and blood pressure.
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Satkoski JA, Malhi R, Kanthaswamy S, Tito R, Malladi V, Smith D. Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta). BMC Genomics 2008; 9:256. [PMID: 18510772 PMCID: PMC2443142 DOI: 10.1186/1471-2164-9-256] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Accepted: 05/29/2008] [Indexed: 11/29/2022] Open
Abstract
Background Rhesus macaques (Macaca mulatta) are the primate most used for biomedical research, but phenotypic differences between Indian-origin and Chinese rhesus macaques have encouraged genetic methods for identifying genetic differences between these two populations. The completion of the rhesus genome has led to the identification of many single nucleotide polymorphisms (SNPs) in this species. These single nucleotide polymorphisms have many advantages over the short tandem repeat (STR) loci currently used to assay genetic variation. However, the number of currently identified polymorphisms is too small for whole genome analysis or studies of quantitative trait loci. To that end, we tested a combination of methods to identify large numbers of high-confidence SNPs, and screen those with high minor allele frequencies (MAF). Results By testing our previously reported single nucleotide polymorphisms, we identified a subset of high-confidence, high-MAF polymorphisms. Resequencing revealed a large number of regionally specific SNPs not identified through a single pyrosequencing run. By resequencing a pooled sample of four individuals, we reliably identified loci with a MAF of at least 12.5%. Finally, we found that when applied to a larger, geographically variable sample of rhesus, a large proportion of our loci were variable in both populations, and very few loci were ancestry informative. Despite this fact, the SNP loci were more effective at discriminating Indian and Chinese rhesus than STR loci. Conclusion Pyrosequencing and pooled resequencing are viable methods for the identification of high-MAF SNP loci in rhesus macaques. These SNP loci are appropriate for screening both the inter- and intra-population genetic variation.
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Affiliation(s)
- Jessica A Satkoski
- Department of Anthropology, University of California-Davis, One Shields Avenue, Davis, CA, USA.
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Morrison AC, Boerwinkle E, Turner ST, Ferrell RE. Regional association-based fine-mapping for sodium-lithium countertransport on chromosome 10. Am J Hypertens 2008; 21:117-21. [PMID: 18091754 DOI: 10.1038/ajh.2007.17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Increased erythrocyte sodium-lithium countertransport (SLC) has been observed in patients with essential hypertension. Consistent evidence of genetic linkage was shown for SLC on chromosome 10, and a region of interest was localized between 26 and 56 Mb. METHODS This study surveyed single nucleotide polymorphisms (SNPs) in 54 genes that reside in the region of interest, and investigated their association with SLC and blood pressure. These SNPs were genotyped in 1,133 non-Hispanic white individuals from 255 pedigrees comprising the second phase of the Rochester Family Heart Study. The variance-components-based genetics software package SOLAR was used for evaluating whether an SNP contributed to a significant fraction of the trait heritability. RESULTS Of the 77 SNPs surveyed in this study across the region of interest, four SNPs were associated with SLC (P < 0.04), five SNPs were associated with blood pressure (P < 0.04), and two SNPs in mannose-binding lectin 2 (MBL2) were associated with both phenotypes. In general, the pairwise linkage disequilibrium among the genotyped SNPs was low. CONCLUSIONS This fine-mapping survey of genetic variation in a linkage region of interest provides overall support for association-mapping for SLC on chromosome 10. Genes significantly associated with systolic blood pressure and/or SLC in these families will be prioritized for future studies.
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Rogers J, Shelton SE, Shelledy W, Garcia R, Kalin NH. Genetic influences on behavioral inhibition and anxiety in juvenile rhesus macaques. GENES BRAIN AND BEHAVIOR 2007; 7:463-9. [PMID: 18045243 DOI: 10.1111/j.1601-183x.2007.00381.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In humans and other animals, behavioral responses to threatening stimuli are an important component of temperament. Among children, extreme behavioral inhibition elicited by novel situations or strangers predicts the subsequent development of anxiety disorders and depression. Genetic differences among children are known to affect risk of developing behavioral inhibition and anxiety, but a more detailed understanding of genetic influences on susceptibility is needed. Nonhuman primates provide valuable models for studying the mechanisms underlying human behavior. Individual differences in threat-induced behavioral inhibition (freezing behavior) in young rhesus monkeys are stable over time and reflect individual levels of anxiety. This study used the well-established human intruder paradigm to elicit threat-induced freezing behavior and other behavioral responses in 285 young pedigreed rhesus monkeys. We examined the overall influence of quantitative genetic variation and tested the specific effect of the serotonin transporter promoter repeat polymorphism. Quantitative genetic analyses indicated that the residual heritability of freezing duration (behavioral inhibition) is h(2) = 0.384 (P = 0.012) and of 'orienting to the intruder' (vigilance) is h(2) = 0.908 (P = 0.00001). Duration of locomotion and hostility and frequency of cooing were not significantly heritable. The serotonin transporter polymorphism showed no significant effect on either freezing or orienting to the intruder. Our results suggest that this species could be used for detailed studies of genetic mechanisms influencing extreme behavioral inhibition, including the identification of specific genes that are involved in predisposing individuals to such behavior.
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Affiliation(s)
- J Rogers
- Department of Genetics, Southwest Foundation for Biomedical Research and Southwest National Primate Research Center, San Antonio, TX 78227, USA.
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A human Na+/H+ antiporter sharing evolutionary origins with bacterial NhaA may be a candidate gene for essential hypertension. Proc Natl Acad Sci U S A 2007; 104:18677-81. [PMID: 18000046 DOI: 10.1073/pnas.0707120104] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analysis of the cation/proton antiporter superfamily has uncovered a previously unknown clade of genes in metazoan genomes, including two previously uncharacterized human isoforms, NHA1 and NHA2, found in tandem on human chromosome 4. The NHA (sodium hydrogen antiporter) family members share significant sequence similarity with Escherichia coli NhaA, including a conserved double aspartate motif in predicted transmembrane 5. We show that HsNHA2 (Homo sapiens NHA2) resides on the plasma membrane and, in polarized MDCK cells, localizes to the apical domain. Analysis of mouse tissues indicates that NHA2 is ubiquitous. When expressed in the yeast Saccharomyces cerevisiae lacking endogenous cation/proton antiporters and pumps, HsNHA2 can confer tolerance to Li(+) and Na(+) ions but not to K(+). HsNHA2 transformants accumulated less Li(+) than the salt-sensitive host; however, mutagenic replacement of the conserved aspartates abolished all observed phenotypes. Functional complementation by HsNHA2 was insensitive to amiloride, a characteristic inhibitor of plasma membrane sodium hydrogen exchanger isoforms, but was inhibited by phloretin. These are hallmarks of sodium-lithium countertransport activity, a highly heritable trait correlating with hypertension. Our findings raise the possibility that NHA genes may contribute to sodium-lithium countertransport activity and salt homeostasis in humans.
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Rogers J, Kochunov P, Lancaster J, Shelledy W, Glahn D, Blangero J, Fox P. Heritability of brain volume, surface area and shape: an MRI study in an extended pedigree of baboons. Hum Brain Mapp 2007; 28:576-83. [PMID: 17437285 PMCID: PMC6871350 DOI: 10.1002/hbm.20407] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
To evaluate baboons (Papio hamadryas) as a primate model for the study of the genetic control of brain size and internal structure, we performed high resolution (<500 microm) magnetic resonance imaging on 109 pedigreed baboons. Quantitative genetic analysis of these MR images using a variance components approach indicates that native (untransformed) brain volume exhibits significant heritability among these baboons (h(2) = 0.52, P = 0.0049), with age and sex also accounting for substantial variation. Using global spatial normalization, we transformed all images to a standard population-specific reference, and recalculated the heritability of brain volume. The transformed images generated heritability estimates of h(2) = 0.82 (P = 0.00022) for total brain volume, h(2) = 0.86 (P = 0.0006) for cerebral volume, h(2) = 0.73 (P = 0.0069) for exposed surface area of the cerebrum and h(2) = 0.67 (P = 0.01) for gray matter volume. Regional differences in the genetic effects on brain structure were calculated using a voxel-based morphometry (VBM) approach. This analysis of regional variation shows that some areas of motor cortex and the superior temporal gyrus show relatively high heritability while other regions (e.g. superior parietal cortex) exhibit lower heritability. The general pattern of regional differences is similar to that observed in previous studies of humans. The present study demonstrates that there is substantial genetic variation underlying individual variation in brain size and structure among Papio baboons, and that broad patterns of genetic influence on variation in brain structure may be similar in baboons and humans.
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Affiliation(s)
- Jeffrey Rogers
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas 78227, USA.
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Cox LA, Mahaney MC, Vandeberg JL, Rogers J. A second-generation genetic linkage map of the baboon (Papio hamadryas) genome. Genomics 2006; 88:274-81. [PMID: 16697552 DOI: 10.1016/j.ygeno.2006.03.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Revised: 03/27/2006] [Accepted: 03/29/2006] [Indexed: 11/29/2022]
Abstract
Construction of genetic linkage maps for nonhuman primate species provides information and tools that are useful for comparative analysis of chromosome structure and evolution and facilitates comparative analysis of meiotic recombination mechanisms. Most importantly, nonhuman primate genome linkage maps provide the means to conduct whole genome linkage screens for localization and identification of quantitative trait loci that influence phenotypic variation in primate models of common complex human diseases such as atherosclerosis, hypertension, and diabetes. In this study we improved a previously published baboon whole genome linkage map by adding more loci. New loci were added in chromosomal regions that did not have sufficient marker density in the initial map. Relatively low heterozygosity loci from the original map were replaced with higher heterozygosity loci. We report in detail on baboon chromosomes 5, 12, and 18 for which the linkage maps are now substantially improved due to addition of new informative markers.
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Affiliation(s)
- Laura A Cox
- Department of Genetics and Southwest National Primate Research Center, Southwest Foundation for Biomedical Research, 7620 NW Loop 410, San Antonio, TX 78227, USA.
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Rogers J, Garcia R, Shelledy W, Kaplan J, Arya A, Johnson Z, Bergstrom M, Novakowski L, Nair P, Vinson A, Newman D, Heckman G, Cameron J. An initial genetic linkage map of the rhesus macaque (Macaca mulatta) genome using human microsatellite loci. Genomics 2006; 87:30-8. [PMID: 16321502 DOI: 10.1016/j.ygeno.2005.10.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2005] [Revised: 09/25/2005] [Accepted: 10/14/2005] [Indexed: 10/25/2022]
Abstract
Rhesus macaques (Macaca mulatta) are the most widely used nonhuman primate species in biomedical research. To create new opportunities for genetic and genomic studies using rhesus monkeys, we constructed a genetic linkage map of the rhesus genome. This map consists of 241 microsatellite loci, all previously mapped in the human genome. These polymorphisms were genotyped in five pedigrees of rhesus monkeys totaling 865 animals. The resulting linkage map covers 2048 cM including all 20 rhesus autosomes, with average spacing between markers of 9.3 cM. Average heterozygosity among those markers is 0.73. This linkage map provides new comparative information concerning locus order and interlocus distances in humans and rhesus monkeys. The map will facilitate whole-genome linkage screens to locate quantitative trait loci (QTLs) that influence individual variation in phenotypic traits related to basic primate anatomy, physiology, and behavior, as well as QTLs relevant to risk factors for human disease.
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Affiliation(s)
- Jeffrey Rogers
- Department of Genetics, Southwest Foundation for Biomedical Research, 7620 N.W., Loop 410, San Antonio, TX 78227, USA.
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Vaccaro O, Cuomo V, Trevisan M, Cirillo M, Panarelli W, Laurenzi M, Mancini M, Riccardi G. Enhanced Na–Li countertransport: a marker of inherited susceptibility to type 2 diabetes. Int J Epidemiol 2005; 34:1123-8. [PMID: 16087689 DOI: 10.1093/ije/dyi160] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED Introduction The association between type 2 diabetes and hypertension has long been described, but the mechanisms remain unclear. Na-Li countertransport (Na-Li CT) activity is viewed as a marker of inherited pre-disposition to hypertension, especially if associated with other metabolic abnormalities. Aim To evaluate whether enhanced Na-Li CT activity is a predictor of type 2 diabetes. METHODS Study participants were 2167 men and women, 30-70 years. Na-Li CT activity, glucose, HDL cholesterol, blood pressure, height, and weight were measured. Six years incidence of diabetes (WHO) was assessed. RESULTS Baseline Na-Li CT activity was significantly higher for people who developed diabetes at follow-up (n = 101) than for those who remained non-diabetic (364 +/- 184 vs 300 +/- 150 micromol/l RBC/h, P < 0.001). This finding was confirmed after correction for obesity, hypertension, and blood glucose. Six years' incidence of diabetes increased across tertiles of baseline Na-Li CT activity--from 2 to 7%--with a significant linear trend (P < 0.001). In multivariate analyses Na-Li CT is a significant predictor of diabetes independent of age, BMI, HDL cholesterol, hypertension, and plasma glucose; based on exponentiation of the regression coefficient Na-Li CT higher by 154 micromol (i.e. 1 SD of the population mean) was associated with a 36% greater risk of incident diabetes. CONCLUSIONS Prospective data from the present study show for the first time enhanced Na-Li CT activity is a significant predictor of development of diabetes in adults, thus suggesting that it could be viewed as a pre-clinical, possibly genetic, marker of inherited susceptibility to type 2 diabetes.
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Affiliation(s)
- Olga Vaccaro
- Department of Clinical and Experimental Medicine, Federico II University of Naples, Napoli, Italy.
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Hasstedt SJ, Camp NJ, Hopkins PN, Coon H, McKinney JT, Cawthon RM, Hunt SC. Model-fitting and linkage analysis of sodium–lithium countertransport. Eur J Hum Genet 2004; 12:1055-61. [PMID: 15383825 DOI: 10.1038/sj.ejhg.5201262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Increased sodium-lithium countertransport activity (SLC) associates with hypertension and is highly heritable, yet the underlying genes remain unknown. SLC, measured on 1113 and remeasured 2-3 years later on 675 adult members of 48 Utah pedigrees, was tested for candidate gene association, major locus inheritance, and linkage to genome scan markers using a bivariate model with genotype-specific effects of age, body mass index (BMI), and triglycerides level (TG). No effect of the alpha-adducin Gly460Trp polymorphism on SLC was found. In contrast, SLC increased with age in carriers of apolipoproteinE varepsilon2 (85 individuals; 8.7% of the sample) and decreased in noncarriers. Model-fitting analyses inferred two additional loci with genotype-specific responses to BMI and TG. Using the inferred model, lod scores >2 were obtained for D3S3038, D11S4464, and D10S677 for the BMI-responsive locus, and for D8S1048 for the TG-responsive locus.
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Affiliation(s)
- Sandra J Hasstedt
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA.
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Williamson DE, Coleman K, Bacanu SA, Devlin BJ, Rogers J, Ryan ND, Cameron JL. Heritability of fearful-anxious endophenotypes in infant rhesus macaques: a preliminary report. Biol Psychiatry 2003; 53:284-91. [PMID: 12586447 DOI: 10.1016/s0006-3223(02)01601-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Research efforts to discover the genetic underpinnings of anxiety and depression is challenging because of the etiologic heterogeneity inherent to these disorders. These efforts might be aided by the study of related behavioral phenotypes in model organisms, such as monkeys. METHODS Eighty-five rhesus monkeys (Macaca mulatta) from the Oregon National Primate Research Center were drawn from a standard matriarchal colony and tested for behavioral response in four testing paradigms designed to elicit fearful-anxious reactions. Heritabilities were estimated using variance component-based quantitative genetic analyses with much of the genetic information arising from paternal half-sibs. RESULTS Individual behaviors reflecting increased distress responses (e.g., vocalizations and teeth grinding) and behavioral inhibition (e.g., latency to leave mother, latency to inspect novel fruit) showed significant heritability, even though a small number of monkeys were assessed. Exploratory factor analyses identified seven clusters of behaviors across tests, some of which were found to be heritable. CONCLUSIONS These results indicate that several specific fearful-anxious behaviors in infant rhesus monkeys are heritable within this colony. Accordingly, these phenotypes, which are believed to represent the genetic liability for anxiety and depression, are good candidates for further genetic investigation in this population.
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Affiliation(s)
- Douglas E Williamson
- Department of Psychiatry, University of Pittsburgh Medical Center, Western Psychiatric Institute and Clinic, Pittsburgh, Pennsylvania 15213, USA
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Wierzbicki AS. Lipid lowering: another method of reducing blood pressure? J Hum Hypertens 2002; 16:753-60. [PMID: 12444536 DOI: 10.1038/sj.jhh.1001483] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2002] [Accepted: 09/02/2002] [Indexed: 11/08/2022]
Abstract
Modern management of cardiovascular risk depends on assessment of cardiovascular risk factors. Hypertension and hyperlipidaemia are synergistic risk factors for cardiovascular events. Both show a degree of cross-correlation through sharing mechanisms of pathogenesis including insulin resistance and endothelial dysfunction. This article reviews the common pathways leading to dyslipidaemia and hypertension and the effects diet and lipid-lowering drug therapies have had on correcting blood pressure in patients with essential hypertension. Both statins and fibrates have shown a capability to lower blood pressure by up to 8/5 and 15/10 mmHg respectively, in some small-scale clinical trials and have effects on arterial wall structure and hence pulse wave velocity. This blood pressure action may account for some of the clinical effects of lipid-lowering drugs on cardiovascular risk. Thus, lipid lowering may provide an additional method of correcting hypertension in some high-risk patients. However, data from large-scale intervention trials are either absent or ambiguous. Definitive large-scale trials to investigate the antihypertensive effects of lipid-lowering drugs are required, although end point studies examining the interaction of lipid-lowering and antihypertensive drugs to determine optimum combinations are already under way.
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Affiliation(s)
- A S Wierzbicki
- Department of Chemical Pathology, St Thomas' Hospital, London, UK
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27
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Martin LJ, Mahaney MC, Bronikowski AM, Carey KD, Dyke B, Comuzzie AG. Lifespan in captive baboons is heritable. Mech Ageing Dev 2002; 123:1461-7. [PMID: 12425953 DOI: 10.1016/s0047-6374(02)00083-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The effects of aging are evident in multiple organ systems, tissues, cell types, and molecules; all complex phenotypes affected by multiple shared and unique environmental factors and genes, which makes identifying the role of genetics in human aging difficult. Researchers have used yeast, nematodes, fruit flies, and mice to search for genes that influence the aging process. Given the phylogenetic distance and anatomic and physiologic dissimilarities of these organisms from humans, directly extrapolating these results to our species is problematic. However, nonhuman primates have a high degree of genetic, anatomic and physiologic similarity with humans and, thus, they may assist in the detection, characterization, and identification of genetic and environmental influences on human aging. Our goal is to demonstrate that effects of genes on variation in lifespan, a surrogate measure of aging, can be detected in a nonhuman primate species. Using variance component analysis, heritability of age at death was estimated to be 0.23+/-0.08 (P=0.0003) in 674 baboons from the Southwest Foundation for Biomedical Research (SFBR). This research demonstrates that lifespan is under partial genetic control. Given these findings, we believe that the baboon has potential as a model of human aging.
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Affiliation(s)
- Lisa J Martin
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78245-0549, USA.
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28
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Abstract
Cellular phenotypes have been used in the search for genes or loci harboring genes in control of blood pressure in animals and humans. Preliminary findings using cellular phenotypes confirm that multiple genes contribute to the development of essential hypertension, consistent with the polygenic nature of this disorder. Although these results are promising, no loci have been unequivocally identified as causative for human hypertension. Cellular phenotypes, if combined with large-scale studies and evolving methodologies and databases for the human genome, could play an integral role in the search for genes causing essential hypertension.
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Affiliation(s)
- Jeffrey P Gardner
- Room F-464, MSB, Hypertension Research Center, University of Medicine and Dentistry of New Jersey, 185 South Orange Avenue, Newark, NJ 07103-2714, USA.
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