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Ji MT, Pashankar N, Harter AM, Nemesh M, Przybyl KJ, Mulligan MK, Chen H, Redei EE. Limited WKY chromosomal regions confer increases in anxiety and fear memory in a F344 congenic rat strain. Physiol Genomics 2024; 56:327-342. [PMID: 38314698 PMCID: PMC11283897 DOI: 10.1152/physiolgenomics.00114.2023] [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: 10/05/2023] [Revised: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 02/07/2024] Open
Abstract
This study investigated the interaction between genetic differences in stress reactivity/coping and environmental challenges, such as acute stress during adolescence on adult contextual fear memory and anxiety-like behaviors. Fischer 344 (F344) and the inbred F344;WKY-Stresp3/Eer congenic strain (congenic), in which chromosomal regions from the Wistar-Kyoto (WKY) strain were introgressed into the F344 background, were exposed to a modified forced swim test during adolescence, while controls were undisturbed. In adulthood, fear learning and memory, assessed by contextual fear conditioning, were significantly greater in congenic animals compared with F344 animals, and stress during adolescence increased them even further in males of both strains. Anxiety-like behavior, measured by the open field test, was also greater in congenic than F344 animals, and stress during adolescence increased it further in both strains of adult males. Whole genome sequencing of the F344;WKY-Stresp3/Eer strain revealed an enrichment of WKY genotypes in chromosomes 9, 14, and 15. An example of functional WKY sequence variations in the congenic strain, cannabinoid receptor interacting protein 1 (Cnrip1) had a Cnrip1 transcript isoform that lacked two exons. Although the original hypothesis that the genetic predisposition to increased anxiety of the WKY donor strain would exaggerate fear memory relative to the background strain was confirmed, the consequences of adolescent stress were strain independent but sex dependent in adulthood. Molecular genomic approaches combined with genetic mapping of WKY sequence variations in chromosomes 9, 14, and 15 could aid in finding quantitative trait genes contributing to the variation in fear memory.NEW & NOTEWORTHY This study found that 1) whole genome sequencing of congenic strains should be a criterion for their recognition; 2) sequence variations between Wistar-Kyoto and Fischer 344 strains at regions of chromosomes 9, 14, and 15 contribute to differences in contextual fear memory and anxiety-like behaviors; and 3) stress during adolescence affects these behaviors in males, but not females, and is independent of strain.
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Affiliation(s)
- Michelle T Ji
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Neha Pashankar
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Aspen M Harter
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Mariya Nemesh
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Katherine J Przybyl
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Megan K Mulligan
- Department of Genetics, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Eva E Redei
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
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Gokula V, Terrero D, Joe B. Six Decades of History of Hypertension Research at the University of Toledo: Highlighting Pioneering Contributions in Biochemistry, Genetics, and Host-Microbiota Interactions. Curr Hypertens Rep 2022; 24:669-685. [PMID: 36301488 PMCID: PMC9708772 DOI: 10.1007/s11906-022-01226-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW The study aims to capture the history and lineage of hypertension researchers from the University of Toledo in Ohio and showcase their collective scientific contributions dating from their initial discoveries of the physiology of adrenal and renal systems and genetics regulating blood pressure (BP) to its more contemporary contributions including microbiota and metabolomic links to BP regulation. RECENT FINDINGS The University of Toledo College of Medicine and Life Sciences (UTCOMLS), previously known as the Medical College of Ohio, has contributed significantly to our understanding of the etiology of hypertension. Two of the scientists, Patrick Mulrow and John Rapp from UTCOMLS, have been recognized with the highest honor, the Excellence in Hypertension award from the American Heart Association for their pioneering work on the physiology and genetics of hypertension, respectively. More recently, Bina Joe has continued their legacy in the basic sciences by uncovering previously unknown novel links between microbiota and metabolites to the etiology of hypertension, work that has been recognized by the American Heart Association with multiple awards. On the clinical research front, Christopher Cooper and colleagues lead the CORAL trials and contributed importantly to the investigations on renal artery stenosis treatment paradigms. Hypertension research at this institution has not only provided these pioneering insights, but also grown careers of scientists as leaders in academia as University Presidents and Deans of Medical Schools. Through the last decade, the university has expanded its commitment to Hypertension research as evident through the development of the Center for Hypertension and Precision Medicine led by Bina Joe as its founding Director. Hypertension being the top risk factor for cardiovascular diseases, which is the leading cause of human mortality, is an important area of research in multiple international universities. The UTCOMLS is one such university which, for the last 6 decades, has made significant contributions to our current understanding of hypertension. This review is a synthesis of this rich history. Additionally, it also serves as a collection of audio archives by more recent faculty who are also prominent leaders in the field of hypertension research, including John Rapp, Bina Joe, and Christopher Cooper, which are cataloged at Interviews .
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Affiliation(s)
- Veda Gokula
- Center for Hypertension and Precision Medicine, Department of Physiology and Pharmacology, College of Medicine and Life Sciences, University of Toledo College of Medicine and Life Sciences, Block Health Science Building, 3000 Arlington Ave, Toledo, OH, 43614-2598, USA
| | - David Terrero
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy, University of Toledo, Toledo, OH, USA
| | - Bina Joe
- Center for Hypertension and Precision Medicine, Department of Physiology and Pharmacology, College of Medicine and Life Sciences, University of Toledo College of Medicine and Life Sciences, Block Health Science Building, 3000 Arlington Ave, Toledo, OH, 43614-2598, USA.
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Mei X, Mell B, Cheng X, Yeo JY, Yang T, Chiu N, Joe B. Beyond the gastrointestinal tract: oral and sex-specific skin microbiota are associated with hypertension in rats with genetic disparities. Physiol Genomics 2022; 54:242-250. [PMID: 35503026 PMCID: PMC9208435 DOI: 10.1152/physiolgenomics.00169.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/18/2022] [Accepted: 04/28/2022] [Indexed: 11/22/2022] Open
Abstract
Current knowledge of the link between microbiota and hypertension is limited to the gut. Besides the gut, oral cavity and skin are other locations where sodium chloride (NaCl) is in direct contact with microbiota. Although oral nitrate-reducing bacteria generate nitric oxide, which leads to vasodilation and lowering of blood pressure (BP), the skin excretes sodium via sweat glands and is an important site for sodium and BP homeostasis. However, knowledge on the contributions of oral and skin microbiota to BP regulation, is limited. Therefore, the current study was conducted to compare the tripartite relationship between site, sex, and genetic effects on the composition of oral, skin, and gut microbiota impacting hypertension. Microbiota were profiled from the oral cavity, skin, and feces of both male and female hypertensive Dahl salt-sensitive (S) and congenic rats with genomic substitutions on rat chromosomes (RNO) 1, 5, 9, and 10, demonstrating disparate BP effects. Sex-specific differences in β-diversity were observed only in skin microbiota. The most abundant taxa of the oral and skin microbiota were Actinobacteria and Cyanobacteria, respectively. Oral Actinobacteria were inversely associated with BP. Although the abundance of oral Actinobacteria was upregulated by the BP locus on RNO10 in both sexes, depletion of skin Cyanobacteria decreased the protection from hypertension in the RNO5 female, but not male, congenic strain. In conclusion, to our knowledge this is the first study to identify specific microbiota in sites other than gut as contributors to BP regulation. Notably, both oral Actinobacteria and skin Cyanobacteria were beneficial for lowering BP.
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Affiliation(s)
- Xue Mei
- Department of Physiology and Pharmacology, Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Blair Mell
- Department of Physiology and Pharmacology, Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Xi Cheng
- Department of Physiology and Pharmacology, Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Ji-Youn Yeo
- Department of Physiology and Pharmacology, Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Tao Yang
- Department of Physiology and Pharmacology, Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Nathaline Chiu
- Department of Physiology and Pharmacology, Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Bina Joe
- Department of Physiology and Pharmacology, Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
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Rapp JP, Joe B. Dissecting Epistatic QTL for Blood Pressure in Rats: Congenic Strains versus Heterogeneous Stocks, a Reality Check. Compr Physiol 2019; 9:1305-1337. [PMID: 31688958 DOI: 10.1002/cphy.c180038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Advances in molecular genetics have provided well-defined physical genetic maps and large numbers of genetic markers for both model organisms and humans. It is now possible to gain a fundamental understanding of the genetic architecture underlying quantitative traits, of which blood pressure (BP) is an important example. This review emphasizes analytical techniques and results obtained using the Dahl salt-sensitive (S) rat as a model of hypertension by presenting results in detail for three specific chromosomal regions harboring genetic elements of increasing complexity controlling BP. These results highlight the critical importance of genetic interactions (epistasis) on BP at all levels of structure, intragenic, intergenic, intrachromosomal, interchromosomal, and across whole genomes. In two of the three examples presented, specific DNA structural variations leading to biochemical, physiological, and pathological mechanisms are well defined. This proves the usefulness of the techniques involving interval mapping followed by substitution mapping using congenic strains. These classic techniques are compared to newer approaches using sophisticated statistical analysis on various segregating or outbred model-organism populations, which in some cases are uniquely useful in demonstrating the existence of higher-order interactions. It is speculated that hypertension as an outlier quantitative phenotype is dependent on higher-order genetic interactions. The obstacle to the identification of genetic elements and the biochemical/physiological mechanisms involved in higher-order interactions is not theoretical or technical but the lack of future resources to finish the job of identifying the individual genetic elements underlying the quantitative trait loci for BP and ascertaining their molecular functions. © 2019 American Physiological Society. Compr Physiol 9:1305-1337, 2019.
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Affiliation(s)
- John P Rapp
- Physiological Genomics Laboratory, Department of Physiology and Pharmacology, Center for Hypertension and Precision Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Bina Joe
- Physiological Genomics Laboratory, Department of Physiology and Pharmacology, Center for Hypertension and Precision Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
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Abstract
BACKGROUND Previously, using linkage analysis and substitution mapping, two closely-linked interactive blood pressure quantitative trait loci (QTLs), BP QTL1 and BP QTL2, were located within a 13.96 Mb region from 117894038 to 131853815 bp (RGSC 3.4 version) on rat chromosome 5 (RNO5). This was done by using a series of congenic strains consisting of genomic segments of the Dahl salt-sensitive (S) rat substituted with that of the normotensive Lewis (LEW) rat. The interactive nature of the two loci was further confirmed by the construction and characterization of a panel of S.LEW bicongenic strains and corresponding S.LEW monocongenic strains, which provided definitive evidence of epistasis (genetic interaction) between BP QTL1 (7.77 Mb) and BP QTL2 (4.18 Mb). The purpose of this work was to further map these interacting QTLs. METHOD A new panel of seven new S.LEW bicongenic strains was constructed and characterized for BP. RESULTS The data obtained from these new strains further resolved BP QTL1 from 7.77 to 2.93 Mb. Further, BP QTL2 was traceable as not being a single QTL, but a composite of at least three QTLs, LEW alleles at two of which located within 2.26 Mb and 175 kb lowered BP but the third one located within 1.31 Mb increased BP. CONCLUSION Lack of coding variation within any of the regions further mapped within the previous QTL2 suggests noncoding variation as likely responsible for the observed epistasis.
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Padmanabhan S, Joe B. Towards Precision Medicine for Hypertension: A Review of Genomic, Epigenomic, and Microbiomic Effects on Blood Pressure in Experimental Rat Models and Humans. Physiol Rev 2017; 97:1469-1528. [PMID: 28931564 PMCID: PMC6347103 DOI: 10.1152/physrev.00035.2016] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 04/28/2017] [Accepted: 04/29/2017] [Indexed: 12/11/2022] Open
Abstract
Compelling evidence for the inherited nature of essential hypertension has led to extensive research in rats and humans. Rats have served as the primary model for research on the genetics of hypertension resulting in identification of genomic regions that are causally associated with hypertension. In more recent times, genome-wide studies in humans have also begun to improve our understanding of the inheritance of polygenic forms of hypertension. Based on the chronological progression of research into the genetics of hypertension as the "structural backbone," this review catalogs and discusses the rat and human genetic elements mapped and implicated in blood pressure regulation. Furthermore, the knowledge gained from these genetic studies that provide evidence to suggest that much of the genetic influence on hypertension residing within noncoding elements of our DNA and operating through pervasive epistasis or gene-gene interactions is highlighted. Lastly, perspectives on current thinking that the more complex "triad" of the genome, epigenome, and the microbiome operating to influence the inheritance of hypertension, is documented. Overall, the collective knowledge gained from rats and humans is disappointing in the sense that major hypertension-causing genes as targets for clinical management of essential hypertension may not be a clinical reality. On the other hand, the realization that the polygenic nature of hypertension prevents any single locus from being a relevant clinical target for all humans directs future studies on the genetics of hypertension towards an individualized genomic approach.
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Affiliation(s)
- Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; and Center for Hypertension and Personalized Medicine; Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Bina Joe
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; and Center for Hypertension and Personalized Medicine; Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
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Cheng X, Waghulde H, Mell B, Morgan EE, Pruett-Miller SM, Joe B. Positional cloning of quantitative trait nucleotides for blood pressure and cardiac QT-interval by targeted CRISPR/Cas9 editing of a novel long non-coding RNA. PLoS Genet 2017; 13:e1006961. [PMID: 28827789 PMCID: PMC5578691 DOI: 10.1371/journal.pgen.1006961] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/31/2017] [Accepted: 08/07/2017] [Indexed: 01/11/2023] Open
Abstract
Multiple GWAS studies have reported strong association of cardiac QT-interval to a region on HSA17. Interestingly, a rat locus homologous to this region is also linked to QT-intervals. The high resolution positional mapping study located the rat QT-interval locus to a <42.5kb region on RNO10. This region contained no variants in protein-coding sequences, but a prominent contiguous 19bp indel polymorphism was noted within a novel predicted long non-coding RNA (lncRNA), which we named as Rffl-lnc1. To assess the candidacy of this novel lncRNA on QT-interval, targeted CRISPR/Cas9 based genome-engineering approaches were applied on the rat strains used to map this locus. Targeted disruption of the rat Rffl-lnc1 locus caused aberrant, short QT-intervals and elevated blood pressure. Further, to specifically examine the significance of the 19bp polymorphism within the Rffl-lnc1 locus, a CRISPR/Cas9 based targeted knock-in rescue model was constructed by inserting the 19bp into the strain which contained the deletion polymorphism. The knock-in alleles successfully rescued the aberrant QT-interval and blood pressure phenotypes. Further studies revealed that the 19bp polymorphism was necessary and sufficient to recapitulate the phenotypic effect of the previously mapped <42.5kb rat locus. To our knowledge, this study is the first demonstration of a combination of both CRISPR/Cas9 based targeted disruption as well as CRISPR/Cas9 based targeted knock-in rescue approaches applied for a mammalian positional cloning study, which defines the quantitative trait nucleotides (QTNs) within a rat long non-coding RNA as being important for the pleiotropic regulation of both cardiac QT-intervals and blood pressure. Diseases of the cardiovascular system such as essential hypertension do not have a clear cause, but are known to run in families. The inheritance patterns of essential hypertension and other cardiac diseases suggest that they are not due to a single defective gene but instead are caused by multiple genetic defects that are inherited together in a patient. This complex inheritance makes it difficult to pinpoint the underlying defects. Here, we describe a panel of genetically-engineered rats, using which we have discovered a novel gene, which does not code for any protein, as a gene required for maintenance of normal blood pressure. Structural defects within this non-coding RNA cause hypertension and cardiac short-QT interval. Further, by performing genome surgery to correct the gene defect, we demonstrate the precise error in nucleotides that was inherited and caused hypertension and cardiac short-QT interval syndrome.
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Affiliation(s)
- Xi Cheng
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - Harshal Waghulde
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - Blair Mell
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - Eric E. Morgan
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
- Department of Radiology, University of Toledo Medical Center, Toledo, OH, United States of America
| | - Shondra M. Pruett-Miller
- Department of Cell & Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Bina Joe
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
- * E-mail:
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Cheng X, Joe B. Circular RNAs in rat models of cardiovascular and renal diseases. Physiol Genomics 2017; 49:484-490. [PMID: 28778982 DOI: 10.1152/physiolgenomics.00064.2017] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 07/25/2017] [Accepted: 07/27/2017] [Indexed: 12/16/2022] Open
Abstract
Circular RNAs (circRNAs) have emerged as an important new class of genomic regulatory molecules contributing to the development of various diseases, but their relevance to the development and progression of hypertension remains largely unknown. A major impediment to begin studying circRNAs in rat models of inherited hypertension is that the rat as a valuable model of human diseases lags far behind the mouse and human in providing knowledge on circRNAs. In this study, a genome-wide circRNA profiling was performed from four rat strains that are widely used in hypertension research: the Dahl salt-sensitive rat (S), the Dahl salt-resistant rat (R), the spontaneously hypertensive rat (SHR), and the Wistar Kyoto rat (WKY). Combined hybridization data obtained from these four strains allowed for the identification of 12,846 circRNAs as being expressed in the rat kidneys. Out of these, 318 and 110 circRNAs were differentially expressed with a fold change > 1.5 (P < 0.05) in S vs. R and SHR vs. WKY, respectively. Among these circRNAs, circRNA/microRNA interaction was predicted since circRNAs are known as microRNA sponges to sequester microRNAs. Several circRNAs were further validated by quantitative real-time PCR. To our knowledge, our study is the primary report of profiling circRNAs in renal tissue and illustrates that circRNAs could be candidate genetic factors controlling blood pressure.
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Affiliation(s)
- Xi Cheng
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio;
| | - Bina Joe
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
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Nie Y, Kumarasamy S, Waghulde H, Cheng X, Mell B, Czernik PJ, Lecka-Czernik B, Joe B. High-resolution mapping of a novel rat blood pressure locus on chromosome 9 to a region containing the Spp2 gene and colocalization of a QTL for bone mass. Physiol Genomics 2016; 48:409-19. [PMID: 27113531 DOI: 10.1152/physiolgenomics.00004.2016] [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] [Received: 01/05/2016] [Accepted: 04/20/2016] [Indexed: 01/11/2023] Open
Abstract
Through linkage analysis of the Dahl salt-sensitive (S) rat and the spontaneously hypertensive rat (SHR), a blood pressure (BP) quantitative trait locus (QTL) was previously located on rat chromosome 9. Subsequent substitution mapping studies of this QTL revealed multiple BP QTLs within the originally identified logarithm of odds plot by linkage analysis. The focus of this study was on a 14.39 Mb region, the distal portion of which remained unmapped in our previous studies. High-resolution substitution mapping for a BP QTL in the setting of a high-salt diet indicated that an SHR-derived congenic segment of 787.9 kb containing the gene secreted phosphoprotein-2 (Spp2) lowered BP and urinary protein excretion. A nonsynonymous G/T polymorphism in the Spp2 gene was detected between the S and S.SHR congenic rats. A survey of 45 strains showed that the T allele was rare, being detected only in some substrains of SHR and WKY. Protein modeling prediction through SWISSPROT indicated that the predicted protein product of this variant was significantly altered. Importantly, in addition to improved cardiovascular and renal function, high salt-fed congenic animals carrying the SHR T variant of Spp2 had significantly lower bone mass and altered bone microarchitecture. Total bone volume and volume of trabecular bone, cortical thickness, and degree of mineralization of cortical bone were all significantly reduced in congenic rats. Our study points to opposing effects of a congenic segment containing the prioritized candidate gene Spp2 on BP and bone mass.
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Affiliation(s)
- Ying Nie
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Sivarajan Kumarasamy
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Harshal Waghulde
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Xi Cheng
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Blair Mell
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Piotr J Czernik
- Center for Diabetes and Endocrine Research, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio; and Department of Orthopedics, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Beata Lecka-Czernik
- Center for Diabetes and Endocrine Research, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio; and Department of Orthopedics, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Bina Joe
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio;
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Joe B. Dr Lewis Kitchener Dahl, the Dahl rats, and the "inconvenient truth" about the genetics of hypertension. Hypertension 2015; 65:963-9. [PMID: 25646295 PMCID: PMC4393342 DOI: 10.1161/hypertensionaha.114.04368] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/29/2014] [Indexed: 12/28/2022]
Abstract
Lewis K. Dahl is regarded as an iconic figure in the field of hypertension research. During the 1960s and 1970s he published several seminal articles in the field that shed light on the relationship between salt and hypertension. Further, the Dahl rat models of hypertension that he developed by a selective breeding strategy are among the most widely used models for hypertension research. To this day, genetic studies using this model are ongoing in our laboratory. While Dr. Dahl is known for his contributions to the field of hypertension, very little, if any, of his personal history is documented. This article details a short biography of Dr. Lewis Dahl, the history behind the development of the Dahl rats and presents an overview of the results obtained through the genetic analysis of the Dahl rat as an experimental model to study the inheritance of hypertension.
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Affiliation(s)
- Bina Joe
- From the Department of Physiology and Pharmacology, Center for Hypertension and Personalized Medicine and Program in Physiological Genomics, University of Toledo College of Medicine and Life Sciences, OH.
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Mell B, Jala VR, Mathew AV, Byun J, Waghulde H, Zhang Y, Haribabu B, Vijay-Kumar M, Pennathur S, Joe B. Evidence for a link between gut microbiota and hypertension in the Dahl rat. Physiol Genomics 2015; 47:187-97. [PMID: 25829393 DOI: 10.1152/physiolgenomics.00136.2014] [Citation(s) in RCA: 282] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/26/2015] [Indexed: 12/20/2022] Open
Abstract
The gut microbiota plays a critical role in maintaining physiological homeostasis. This study was designed to evaluate whether gut microbial composition affects hypertension. 16S rRNA genes obtained from cecal samples of Dahl salt-sensitive (S) and Dahl salt-resistant (R) rats were sequenced. Bacteria of the phylum Bacteroidetes were higher in the S rats compared with the R rats. Furthermore, the family S24-7 of the phylum Bacteroidetes and the family Veillonellaceae of the phylum Firmicutes were higher in the S rats compared with the R rats. Analyses of the various phylogenetic groups of cecal microbiota revealed significant differences between S and R rats. Both strains were maintained on a high-salt diet, administered antibiotics for ablation of microbiota, transplanted with S or R rat cecal contents, and monitored for blood pressure (BP). Systolic BP of the R rats remained unaltered irrespective of S or R rat cecal transplantation. Surprisingly, compared with the S rats given S rat cecal content, systolic BP of the S rats given a single bolus of cecal content from R rats was consistently and significantly elevated during the rest of their life, and they had a shorter lifespan. A lower level of fecal bacteria of the family Veillonellaceae and increased plasma acetate and heptanoate were features associated with the increased BP observed in the S rats given R rat microbiota compared with the S rats given S rat microbiota. These data demonstrate a link between microbial content and BP regulation and, because the S and R rats differ in their genomic composition, provide the necessary basis to further examine the relationship between the host genome and microbiome in the context of BP regulation in the Dahl rats.
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Affiliation(s)
- Blair Mell
- Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Venkatakrishna R Jala
- James Graham Brown Cancer Center, Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky
| | - Anna V Mathew
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, Michigan; and
| | - Jaeman Byun
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, Michigan; and
| | - Harshal Waghulde
- Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Youjie Zhang
- Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Bodduluri Haribabu
- James Graham Brown Cancer Center, Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky
| | - Matam Vijay-Kumar
- Department of Nutritional Sciences and Medicine, The Pennsylvania State University, University Park, Pennsylvania
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, Michigan; and
| | - Bina Joe
- Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio;
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Gopalakrishnan K, Kumarasamy S, Mell B, Joe B. Genome-wide identification of long noncoding RNAs in rat models of cardiovascular and renal disease. Hypertension 2014; 65:200-10. [PMID: 25385761 DOI: 10.1161/hypertensionaha.114.04498] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Long noncoding RNAs (lncRNAs) are an emerging class of genomic regulatory molecules reported in various species. In the rat, which is one of the major mammalian model organisms, discovery of lncRNAs on a genome-wide scale is lagging. Renal lncRNA sequencing and lncRNA transcriptome analysis were conducted in 3 rat strains that are widely used in cardiovascular and renal research: the Dahl salt-sensitive rat, the spontaneously hypertensive rat, and the Dahl salt-resistant rat. Through the RNA sequencing approach, 3273 transcripts were identified as rat lncRNAs. A majority of lncRNAs were without predicted target genes. Differential expression of 273 and 749 lncRNAs was detected between Dahl salt-sensitive versus Dahl salt-resistant and Dahl salt-sensitive versus spontaneously hypertensive rat comparisons, respectively. To couple the observed differential expression of lncRNAs with the status of mRNAs, an mRNA transcriptome analysis was conducted. Several cis mRNA genes were coregulated with lncRNAs. Of these, the protein expression status of 4 target genes, Asb3, Chac2, Pex11b, and Sp5, were differentially expressed between the relevant strain comparisons, thereby suggesting that the differentially expressed lncRNAs associated with these genes are candidate genetic determinants of blood pressure. This study serves as a first-generation catalog of rat lncRNAs and illustrates the prioritization of lncRNAs as candidates for complex polygenic traits.
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Affiliation(s)
- Kathirvel Gopalakrishnan
- From the Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, OH
| | - Sivarajan Kumarasamy
- From the Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, OH
| | - Blair Mell
- From the Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, OH
| | - Bina Joe
- From the Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, OH.
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13
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Wang X, Zhang D, Tzeng JY. Pathway-guided identification of gene-gene interactions. Ann Hum Genet 2014; 78:478-91. [PMID: 25227508 PMCID: PMC4363308 DOI: 10.1111/ahg.12080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 07/03/2014] [Indexed: 12/26/2022]
Abstract
Assessing gene-gene interactions (GxG) at the gene level can permit examination of epistasis at biologically functional units with amplified interaction signals from marker-marker pairs. While current gene-based GxG methods tend to be designed for two or a few genes, for complex traits, it is often common to have a list of many candidate genes to explore GxG. We propose a regression model with pathway-guided regularization for detecting interactions among genes. Specifically, we use the principal components to summarize the SNP-SNP interactions between a gene pair, and use an L1 penalty that incorporates adaptive weights based on biological guidance and trait supervision to identify important main and interaction effects. Our approach aims to combine biological guidance and data adaptiveness, and yields credible findings that may be likely to shed insights in order to formulate biological hypotheses for further molecular studies. The proposed approach can be used to explore the GxG with a list of many candidate genes and is applicable even when sample size is smaller than the number of predictors studied. We evaluate the utility of the proposed method using simulation and real data analysis. The results suggest improved performance over methods not utilizing pathway and trait guidance.
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Affiliation(s)
- Xin Wang
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Daowen Zhang
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Jung-Ying Tzeng
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, National Cheng-Kung University, Tainan, Taiwan
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14
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Wang X, Epstein MP, Tzeng JY. Analysis of gene-gene interactions using gene-trait similarity regression. Hum Hered 2014; 78:17-26. [PMID: 24969398 DOI: 10.1159/000360161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 01/30/2014] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Gene-gene interactions (G×G) are important to study because of their extensiveness in biological systems and their potential in explaining missing heritability of complex traits. In this work, we propose a new similarity-based test to assess G×G at the gene level, which permits the study of epistasis at biologically functional units with amplified interaction signals. METHODS Under the framework of gene-trait similarity regression (SimReg), we propose a gene-based test for detecting G×G. SimReg uses a regression model to correlate trait similarity with genotypic similarity across a gene. Unlike existing gene-level methods based on leading principal components (PCs), SimReg summarizes all information on genotypic variation within a gene and can be used to assess the joint/interactive effects of two genes as well as the effect of one gene conditional on another. RESULTS Using simulations and a real data application to the Warfarin study, we show that the SimReg G×G tests have satisfactory power and robustness under different genetic architecture when compared to existing gene-based interaction tests such as PC analysis or partial least squares. A genome-wide association study with approx. 20,000 genes may be completed on a parallel computing system in 2 weeks.
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Affiliation(s)
- Xin Wang
- Bioinformatics Research Center, North Carolina State University, Raleigh, N.C., USA
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