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Sheng Yang,
Akiko Takizawa,
Jamie Foeckler,
Allison Zappa,
Monika Gjoka,
Rebecca Schilling,
Colin Hansen,
Haiyan Xu,
Shawn Kalloway,
Michael Grzybowski,
Gregory D Davis, Howard J Jacob,
Aron M Geurts
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ABSTRACT: The lack of rat embryonic stem cells (ESCs) and approaches for manipulation of their genomes have restricted the ability to create new genetic models and to explore the function of a single gene in complex diseases in the laboratory rat. The recent breakthrough in isolating germline-competent ESCs from rat and subsequent demonstration of gene knockout has propelled the field forward, but such tools do not yet exist for many disease-model rat strains. Here we derive new ESCs from several commonly used rat models including the Dahl Salt Sensitive (SS), the sequenced Brown Norway (BN), and Fischer (F344) rat and establish the first germline-competent ESCs from a hypertension disease model strain, the Fawn Hooded Hypertensive (FHH) rat. Genetic manipulations including transgenesis mediated by lentivirus, routine homologous recombination, and homologous recombination mediated by zinc-finger nucleases (ZFNs) were performed effectively in FHH rat ESCs. Our results showed these rat ESC lines, isolated from inner cell masses using mechanical splitting, had germline competency; the Pparg gene locus and homologous genomic region to the mouse Rosa26 locus can be targeted effectively in these rat ESCs. Furthermore, our results also demonstrated that ZFNs increased the efficiency of proper homologous recombination in FHH rat ESCs using targeting vectors with short homology arms. These rat ESC lines and advancements in genetic manipulation pave the way to novel genetic approaches in this valuable biomedical model species and for exploration of complex disease in these strains.
Stem cells and development 05/2013; · 4.15 Impact Factor
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ABSTRACT: Renin was the first blood pressure (BP) quantitative trait locus mapped by linkage analysis in the rat. Subsequent BP linkage and congenic studies capturing different portions of the renin region have returned conflicting results, suggesting that multiple interdependent BP loci may be residing in the chromosome 13 BP quantitative trait locus that includes Renin. We used SS-13BN congenic strains to map 2 BP loci in the Renin region (chr13: 45.2-49.0 Mb). We identified a 1.1-Mb protective Brown Norway region around Renin (chr13: 46.1-47.2 Mb) that significantly decreased BP by 32 mm Hg. The Renin protective BP locus was offset by an adjacent hypertensive locus (chr13: 47.2-49.0 Mb) that significantly increased BP by 29 mm Hg. Sequence analysis of the protective and hypertensive BP loci revealed 1433 and 2063 variants between Dahl salt-sensitive/Mcwi and Brown Norway rats, respectively. To further reduce the list of candidate variants, we regenotyped an overlapping SS-13SR congenic strain (S/renrr) with a previously reported BP phenotype. Sequence comparison among Dahl salt-sensitive, Dahl R, and Brown Norway reduced the number of candidate variants in the 2 BP loci by 42% for further study. Combined with previous studies, these data suggest that at least 4 BP loci reside within the 30-cM chromosome 13 BP quantitative trait locus that includes Renin.
Hypertension 03/2013; · 6.21 Impact Factor
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ABSTRACT: Whole exome sequencing (WES) is currently used to identify the genetic etiologies of many diseases, especially monogenic disorders. Ng et al., in 2009, completed the first proof-of-principle study demonstrating the feasibility of using exome sequencing to identify causal variants for diseases, specifically Freeman-Sheldon syndrome.(1) Within two years, there was a marked increase in publications presenting WES data and the pace continues to accelerate (Figure 1). In 2010, WES began to be used for clinical diagnoses, particularly for Mendelian disorders. In early 2011, Worthey et al(2) used exome sequencing to facilitate clinical diagnosis and modify treatment in a single case. Despite many of the successes resulting from exome sequencing, more than half of the approximately 7,000 known or suspected Mendelian disorders have not yet been discovered,(3) highlighting the need for more genetic, mechanistic and clinical studies, particularly if the data are to be used clinically. Moreover, as our knowledge of the genome increases, examples of some of the complexities associated with genotypic-phenotypic relationships further substantiate the need for both additional genomic annotation and many more sequenced genomes with phenotypic information. Some of these complexities include: 1) variants in the same genes may lead to different clinical manifestations or phenotypes; 2) what appear to be similar phenotypic observations may result from different causal disease variants operating through distinct pathophysiological mechanisms; and 3) the recent ENCODE papers which suggest that up to 80% of the human genome is functional.(4).
Circulation 02/2013; · 14.74 Impact Factor
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ABSTRACT: Hypertension and renal damage in Dahl SS rats are associated with increased infiltrating immune cells in the kidney. To examine the role of infiltrating immune cells in this disease process, a zinc finger nuclease targeting bases 672-706 of recombination activating gene 1 (Rag1) was injected into the pronucleus of Dahl SS (SS/JrHsdMcwi) strain embryos and implanted in pseudopregnant females. This strategy yielded a rat strain with a 13 base frame-shift mutation in the target region of Rag1 and a deletion of immunoreactive Rag1 protein in the thymus. Flow cytometry demonstrated that the Rag1 null mutant rats have a significant reduction in T- and B-lymphocytes in the circulation and spleen. Studies were performed on SS and Rag1 null rats fed a 4.0% NaCl diet for three weeks. The infiltration of T-cells into the kidney following high salt was significantly blunted in the Rag1 null rats (1.7±0.6 x 10(5) cells/kidney) compared to the Dahl SS (5.6±0.9 x 10(5) cells/kidney). Accompanying the reduction in infiltration of immune cells in the kidney, mean arterial blood pressure and urinary albumin excretion rat were significantly lower in Rag1 null mutants (158±3 mmHg and 60±16 mg/day, respectively) than in SS rats (180±11 mmHg and 251±37 mg/day). Finally, a histological analysis revealed that the glomerular and tubular damage in the kidneys of the SS rats fed high salt was also attenuated in the Rag1 mutants. These studies demonstrate the importance of renal infiltration of immune cells in the pathogenesis of hypertension and renal damage in Dahl SS rats.
AJP Regulatory Integrative and Comparative Physiology 01/2013; · 3.34 Impact Factor
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ABSTRACT: We previously reported that the fawn-hooded hypertensive (FHH) rat is a natural Rab38 knockout, supported by a congenic animal (FHH.BN-Rab38) having less proteinuria than FHH animals. Because these congenic animals contain Brown Norway (BN) alleles for five other named genes; however, a causal role for Rab38 in the FHH phenotype remains uncertain. Here, we used transgenic and knockout models to validate Rab38 and to exclude other genes within the 1.5 Mb congenic region from involvement in causing the FHH phenotype. Transgenic rats homozygous for the wild-type Rab38 BN allele on the FHH background exhibited phenotypic rescue, having 43% lower proteinuria and 75% lower albuminuria than nontransgenic FHH littermates. Conversely, knockout of the Rab38 gene on the FHH.BN-Rab38 congenic line recapitulated a proteinuric phenotype indistinguishable from the FHH strain. In addition, in cultured proximal tubule LLC-PK1 cells, knockdown of Rab38 mRNA significantly decreased endocytosis of colloidal gold-coupled albumin, supporting the hypothesis that Rab38 modulates proteinuria through effects on tubular re-uptake and not by altering glomerular permeability. Taken together, these findings validate Rab38 as a gene having a causal role in determining the phenotype of the FHH rat, which models hypertension-associated renal disease. Furthermore, our data suggest that Rab38 affects urinary protein excretion via effects in the proximal tubule.
Journal of the American Society of Nephrology 01/2013; · 9.66 Impact Factor
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ABSTRACT: The present study employed a zinc-finger nuclease strategy to create heterozygous knockout (KO) rats for the transforming growth factor-β1 (Tgfb1) gene on the Dahl SS/Jr genetic background (TGFβ1(+/-) Dahl S). Intercrossing TGFβ1(+/-) rats did not produce any homozygous KO rats (66.4% +/-, 33.6% +/+), indicating that the mutation is embryonic lethal. Six-week old wild-type (WT) littermates and TGFβ1(+/-) Dahl S rats were fed a 0.4% (low salt, LS) or 8% NaCl (high salt, HS) diet for 5 weeks. Renal cortical expression of TGFβ1, urinary TGFβ1 excretion, proteinuria, glomerular injury and tubulointerstitial fibrosis (TIF), and systolic blood pressure were similar in WT and TGFβ1(+/-) Dahl S rats maintained on the LS diet. The expression and urinary excretion of TGFβ1 increased to a greater extent in WT than in TGFβ1(+/-) Dahl S rats fed a HS diet for 1 week. Systolic blood pressure rose by the same extent to 235±2 mmHg in WT and 239±4 mmHg in TGFβ1(+/-) Dahl S rats fed a HS diet for 5 weeks. However, urinary protein excretion (UPE) was significantly lower in TGFβ1(+/-) Dahl S than in the WT animals. The degree of glomerular injury and renal cortical and outer medullary fibrosis was markedly less in TGFβ1(+/-) than in WT rats. These findings suggest that the loss of one copy of the TGFβ1 gene blunts the increase in renal TGFβ1 protein expression and slows the progression of proteinuria, glomerulosclerosis, and renal interstitial fibrosis in Dahl S rats fed a HS diet independent of changes in blood pressure.
Physiological Genomics 12/2012; · 2.73 Impact Factor
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ABSTRACT: This study examined the effect of substitution of a 2.4 megabase pair (Mbp) region of Brown Norway (BN) rat chromosome 1 (RNO1) between 258.8 and 261.2 Mbp onto the genetic background of Fawn Hooded Hypertensive (FHH) rats on autoregulation of renal blood flow (RBF), myogenic response of renal afferent arterioles (AF-art), K(+) channel activity in renal vascular smooth muscle cells (VSMCs) and development of proteinuria and renal injury. FHH rats exhibited poor autoregulation of RBF, while FHH.1BN congenic strains with the 2.4 Mbp BN region exhibited nearly perfect autoregulation of RBF. The diameter of AF-art from FHH rats increased in response to pressure but decreased in congenic strains containing the 2.4 Mbp BN region. Protein excretion and glomerular and interstitial damage were significantly higher in FHH rats than in congenic strains containing the 2.4 Mbp BN region. K(+) channel current was 5-fold greater in VSMCs from renal arterioles of FHH rats than cells obtained from congenic strains containing the 2.4 Mbp region. Sequence analysis of the known and predicted genes in the 2.4 Mbp region of FHH revealed amino acid altering variants in the exons of three genes; Add3, Rbm20 and Soc-2. Quantitative-PCR studies indicated that Mxi1 and Rbm20 were differentially expressed in the renal vasculature of FHH and FHH.1BN congenic strain F. These data indicate that transfer of this 2.4 Mbp region from BN to FHH rats restores the myogenic response of AF-art and autoregulation of RBF, decreases K(+) current and slows the progression of proteinuria and renal injury.
AJP Renal Physiology 12/2012; · 4.42 Impact Factor
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ABSTRACT: The laboratory rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have relevance to human physiology and disease. The Rat Genome Database (RGD, http://rgd.mcw.edu) is a model organism database that provides access to a wide variety of curated rat data including disease associations, phenotypes, pathways, molecular functions, biological processes, and cellular components for genes, quantitative trait loci, and strains. We present an overview of the database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the rat. Curr. Protoc. Bioinform. 40:1.14.1-1.14.27. © 2012 by John Wiley & Sons, Inc.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 12/2012; Chapter 1:Unit1.14.
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Chun Yang,
Francesco C Stingo,
Kwang Woo Ahn,
Pengyuan Liu,
Marina Vannucci,
Purushottam W Laud,
Meredith Skelton,
Paul O'Connor,
Terry Kurth,
Robert P Ryan,
Carol Moreno,
Shirng-Wern Tsaih,
Giannino Patone,
Oliver Hummel, Howard J Jacob,
Mingyu Liang,
Allen W Cowley
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ABSTRACT: Studies of transcriptome profiles have provided new insights into mechanisms underlying the development of hypertension. Cell type heterogeneity in tissue samples, however, has been a significant hindrance in these studies. We performed a transcriptome analysis in medullary thick ascending limbs of the loop of Henle isolated from Dahl salt-sensitive rats. Genes differentially expressed between Dahl salt-sensitive rats and salt-insensitive consomic SS.13(bn) rats on either 0.4% or 7 days of 8.0% NaCl diet (n=4) were highly enriched for genes located on chromosome 13, the chromosome substituted in the SS.13(bn) rat. A pathway involving cell proliferation and cell cycle regulation was identified as one of the most highly ranked pathways based on differentially expressed genes and by a Bayesian model analysis. Immunofluorescent analysis indicated that just 1 week of a high-salt diet resulted in a severalfold increase in proliferative medullary thick ascending limb cells in both rat strains, and that Dahl salt-sensitive rats exhibited a significantly greater proportion of medullary thick ascending limb cells in a proliferative state than in SS.13(bn) rats (15.0±1.4% versus 10.1±0.6%; n=7-9; P<0.05). The total number of cells per medullary thick ascending limb section analyzed was not different between the 2 strains. The study revealed alterations in regulatory pathways in Dahl salt-sensitive rats in tissues highly enriched for a single cell type, leading to the unexpected finding of a greater increase in the number of proliferative medullary thick ascending limb cells in Dahl salt-sensitive rats on a high-salt diet.
Hypertension 11/2012; · 6.21 Impact Factor
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Nadine Beetz,
Pavel Hamet,
Michael D Harrison,
Mary Kaldunski,
Maria Augusta Vieira-Coelho,
Daniel Gaudet,
Marc Brede,
Mathias W Seeliger,
Rolf Nüsing,
Johanne Tremblay, [......],
Michal J Urbanski,
Ulrich Broeckel,
Stefan Lorkowski, Howard J Jacob,
Anika Sietmann,
Lutz Hein,
Allen W Cowley,
Jennifer Kaufling,
Theodore A Kotchen,
Martin Biel
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ABSTRACT: This study examined the effects of transfer of a 2.4 Mbp region of rat chromosome 1 (RNO1) from Brown Norway (BN) into Fawn Hooded Hypertensive (FHH) rats on autoregulation (AR) of cerebral blood flow (CBF) and the myogenic response of middle cerebral arteries (MCA). AR of CBF was poor in FHH and FHH.1(BN) AR(-) congenic strains that excluded the critical 2.4 Mbp region. In contrast, AR was restored in FHH.1(BN) AR(+) congenic strains that included this region. The diameter of MCA of FHH rats increased from 140 ± 14 to 157±18 μm when transmural pressure was increased from 40 to 140 mmHg but it decreased from 137 ± 5 to 94 ± 7 μm in FHH.1(BN) AR(+) congenic strains. Transient occlusion of MCA reduced CBF by 80% in all strains. However, the hyperemic response following ischemia was significantly greater in FHH and AR(-) rats than that seen in AR(+) congenic strains (AR(-): 173 ± 11% versus AR(+): 124 ± 5%). Infarct size and edema formation were also significantly greater in an AR(-) strain (38.6 ± 2.6% and 12.1 ± 2%) than in AR(+) congenic strains (27.6 ± 1.8 %; 6.5 ± 0.9%). These results indicate that there is a gene in the 2.4 Mbp region of RNO1 that alters the development of myogenic tone in cerebral arteries. Transfer of this region from BN to FHH rats restores AR of CBF, vascular reactivity and reduces cerebral injury after transient occlusion and reperfusion of the MCA.
AJP Heart and Circulatory Physiology 11/2012; · 3.71 Impact Factor
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ABSTRACT: Previous studies have identified multiple blood pressure and renal disease quantitative trait loci located on rat chromosome 12. In the present study, we narrowed blood pressure loci using a series of overlapping Dahl salt-sensitive/Mcwi (SS)-12 Brown Norway (BN) congenic lines. We found that transferring 6.1 Mb of SS chromosome 12 (13.4-19.5 Mb) onto the consomic SS-12(BN) background significantly elevated blood pressure on 1% NaCl (146 ± 6 versus 127 ± 1 mm Hg; P<0.001) and 8% NaCl diets (178 ± 7 versus 144 ± 2 mm Hg; P<0.001). Compared with the SS-12(BN) consomic, these animals also had significantly elevated albumin (218 ± 31 versus 104 ± 8 mg/d; P<0.001) and protein excretion (347 ± 41 versus 195 ± 12 mg/d; P<0.001) on a 1% NaCl diet. Elevated blood pressure, albuminuria, and proteinuria coincided with greater renal and cardiac damage, demonstrating that SS allele(s) within the 6.1 Mb congenic interval are associated with strong cardiovascular disease phenotypes. Sequence analysis of the 6.1 Mb congenic region revealed 12 673 single nucleotide polymorphisms between SS and BN rats. Of these polymorphisms, 293 lie within coding regions, and 18 resulted in nonsynonymous changes in conserved genes, of which 5 were predicted to be potentially damaging to protein function. Syntenic regions in human chromosome 7 have also been identified in multiple linkage and association studies of cardiovascular disease, suggesting that genetic variants underlying cardiovascular phenotypes in this congenic strain can likely be translated to a better understanding of human hypertension.
Hypertension 08/2012; 60(4):942-8. · 6.21 Impact Factor
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ABSTRACT: Background/Aims: Recent studies have highlighted the importance of gene by diet interactions in contributing to risk factors of metabolic syndrome. We used a consomic rat panel, in which a chromosome of the Brown Norway (BN) strain is introgressed onto the background of the Dahl salt-sentitive (SS) strain, to test the hypothesis that these animals will be useful for dissecting gene by diet interactions involved in metabolic syndrome. Methods: We placed the parental SS and BN strains on a low-fat/high-carbohydrate (LF) or high-fat/low-carbohydrate (HF) diet for 22 weeks and measured several indices of metabolic syndrome. We then investigated the effect of diet in eight consomic rat strains. Results: We show that the HF diet resulted in significantly increased levels of fasting plasma cholesterol and triglycerides in the SS strain, with no effect in the BN. Both strains responded to the HF diet with slight increases in body weight. SSBN8 was the only consomic strain that resembled that of the BN, with low levels of fasting cholesterol and triglycerides even on the HF diet. Conclusions: These results indicate that BN chromosome 8 harbors a gene or genes that confer protection against dyslipidemia caused by the HF diet.
Journal of Nutrigenetics and Nutrigenomics 06/2012; 5(2):81-93. · 1.14 Impact Factor
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ABSTRACT: Human data and animal models of autosomal recessive polycystic kidney disease (ARPKD) suggest that genetic factors modulate the onset and severity of the disease. We report here for the first time that ARPKD susceptibility is attenuated by introgressing the mutated Pkhd1 disease allele from the polycystic kidney (PCK) rat onto the FHH (Fawn-Hooded Hypertensive) genetic background. Compared with PCK, the FHH.Pkhd1 strain had significantly decreased renal cyst formation that coincided with a threefold reduction in mean kidney weights. Further analysis revealed that the FHH. Pkhd1 is protected from increased blood pressure as well as elevated plasma creatinine and blood urea nitrogen levels. On the other hand, liver weight and biliary cystogenesis revealed no differences between PCK and FHH.Pkdh1, indicating that genes within the FHH genetic background prevent the development of renal, but not hepatic, manifestations of ARPKD. Microarray expression analysis of kidneys from 30-day-old PCK rats revealed increased expression of genes previously identified in PKD renal expression profiles, such as inflammatory response, extracellular matrix synthesis, and cell proliferation genes among others, whereas the FHH.Pkhd1 did not show activation of these common markers of disease. This newly developed strain can serve as a tool to map modifier genes for renal disease in ARPKD and provides further insight into disease variability and pathophysiology.
Physiological Genomics 06/2012; 44(15):741-53. · 2.73 Impact Factor
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ABSTRACT: The rat is a well-established model for hypertension research, in both physiologic and pharmacologic study. Quantitative trait
loci (QTL) for blood pressure and related phenotypes have been described on every rat chromosome; therefore, more simplified
models must be generated to identify and study the function of the gene(s) located by QTL analysis. Designer rat strains,
such as congenic and consomic strains, which share phenotypic and genotypic characteristics with humans but with a greatly
simplified genetic background, would yield a powerful platform for functional studies, especially when combined with microarray
technologies. Development of these designer rats would result in better-defined disease models that can be used in physiologic
and applied pharmacologic studies to better treat human essential hypertension.
Current Hypertension Reports 04/2012; 3(1):12-18. · 2.50 Impact Factor
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ABSTRACT: Heightened interest in relevant models for human disease increases the need for improved methods for germline transgenesis.
We describe a significant improvement in the creation of transgenic laboratory mice and rats by chemical modification of Sleeping Beauty transposons. Germline transgenesis in mice and rats was significantly enhanced by in vitro cytosine-phosphodiester-guanine
methylation of transposons prior to injection. Heritability of transgene alleles was also greater from founder mice generated
with methylated versus non-methylated transposon. The artificial methylation was reprogrammed in the early embryo, leading
to founders that express the transgenes. We also noted differences in transgene insertion number and structure (single-insert
versus concatemer) based on the influence of methylation and plasmid conformation (linear versus supercoiled), with supercoiled
substrate resulting in efficient transpositional transgenesis (TnT) with near elimination of concatemer insertion. Combined,
these substrate modifications resulted in increases in both the frequency of transgenic founders and the number of transgenes
per founder, significantly elevating the number of potential transgenic lines. Given its simplicity, versatility and high
efficiency, TnT with enhanced Sleeping Beauty components represents a compelling non-viral approach to modifying the mammalian germline.
KeywordsSleeping Beauty–Transposon–Transgenesis–Mouse–Rat–Methylation
Transgenic Research 04/2012; 20(1):29-45. · 2.75 Impact Factor
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ABSTRACT: This study examined whether substitution of chromosome 5 containing the CYP4A genes from Brown Norway rat onto the Dahl S salt-sensitive (SS) genetic background upregulates the renal production of 20-HETE and attenuates the development of hypertension. The expression of CYP4A protein and the production of 20-HETE were significantly higher in the renal cortex and outer medulla of SS.5(BN) (chromosome 5-substituted Brown Norway rat) consomic rats fed either a low-salt (LS) or high-salt (HS) diet than that seen in SS rats. The increase in the renal production of 20-HETE in SS.5(BN) rats was associated with elevated expression of CYP4A2 mRNA. MAP measured by telemetry rose from 117 ± 1 to 183 ± 5 mmHg in SS rats fed a HS diet for 21 days, but only increased to 151 ± 5 mmHg in SS.5(BN) rats. The pressure-natriuretic and diuretic responses were twofold higher in SS.5(BN) rats compared with SS rats. Protein excretion rose to 354 ± 17 mg/day in SS rats fed a HS diet for 21 days compared with 205 ± 13 mg/day in the SS.5(BN) rats, and the degree of glomerular injury was reduced. Baseline glomerular capillary pressure (Pgc) was similar in SS.5(BN) rats (43 ± 1 mmHg) and Dahl S (44 ± 2 mmHg) rats. However, Pgc increased to 59 ± 3 mmHg in SS rats fed a HS diet for 7 days, while it remained unaltered in SS.5(BN) rats (43 ± 2 mmHg). Chronic administration of an inhibitor of the synthesis of 20-HETE (HET0016, 10 mg·kg(-1)·day(-1) iv) reversed the antihypertensive phenotype seen in the SS.5(BN) rats. These findings indicate that the transfer of chromosome 5 from the BN rat onto the SS genetic background increases the renal expression of CYP4A protein and the production of 20-HETE and that 20-HETE contributes to the antihypertensive and renoprotective effects seen in the SS.5(BN) consomic strain.
AJP Regulatory Integrative and Comparative Physiology 03/2012; 302(10):R1209-18. · 3.34 Impact Factor
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Caitlin C O'Meara,
Michelle M Lutz,
Allison B Sarkis,
Haiyan Xu,
Rajendra K Kothinti,
Matthew Hoffman,
Carol Moreno,
Niloofar M Tabatabai,
Jozef Lazar,
Richard J Roman, Howard J Jacob
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ABSTRACT: The combined transfer of two renal function quantitative trait loci (QTLs), Rf-1 (rat chromosome 1) and Rf-4 (rat chromosome 14), from the Fawn-hooded hypertensive rat onto the August Copenhagen Irish genetic background significantly increases proteinuria and demonstrates an interaction between these QTLs. Because the original Rf-4 congenic region is 61.9 Mbp, it is necessary to reduce this interval to feasibly search for variants responsible for renal susceptibility in this region. Here, we generated a minimal congenic line (Rf-1a+4_a) to identify a 4.1-Mb region of the Rf-4 QTL that significantly contributes to the severity of proteinuria in the Fawn-hooded hypertensive rat. Rf-1a+4_a animals have an increased glomerular permeability to albumin without significant changes in BP, indicating that at least one genetic element in this refined region directly affects renal function. Sequence analysis revealed no variants predicted to damage protein function, implying that regulatory elements are responsible for the Rf-4 phenotype. Multiple human studies, including recent genome-wide association studies, link the homologous human region with susceptibility to renal disease, suggesting that this congenic line is an important model for studying pathways that contribute to the progression of kidney disease.
Journal of the American Society of Nephrology 02/2012; 23(5):825-33. · 9.66 Impact Factor
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Stanley J F Laulederkind,
Marek Tutaj,
Mary Shimoyama,
G Thomas Hayman,
Timothy F Lowry,
Rajni Nigam,
Victoria Petri,
Jennifer R Smith,
Shur-Jen Wang,
Jeff de Pons,
Melinda R Dwinell, Howard J Jacob
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ABSTRACT: The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses over 40 000 rat gene records, as well as human and mouse orthologs, 1857 rat and 1912 human quantitative trait loci (QTLs) and 2347 rat strains. Biological information curated for these data objects includes disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components. RGD uses more than a dozen different ontologies to standardize annotation information for genes, QTLs and strains. That means a lot of time can be spent searching and browsing ontologies for the appropriate terms needed both for curating and mining the data. RGD has upgraded its ontology term search to make it more versatile and more robust. A term search result is connected to a term browser so the user can fine-tune the search by viewing parent and children terms. Most publicly available term browsers display a hierarchical organization of terms in an expandable tree format. RGD has replaced its old tree browser format with a 'driller' type of browser that allows quicker drilling up and down through the term branches, which has been confirmed by testing. The RGD ontology report pages have also been upgraded. Expanded functionality allows more choice in how annotations are displayed and what subsets of annotations are displayed. The new ontology search, browser and report features have been designed to enhance both manual data curation and manual data extraction. DATABASE URL: http://rgd.mcw.edu/rgdweb/ontology/search.html.
Database The Journal of Biological Databases and Curation 01/2012; 2012:bas016. · 2.07 Impact Factor
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ABSTRACT: Impaired regulation of renin in Dahl salt-sensitive rats (SS/JRHsdMcwi, SS) contributes to attenuated angiogenesis in this strain. This study examined angiogenic function and genomic structure of regions surrounding the renin gene using subcongenic strains of the SS and BN/NHsdMcwi (BN) rat to identify important genomic variations between SS and BN involved in angiogenesis. Three candidate regions on Chr 13 were studied: two congenic strains containing 0.89 and 2.62 Mb portions of BN Chr 13 that excluded the BN renin allele and a third strain that contained a 2.02 Mb overlapping region that included the BN renin allele. Angiogenesis induced by electrical stimulation of the tibialis anterior muscle was attenuated in the SS compared with the BN. Congenics carrying the SS renin allele had impaired angiogenesis, while strains carrying the BN renin allele had angiogenesis restored. The exception was a congenic including a region of BN genome 0.4 Mb distal to renin that restored both renin regulation and angiogenesis. This suggests that there is a distant regulatory element in the BN capable of restoring normal regulation of the SS renin allele. The importance of ANG II in the restored angiogenic response was demonstrated by blocking with losartan. Sequencing of the 4.05 Mb candidate region in SS and BN revealed a total of 8,850 SNPs and other sequence variants. An analysis of the genes and their variants in the region suggested a number of pathways that may explain the impaired regulation of renin and angiogenesis in the SS rat.
Physiological Genomics 04/2011; 43(13):808-17. · 2.73 Impact Factor
