Loci of intestinal distress in cystic fibrosis knockout mice

2003 ◽  
Vol 12 (2) ◽  
pp. 79-84 ◽  
Author(s):  
Christina K. Haston ◽  
Lap-Chee Tsui

The strain-dependent survival of cystic fibrosis (CF) knockout mice has been used to map a modifier of CF, Cfm1, in mice and, subsequently, in humans. To identify additional modifiers of the CF phenotype, in this study, the survival of F2 CF mice derived from a cross between congenic C57BL/6J CF and BALB/cJ CF heterozygotes was followed up to 12 wk of age. A genome-wide linkage scan completed in F2 CF mice revealed a chromosome 10 locus ( P = 1.2 × 10−4) to predict for intestinal distress in CF male mice. An X chromosome locus for which non-Mendelian inheritance favoring B6 alleles in the surviving CF mice and BALB alleles in mice of a control population, was identified. The survival of female mice, both F2 CF and F2 control, was linked to loci on chromosomes 3 and 5. The identification of additional putative CF modifier loci may permit further genetic dissection of the complex CF phenotype.

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 441
Author(s):  
Fanny Pineau ◽  
Davide Caimmi ◽  
Sylvie Taviaux ◽  
Maurane Reveil ◽  
Laura Brosseau ◽  
...  

Cystic fibrosis (CF) is a chronic genetic disease that mainly affects the respiratory and gastrointestinal systems. No curative treatments are available, but the follow-up in specialized centers has greatly improved the patient life expectancy. Robust biomarkers are required to monitor the disease, guide treatments, stratify patients, and provide outcome measures in clinical trials. In the present study, we outline a strategy to select putative DNA methylation biomarkers of lung disease severity in cystic fibrosis patients. In the discovery step, we selected seven potential biomarkers using a genome-wide DNA methylation dataset that we generated in nasal epithelial samples from the MethylCF cohort. In the replication step, we assessed the same biomarkers using sputum cell samples from the MethylBiomark cohort. Of interest, DNA methylation at the cg11702988 site (ATP11A gene) positively correlated with lung function and BMI, and negatively correlated with lung disease severity, P. aeruginosa chronic infection, and the number of exacerbations. These results were replicated in prospective sputum samples collected at four time points within an 18-month period and longitudinally. To conclude, (i) we identified a DNA methylation biomarker that correlates with CF severity, (ii) we provided a method to easily assess this biomarker, and (iii) we carried out the first longitudinal analysis of DNA methylation in CF patients. This new epigenetic biomarker could be used to stratify CF patients in clinical trials.


Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 643
Author(s):  
Thibaud Kuca ◽  
Brandy M. Marron ◽  
Joana G. P. Jacinto ◽  
Julia M. Paris ◽  
Christian Gerspach ◽  
...  

Genodermatosis such as hair disorders mostly follow a monogenic mode of inheritance. Congenital hypotrichosis (HY) belong to this group of disorders and is characterized by abnormally reduced hair since birth. The purpose of this study was to characterize the clinical phenotype of a breed-specific non-syndromic form of HY in Belted Galloway cattle and to identify the causative genetic variant for this recessive disorder. An affected calf born in Switzerland presented with multiple small to large areas of alopecia on the limbs and on the dorsal part of the head, neck, and back. A genome-wide association study using Swiss and US Belted Galloway cattle encompassing 12 cases and 61 controls revealed an association signal on chromosome 29. Homozygosity mapping in a subset of cases refined the HY locus to a 1.5 Mb critical interval and subsequent Sanger sequencing of protein-coding exons of positional candidate genes revealed a stop gain variant in the HEPHL1 gene that encodes a multi-copper ferroxidase protein so-called hephaestin like 1 (c.1684A>T; p.Lys562*). A perfect concordance between the homozygous presence of this most likely pathogenic loss-of-function variant and the HY phenotype was found. Genotyping of more than 700 purebred Swiss and US Belted Galloway cattle showed the global spread of the mutation. This study provides a molecular test that will permit the avoidance of risk matings by systematic genotyping of relevant breeding animals. This rare recessive HEPHL1-related form of hypotrichosis provides a novel large animal model for similar human conditions. The results have been incorporated in the Online Mendelian Inheritance in Animals (OMIA) database (OMIA 002230-9913).


2021 ◽  
Vol 17 (6) ◽  
pp. e1009681
Author(s):  
Wontae Hwang ◽  
Ji Hyun Yong ◽  
Kyung Bae Min ◽  
Kang-Mu Lee ◽  
Ben Pascoe ◽  
...  

Pseudomonas aeruginosa (PA) is an opportunistic pathogen that causes diverse human infections including chronic airway infection in patients with cystic fibrosis (CF). Comparing the genomes of CF and non-CF PA isolates has great potential to identify the genetic basis of pathogenicity. To gain a deeper understanding of PA adaptation in CF airways, we performed a genome-wide association study (GWAS) on 1,001 PA genomes. Genetic variations identified among CF isolates were categorized into (i) alterations in protein-coding regions, either large- or small-scale, and (ii) polymorphic variation in intergenic regions. We introduced each CF-associated genetic alteration into the genome of PAO1, a prototype PA strain, and validated the outcomes experimentally. Loci readily mutated among CF isolates included genes encoding a probable sulfatase, a probable TonB-dependent receptor (PA2332~PA2336), L-cystine transporter (YecS, PA0313), and a probable transcriptional regulator (PA5438). A promoter region of a heme/hemoglobin uptake outer membrane receptor (PhuR, PA4710) was also different between the CF and non-CF isolate groups. Our analysis highlights ways in which the PA genome evolves to survive and persist within the context of chronic CF infection.


2019 ◽  
Vol 71 (4) ◽  
pp. 1614-1627 ◽  
Author(s):  
Giovanni Melandri ◽  
Ankush Prashar ◽  
Susan R McCouch ◽  
Gerard van der Linden ◽  
Hamlyn G Jones ◽  
...  

Abstract Drought-stressed plants display reduced stomatal conductance, which results in increased leaf temperature by limiting transpiration. In this study, thermal imaging was used to quantify the differences in canopy temperature under drought in a rice diversity panel consisting of 293 indica accessions. The population was grown under paddy field conditions and drought stress was imposed for 2 weeks at flowering. The canopy temperature of the accessions during stress negatively correlated with grain yield (r= –0.48) and positively with plant height (r=0.56). Temperature values were used to perform a genome-wide association (GWA) analysis using a 45K single nucleotide polynmorphism (SNP) map. A quantitative trait locus (QTL) for canopy temperature under drought was detected on chromosome 3 and fine-mapped using a high-density imputed SNP map. The candidate genes underlying the QTL point towards differences in the regulation of guard cell solute intake for stomatal opening as the possible source of temperature variation. Genetic variation for the significant markers of the QTL was present only within the tall, low-yielding landraces adapted to drought-prone environments. The absence of variation in the shorter genotypes, which showed lower leaf temperature and higher grain yield, suggests that breeding for high grain yield in rice under paddy conditions has reduced genetic variation for stomatal response under drought.


2014 ◽  
Vol 66 (1) ◽  
pp. 293-306 ◽  
Author(s):  
Yoshiaki Ueda ◽  
Felix Frimpong ◽  
Yitao Qi ◽  
Elsa Matthus ◽  
Linbo Wu ◽  
...  

2018 ◽  
Vol 131 (5) ◽  
pp. 1073-1090 ◽  
Author(s):  
Kai Liu ◽  
Xiaoxiao Sun ◽  
Tangyuan Ning ◽  
Xixian Duan ◽  
Qiaoling Wang ◽  
...  

2021 ◽  
Author(s):  
Kyle W. Davis ◽  
Colleen G. Bilancia ◽  
Megan Martin ◽  
Rena Vanzo ◽  
Megan Rimmasch ◽  
...  

AbstractTo identify and prioritize candidate disease genes of the central nervous system (CNS) we created the Neurogenetic Systematic Correlation of Omics-Related Evidence (NeuroSCORE). We used five genome-wide metrics highly associated with neurological phenotypes to score 19,598 protein-coding genes. Genes scored one point per metric, resulting in a range of scores from 0-5. Approximately 13,000 genes were then paired with phenotype data from the Online Mendelian Inheritance in Man (OMIM) database. We used logistic regression to determine the odds ratio of each metric and compared genes scoring 1+ to cause a known CNS-related phenotype compared to genes that scored zero. We tested NeuroSCORE using microarray copy number variants (CNVs) in case-control cohorts, mouse model phenotype data, and gene ontology (GO) and pathway analyses. NeuroSCORE identified 8,296 genes scored ≥1, of which 1,580 are “high scoring” genes (scores ≥3). High scoring genes are significantly associated with CNS phenotypes (OR=5.5, p<2×10−16), enriched in case CNVs, and enriched in mouse ortholog genes associated with behavioral and nervous system abnormalities. GO and pathway analyses showed high scoring genes were enriched in chromatin remodeling, mRNA splicing, dendrite development, and neuron projection. OMIM has no phenotype for 1,062 high scoring genes (67%). Top scoring genes include ANKRD17, CCAR1, CLASP1, DOCK9, EIF4G2, G3BP2, GRIA1, MAP4K4, MARK2, PCBP2, RNF145, SF1, SYNCRIP, TNPO2, and ZSWIM8. NeuroSCORE identifies and prioritizes CNS-disease candidate genes, many not yet associated with any phenotype in OMIM. These findings can help direct future research and improve molecular diagnostics for individuals with neurological conditions.


2018 ◽  
Author(s):  
Haiko Schurz ◽  
Craig J Kinnear ◽  
Chris Gignoux ◽  
Genevieve Wojcik ◽  
Paul D van Helden ◽  
...  

AbstractTuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease with a known human genetic component. Males seem to be more affected than females and in most countries the TB notification rate is twice as high in males as in females. While socio-economic status, behaviour and sex hormones influence the male bias they do not fully account for it. Males have only one copy of the X chromosome, while diploid females are subject to X chromosome inactivation. In addition, the X chromosome codes for many immune-related genes, supporting the hypothesis that X-linked genes could contribute to TB susceptibility in a sex-biased manner. We report the first TB susceptibility genome-wide association study (GWAS) with a specific focus on sex-stratified autosomal analysis and the X chromosome. Individuals from an admixed South African population were genotyped using the Illumina Multi Ethnic Genotyping Array, specifically designed as a suitable platform for diverse and admixed populations. Association testing was done on the autosome and X chromosome in a sex stratified and combined manner. SNP association testing was not statistically significant using a stringent cut-off for significance but revealed likely candidate genes that warrant further investigation. A genome wide interaction analysis detected 16 significant interactions. Finally, the results highlight the importance of sex-stratified analysis as strong sex-specific effects were identified on both the autosome and X chromosome.


2019 ◽  
Vol 105 (5) ◽  
pp. 1401-1415 ◽  
Author(s):  
Melis A Aksit ◽  
Rhonda G Pace ◽  
Briana Vecchio-Pagán ◽  
Hua Ling ◽  
Johanna M Rommens ◽  
...  

Abstract Context Individuals with cystic fibrosis (CF) develop a distinct form of diabetes characterized by β-cell dysfunction and islet amyloid accumulation similar to type 2 diabetes (T2D), but generally have normal insulin sensitivity. CF-related diabetes (CFRD) risk is determined by both CFTR, the gene responsible for CF, and other genetic variants. Objective To identify genetic modifiers of CFRD and determine the genetic overlap with other types of diabetes. Design and Patients A genome-wide association study was conducted for CFRD onset on 5740 individuals with CF. Weighted polygenic risk scores (PRSs) for type 1 diabetes (T1D), T2D, and diabetes endophenotypes were tested for association with CFRD. Results Genome-wide significance was obtained for variants at a novel locus (PTMA) and 2 known CFRD genetic modifiers (TCF7L2 and SLC26A9). PTMA and SLC26A9 variants were CF-specific; TCF7L2 variants also associated with T2D. CFRD was strongly associated with PRSs for T2D, insulin secretion, postchallenge glucose concentration, and fasting plasma glucose, and less strongly with T1D PRSs. CFRD was inconsistently associated with PRSs for insulin sensitivity and was not associated with a PRS for islet autoimmunity. A CFRD PRS comprising variants selected from these PRSs (with a false discovery rate &lt; 0.1) and the genome-wide significant variants was associated with CFRD in a replication population. Conclusions CFRD and T2D have more etiologic and mechanistic overlap than previously known, aligning along pathways involving β-cell function rather than insulin sensitivity. Two CFRD risk loci are unrelated to T2D and may affect multiple aspects of CF. An 18-variant PRS stratifies risk of CFRD in an independent population.


2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Takahisa Yamada ◽  
Hiroyuki Kose ◽  
Takeshi Ohta ◽  
Kozo Matsumoto

The Otsuka Long-Evans Tokushima Fatty (OLETF) rat is an animal model for obese-type, noninsulin-dependent diabetes mellitus (NIDDM) in humans. NIDDM in this rat model was shown to be regulated by multiple genes. We have identified 14 quantitative trait loci (QTLs) responsible for NIDDM (Nidd1-14/of) on chromosomes 1, 5, 7, 8, 9, 11, 12, 14, 16, and 17 by a whole genome search in 160 F2 progenies obtained by mating the OLETF and the F344 rats. Among these loci, two QTLs,Nidd1and2/of, were declared significant loci at a genome-wide level.Nidd3, 8, 9,and13/ofexhibited heterosis: heterozygotes showing significantly higher glucose levels than OLETF or F344 homozygotes. We also found evidence for interaction (epistasis) betweenNidd1/ofandNidd2/of, betweenNidd1/ofandNidd10/of, betweenNidd2/ofandNidd8/of, and betweenNidd2/ofandNidd14/of. Furthermore,Nidd6and11/ofshowed linkage with body weight, andNidd1, 2, 8, 9, 10,and12/ofhad an interaction with body weight. These indicated that NIDDM in the OLETF would have a higher degree of genetic complexity. We suggest several interesting candidate genes located in rat genomic regions forNidd1-14/ofor the syntenic regions in human genome.


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