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Bennett TM, Zhou Y, Meyer KJ, Anderson MG, Shiels A. Whole-exome sequencing prioritizes candidate genes for hereditary cataract in the Emory mouse mutant. G3 (BETHESDA, MD.) 2023; 13:jkad055. [PMID: 36891866 PMCID: PMC10151407 DOI: 10.1093/g3journal/jkad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 03/10/2023]
Abstract
The Emory cataract (Em) mouse mutant has long been proposed as an animal model for age-related or senile cataract in humans-a leading cause of visual impairment. However, the genetic defect(s) underlying the autosomal dominant Em phenotype remains elusive. Here, we confirmed development of the cataract phenotype in commercially available Em/J mice [but not ancestral Carworth Farms White (CFW) mice] at 6-8 months of age and undertook whole-exome sequencing of candidate genes for Em. Analysis of coding and splice-site variants did not identify any disease-causing/associated mutations in over 450 genes known to underlie inherited and age-related forms of cataract and other lens disorders in humans and mice, including genes for lens crystallins, membrane/cytoskeleton proteins, DNA/RNA-binding proteins, and those associated with syndromic/systemic forms of cataract. However, we identified three cataract/lens-associated genes each with one novel homozygous variant including predicted missense substitutions in Prx (p.R167C) and Adamts10 (p.P761L) and a disruptive in-frame deletion variant (predicted missense) in Abhd12 (p.L30_A32delinsS) that were absent in CFW and over 35 other mouse strains. In silico analysis predicted that the missense substitutions in Prx and Adamts10 were borderline neutral/damaging and neutral, respectively, at the protein function level, whereas, that in Abhd12 was functionally damaging. Both the human counterparts of Adamts10 and Abhd12 are clinically associated with syndromic forms of cataract known as Weil-Marchesani syndrome 1 and polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract syndrome, respectively. Overall, while we cannot exclude Prx and Adamts10, our data suggest that Abhd12 is a promising candidate gene for cataract in the Em/J mouse.
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Affiliation(s)
- Thomas M Bennett
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yuefang Zhou
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kacie J Meyer
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Michael G Anderson
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Alan Shiels
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
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Selection Signatures in Italian Livestock Guardian and Herding Shepherd Dogs. Vet Sci 2022; 10:vetsci10010003. [PMID: 36669004 PMCID: PMC9862740 DOI: 10.3390/vetsci10010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Livestock guardian (LGD) and herding shepherd (HSD) dogs have distinct morphological and behavioural characteristics, long selected by farmers and breeders, to accomplish different tasks. This study aimed to find the genomic regions that best differentiate and characterise Italian LGD and HSD. Genomic data of 158 dogs of four LGD and five HSD breeds, obtained with the 170K canine SNPchip, were collected. The two groups were compared using FST and XP-EHH analyses, identifying regions containing 29 genes. Moreover, 16 islands of runs of homozygosity were found in LGD, and 15 in HSD; 4 of them were partially shared. Among the genes found that better differentiated HSD and LGD, several were associated with dog domestication and behavioural aspects; particularly, MSRB3 and LLPH were linked to herding behaviour in previous studies. Others, DYSK, MAP2K5, and RYR, were related to body size and muscle development. Prick ears prevailed in sampled HSD, and drop ears in LGD; this explains the identification of WIF1 and MSRB3 genes. Unexpectedly, a number of genes were also associated with eye development and functionality. These results shed further light on the differences that human selection introduced in dogs aimed at different duties, even in a limited geographic area such as Italy.
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Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences. PLoS One 2022; 17:e0276309. [PMID: 36288367 PMCID: PMC9605288 DOI: 10.1371/journal.pone.0276309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/04/2022] [Indexed: 11/04/2022] Open
Abstract
Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2-71.3 Mb), BTA5 (10.0-19.7 Mb), BTA20 (10.0-19.9 and 20.0-22.7 Mb), and BTA25 (0.5-9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.
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Fang Z, Peltz G. An automated multi-modal graph-based pipeline for mouse genetic discovery. Bioinformatics 2022; 38:3385-3394. [PMID: 35608290 PMCID: PMC9992076 DOI: 10.1093/bioinformatics/btac356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/18/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Our ability to identify causative genetic factors for mouse genetic models of human diseases and biomedical traits has been limited by the difficulties associated with identifying true causative factors, which are often obscured by the many false positive genetic associations produced by a GWAS. RESULTS To accelerate the pace of genetic discovery, we developed a graph neural network (GNN)-based automated pipeline (GNNHap) that could rapidly analyze mouse genetic model data and identify high probability causal genetic factors for analyzed traits. After assessing the strength of allelic associations with the strain response pattern; this pipeline analyzes 29M published papers to assess candidate gene-phenotype relationships; and incorporates the information obtained from a protein-protein interaction network and protein sequence features into the analysis. The GNN model produces markedly improved results relative to that of a simple linear neural network. We demonstrate that GNNHap can identify novel causative genetic factors for murine models of diabetes/obesity and for cataract formation, which were validated by the phenotypes appearing in previously analyzed gene knockout mice. The diabetes/obesity results indicate how characterization of the underlying genetic architecture enables new therapies to be discovered and tested by applying 'precision medicine' principles to murine models. AVAILABILITY AND IMPLEMENTATION The GNNHap source code is freely available at https://github.com/zqfang/gnnhap, and the new version of the HBCGM program is available at https://github.com/zqfang/haplomap. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhuoqing Fang
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gary Peltz
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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Jacinto JGP, Sbarra F, Quaglia A, Gentile A, Drögemüller C. Short communication: Prevalence of deleterious variants causing recessive disorders in Italian Chianina, Marchigiana and Romagnola cattle. Animal 2022; 16:100569. [PMID: 35717834 DOI: 10.1016/j.animal.2022.100569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 11/01/2022] Open
Abstract
In the last two decades, the molecular cause of six monogenic autosomal recessive disorders has been identified in native Italian beef cattle: two different ATP2A1 variants for the pseudomyotonia congenita, the first in Chianina and Romagnola (PMT1) and the second in Romagnola (PMT2); a KDM2B variant for the paunch calf syndrome (PCS) in Marchigiana and Romagnola; a NID1 variant for the congenital cataract (CC) in Romagnola; a LAMB1 variant for the hemifacial microsomia (HFM) in Romagnola; an ABCA12 variant for the ichthyosis fetalis (IF) in Chianina and a FA2H variant for the ichthyosis congenita (IC) in Chianina. The aim of this study was to evaluate the potential impact of these disorders in the affected Italian populations. For this purpose, 3331 Chianina, 2812 Marchigiana and 1680 Romagnola bulls born in the last 40 years were considered. The allelic frequency (AF) of the variant for PMT1 was 1.0% in Romagnola, 4.6% in Marchigiana and 5.9% in Chianina. The AF of the variant for PMT2 was 3.3% in Romagnola and 0% in the other two breeds. The AF of the variant for PCS was 11.7% in Romagnola, 2.0% in Marchigiana and 0% in Chianina. The AF of the variants for CC, HFM, IF and IC resulted below 3%, being the variants detected only in the breed populations in which they were previously reported. Considering a selected male population in the single breed, Chianina showed carrier prevalence of 11.9% for PMT1, 7.7% for IC and 6.4% for IF. Romagnola showed carrier prevalence of 23.4% for PCS, 6.7% for PMT2, 4.1% for HFM, 3.2% for CC and 2.0% for PMT1. Marchigiana showed carrier prevalence of 9.1% for PMT1 and 4.0% for PCS. With respect to the Romagnola cattle, the concerning presence of a total of five defect alleles in the population hampers a general approach based on the prevention of carriers from artificial insemination. However, identification of carriers may allow conscious mating to prevent the risk of homozygous descendants as well as the spread of heterozygous offspring. Therefore, systematic genotyping for all seven known harmful alleles is recommended to prevent risk mating between carriers, in particular to avoid the occurrence of affected offspring.
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Affiliation(s)
- J G P Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse109a, 3012 Bern, Switzerland
| | - F Sbarra
- National Association of Italian Beef-Cattle Breeders, Strada del Vio Viscioloso, 21, 06132 Perugia, Italy
| | - A Quaglia
- National Association of Italian Beef-Cattle Breeders, Strada del Vio Viscioloso, 21, 06132 Perugia, Italy
| | - A Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse109a, 3012 Bern, Switzerland.
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Häfliger IM, Wolf-Hofstetter S, Casola C, Hetzel U, Seefried FR, Drögemüller C. A de novo variant in the bovine ADAMTSL4 gene in an Original Braunvieh calf with congenital cataract. Anim Genet 2022; 53:416-421. [PMID: 35233794 PMCID: PMC9311076 DOI: 10.1111/age.13178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/26/2022]
Abstract
Inherited forms of cataract are a heterogeneous group of eye disorders known in livestock species. Clinicopathological analysis of a single case of impaired vision in a newborn Original Braunvieh calf revealed nuclear cataract. Whole‐genome sequencing of the parent‐offspring trio revealed a de novo mutation of ADAMTSL4 in this case. The heterozygous p.Arg776His missense variant affects a conserved residue of the ADAMTSL4 gene that encodes a secreted glycoprotein expressed in the lens throughout embryonic development. In humans, ADAMTSL4 genetic variants cause recessively inherited forms of subluxation of the lens. Given that ADAMTSL4 is a functional candidate gene for inherited disorders of the lens, we suggest that heterozygosity for the identified missense variant may have caused the congenital cataract in the affected calf. Cattle populations should be monitored for unexplained cataract cases, with subsequent DNA sequencing a hypothesized pathogenic effect of heterozygous ADAMTSL4 variants could be confirmed.
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Affiliation(s)
- Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Christina Casola
- Ophthalmology Section, Equine Department, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Udo Hetzel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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CNGB3 Missense Variant Causes Recessive Achromatopsia in Original Braunvieh Cattle. Int J Mol Sci 2021; 22:ijms222212440. [PMID: 34830323 PMCID: PMC8620519 DOI: 10.3390/ijms222212440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Sporadic occurrence of inherited eye disorders has been reported in cattle but so far pathogenic variants were found only for rare forms of cataract but not for retinopathies. The aim of this study was to characterize the phenotype and the genetic aetiology of a recessive form of congenital day-blindness observed in several cases of purebred Original Braunvieh cattle. Electroretinography in an affected calf revealed absent cone-mediated function, whereas the rods continue to function normally. Brain areas involved in vision were morphologically normal. When targeting cones by immunofluorescence, a decrease in cone number and an accumulation of beta subunits of cone cyclic-nucleotide gated channel (CNGB3) in the outer plexiform layer of affected animals was obvious. Achromatopsia is a monogenic Mendelian disease characterized by the loss of cone photoreceptor function resulting in day-blindness, total color-blindness, and decreased central visual acuity. After SNP genotyping and subsequent homozygosity mapping with twelve affected cattle, we performed whole-genome sequencing and variant calling of three cases. We identified a single missense variant in the bovine CNGB3 gene situated in a ~2.5 Mb homozygous genome region on chromosome 14 shared between all cases. All affected cattle were homozygous carriers of the p.Asp251Asn mutation that was predicted to be deleterious, affecting an evolutionary conserved residue. In conclusion, we have evidence for the occurrence of a breed-specific novel CNGB3-related form of recessively inherited achromatopsia in Original Braunvieh cattle which we have designated OH1 showing an allele frequency of the deleterious allele of ~8%. The identification of carriers will enable selection against this inherited disorder. The studied cattle might serve as an animal model to further elucidate the function of CNGB3 in mammals.
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Case JE, Pederzolli RLA, Clark EG, Fenton H, Kutz SJ, Grahn BH, Rothenburger JL. Congenital cataract and spherophakia leading to starvation in a free-ranging muskox neonate from the Northwest Territories, Canada. J Vet Diagn Invest 2021; 34:160-163. [PMID: 34763579 PMCID: PMC8688975 DOI: 10.1177/10406387211057470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A muskox neonate (Ovibos moschatus) that died of starvation was diagnosed with congenital lenticular anomalies that included spherophakia and hypermature cataract associated with probable lens-induced lymphocytic uveitis and neutrophilic keratitis. Impaired sight as a result of cataract and associated inflammation likely contributed to abandonment and starvation, although maternal death cannot be excluded definitively. Ocular lesions, such as congenital cataracts and spherophakia in neonates, may be important factors affecting survival in free-ranging animals.
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Affiliation(s)
- Julia E Case
- Departments of Ecosystem and Public Health and the Canadian Wildlife Health Cooperative Alberta Region, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Rae-Leigh A Pederzolli
- Departments of Ecosystem and Public Health and the Canadian Wildlife Health Cooperative Alberta Region, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Edward G Clark
- Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Heather Fenton
- Department of Environment and Natural Resources, Government of the Northwest Territories, Yellowknife, Northwest Territories, Canada.,Current address: Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies
| | - Susan J Kutz
- Departments of Ecosystem and Public Health and the Canadian Wildlife Health Cooperative Alberta Region, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Bruce H Grahn
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine and Prairie Ocular Pathology Service, Prairie Diagnostic Services, Saskatoon, Saskatchewan, Canada
| | - Jamie L Rothenburger
- Departments of Ecosystem and Public Health and the Canadian Wildlife Health Cooperative Alberta Region, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
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Zhu H, Zhang Z. Emerging Trends and Research Foci in Cataract Genes: A Bibliometric and Visualized Study. Front Genet 2021; 12:610728. [PMID: 34434212 PMCID: PMC8381374 DOI: 10.3389/fgene.2021.610728] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 07/15/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Approximately 50% of cataracts are associated with genetic factors. Genetic etiology and molecular mechanisms based on gene research increase the understanding of cataracts and provide direction for diagnosis and intervention. In the present study, SCIE papers related to the modeling of cataract gene research from 2010-2019 were evaluated and qualitative and quantitative analyses with modeling performed. Methods: The SCIE database was searched on July 6, 2021 for cataract gene publications and relevant papers published since 2010 were considered for review. Subsequently, 1,904 SCIE papers associated with cataract genes from 2010-2019 were analyzed using a bibliometric method. The publication, country, institution, journal, references, knowledgebase, keywords, and research hotspots of the papers were analyzed using an online analysis platform of literature metrology, bibliographic item co-occurrence matrix builder (BICOMB), CiteSpace V, and VOS viewer analysis tool. Results: 78 countries published the related articles, and the United States ranks of America had the most publications. Two thousand seven hundred and eighty three institutions contributed to the related publications. Fudan University had the most publications. The reference clusters of SCI papers were clustered into six categories, namely, causing congenital cataract-microcornea syndrome, functional snp, cataractous lenses, a1 mutation, foxe3 mutation, cell adhesion gene pvrl3, nid1 gene. The key words representing the research frontiers were cerebrotendinous xanthomatosis (2017-2019), oxidative stress (2017-2019). Conclusion: This study provided a systematic, objective and comprehensive analysis of the literature related to gene research of cataract. Moreover, this study demonstrated the current hotspots and the future trends in the field of gene research of cataract. This review will help ophthalmologist to discern the dynamic evolution of cataract gene research, as well as highlight areas for future research.
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Affiliation(s)
- Hongli Zhu
- Department of Ophthalmology, The 4th People's Hospital of Shenyang, Shenyang, China
| | - Zhichang Zhang
- Department of Computer, School of Intelligent Medicine, China Medical University, Shenyang, China
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CCDC66 frameshift variant associated with a new form of early-onset progressive retinal atrophy in Portuguese Water Dogs. Sci Rep 2020; 10:21162. [PMID: 33273526 PMCID: PMC7712861 DOI: 10.1038/s41598-020-77980-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 11/10/2020] [Indexed: 11/17/2022] Open
Abstract
Aberrant photoreceptor function or morphogenesis leads to blinding retinal degenerative diseases, the majority of which have a genetic aetiology. A variant in PRCD previously identified in Portuguese Water Dogs (PWDs) underlies prcd (progressive rod-cone degeneration), an autosomal recessive progressive retinal atrophy (PRA) with a late onset at 3–6 years of age or older. Herein, we have identified a new form of early-onset PRA (EOPRA) in the same breed. Pedigree analysis suggested an autosomal recessive inheritance. Four PWD full-siblings affected with EOPRA diagnosed at 2–3 years of age were genotyped (173,661 SNPs) along with 2 unaffected siblings, 2 unaffected parents, and 15 unrelated control PWDs. GWAS, linkage analysis and homozygosity mapping defined a 26-Mb candidate region in canine chromosome 20. Whole-genome sequencing in one affected dog and its obligatory carrier parents identified a 1 bp insertion (CFA20:g.33,717,704_33,717,705insT (CanFam3.1); c.2262_c.2263insA) in CCDC66 predicted to cause a frameshift and truncation (p.Val747SerfsTer8). Screening of an extended PWD population confirmed perfect co-segregation of this genetic variant with the disease. Western blot analysis of COS-1 cells transfected with recombinant mutant CCDC66 expression constructs showed the mutant transcript translated into a truncated protein. Furthermore, in vitro studies suggest that the mutant CCDC66 is mislocalized to the nucleus relative to wild type CCDC66. CCDC66 variants have been associated with inherited retinal degenerations (RDs) including canine and murine ciliopathies. As genetic variants affecting the primary cilium can cause ciliopathies in which RD may be either the sole clinical manifestation or part of a syndrome, our findings further support a role for CCDC66 in retinal function and viability, potentially through its ciliary function.
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Murgiano L, Militerno G, Sbarra F, Drögemüller C, G P Jacinto J, Gentile A, Bolcato M. KDM2B-associated paunch calf syndrome in Marchigiana cattle. J Vet Intern Med 2020; 34:1657-1661. [PMID: 32515858 PMCID: PMC7379006 DOI: 10.1111/jvim.15789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Chianina, Romagnola, and Marchigiana are the 3 most important Italian breeds of cattle raised in the Apennine Mountains. Inherited disorders have been reported in the Chianina and Romagnola breeds but not in the Marchigiana breed. Recently, a case resembling recessively inherited KDM2B-associated paunch calf syndrome (PCS) in Romagnola cattle was identified in Marchigiana cattle. HYPOTHESIS/OBJECTIVES To characterize the features of the observed congenital anomaly, evaluate its possible genetic etiology, and determine the prevalence of the deleterious allele in the Marchigiana population. ANIMALS A single stillborn Marchigiana calf was referred for clinicopathological examination because of the presence of PCS-like morphological lesions. METHODS The animal was necropsied and the calf and its parents were genotyped. A PCR-based direct gene test was applied to determine the KDM2B genotype and 114 Marchigiana bulls were genotyped. RESULTS The pathological phenotype included facial deformities, enlarged fluid-filled abdomen, and hepatic fibrosis. The affected animal was the offspring of consanguineous mating and homozygous presence of the KDM2B missense variant was confirmed. Both parents were heterozygous for KDM2B and the prevalence of carriers in a selected population of Marchigiana bulls was <2%. CONCLUSIONS AND CLINICAL IMPORTANCE The characteristic malformations and genetic findings were consistent with the diagnosis of PCS and provide evidence that the deleterious KDM2B variant initially detected in Romagnola cattle also occurs in the Marchigiana breed.
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Affiliation(s)
- Leonardo Murgiano
- Department of Clinical Sciences & Advanced Medicine , University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gianfranco Militerno
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Fiorella Sbarra
- National Association of Italian Beef-Cattle Breeders, Perugia, Italy
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Joana G P Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Arcangelo Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Marilena Bolcato
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
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Braun M, Struck AK, Reinartz S, Heppelmann M, Rehage J, Eule JC, Ciurkiewicz M, Beineke A, Metzger J, Distl O. Study of congenital Morgagnian cataracts in Holstein calves. PLoS One 2019; 14:e0226823. [PMID: 31877171 PMCID: PMC6932804 DOI: 10.1371/journal.pone.0226823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/05/2019] [Indexed: 11/18/2022] Open
Abstract
Cataracts are focal to diffuse opacities of the eye lens causing impaired vision or complete blindness. For bilateral congenital cataracts in Red Holsteins a perfectly cosegregating mutation within the CPAMD8 gene (CPAMD8:g.5995966C>T) has been reported. We genotyped the CPAMD8:g.5995966C>T variant in Holstein calves affected by congenital bilateral congenital cataracts, their unaffected relatives and randomly selected herd mates. Ophthalmological examinations were performed in all affected individuals to confirm a congenital cataract. Whole genome sequencing was employed to screen variants in candidate genes for the Morgagnian cataract phenotype. In the present study, 3/35 cases were confirmed as homozygous mutated and 6/14 obligate carriers. Further 7/46 unaffected animals related with these cases were heterozygous mutated for the CPAMD8:g.5995966C>T variant. However 32 cases with a congenital cataract showed the wild type for the CPAMD8 variant. We did not identify variants in the candidate genes CPAMD8 and NID1 or in their close neighborhood as strongly associated with the congenital cataract phenotype in Holstein calves with the CPAMD8 wild type. In conclusion, the CPAMD8:g.5995966C>T variant is insufficient to explain the majority of Morgagnian congenital cataract phenotypes in Holsteins. It is very likely that congenital bilateral cataracts may be genetically heterogeneous and not yet known variants in genes other than CPAMD8 and NID1 are involved.
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Affiliation(s)
- Marina Braun
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ann-Kathrin Struck
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Sina Reinartz
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Maike Heppelmann
- Clinic for Cattle, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Jürgen Rehage
- Clinic for Cattle, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Johanna Corinna Eule
- Small Animal Clinic, Faculty of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | - Andreas Beineke
- Institute of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
- * E-mail:
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Upadhyay M, Bortoluzzi C, Barbato M, Ajmone‐Marsan P, Colli L, Ginja C, Sonstegard TS, Bosse M, Lenstra JA, Groenen MAM, Crooijmans RPMA. Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs. Evol Appl 2019; 12:951-963. [PMID: 31080507 PMCID: PMC6503822 DOI: 10.1111/eva.12770] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/23/2018] [Accepted: 12/27/2018] [Indexed: 01/10/2023] Open
Abstract
The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might account for the presence of non-European cattle ancestry in these cattle breeds.
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Affiliation(s)
- Maulik Upadhyay
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Chiara Bortoluzzi
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition – DIANA, Nutrigenomics and Proteomics Research Centre – PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre – BioDNAUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Paolo Ajmone‐Marsan
- Department of Animal Science, Food and Nutrition – DIANA, Nutrigenomics and Proteomics Research Centre – PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre – BioDNAUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Licia Colli
- Department of Animal Science, Food and Nutrition – DIANA, Nutrigenomics and Proteomics Research Centre – PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre – BioDNAUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Catarina Ginja
- CIBIO‐InBIO—Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairaoPortugal
| | | | - Mirte Bosse
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | | | - Martien A. M. Groenen
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
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Functional non-coding polymorphism in an EPHA2 promoter PAX2 binding site modifies expression and alters the MAPK and AKT pathways. Sci Rep 2017; 7:9992. [PMID: 28855599 PMCID: PMC5577203 DOI: 10.1038/s41598-017-10117-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/04/2017] [Indexed: 01/11/2023] Open
Abstract
To identify possible genetic variants influencing expression of EPHA2 (Ephrin-receptor Type-A2), a tyrosine kinase receptor that has been shown to be important for lens development and to contribute to both congenital and age related cataract when mutated, the extended promoter region of EPHA2 was screened for variants. SNP rs6603883 lies in a PAX2 binding site in the EPHA2 promoter region. The C (minor) allele decreased EPHA2 transcriptional activity relative to the T allele by reducing the binding affinity of PAX2. Knockdown of PAX2 in human lens epithelial (HLE) cells decreased endogenous expression of EPHA2. Whole RNA sequencing showed that extracellular matrix (ECM), MAPK-AKT signaling pathways and cytoskeleton related genes were dysregulated in EPHA2 knockdown HLE cells. Taken together, these results indicate a functional non-coding SNP in EPHA2 promoter affects PAX2 binding and reduces EPHA2 expression. They further suggest that decreasing EPHA2 levels alters MAPK, AKT signaling pathways and ECM and cytoskeletal genes in lens cells that could contribute to cataract. These results demonstrate a direct role for PAX2 in EPHA2 expression and help delineate the role of EPHA2 in development and homeostasis required for lens transparency.
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Hollmann AK, Dammann I, Wemheuer WM, Wemheuer WE, Chilla A, Tipold A, Schulz-Schaeffer WJ, Beck J, Schütz E, Brenig B. Morgagnian cataract resulting from a naturally occurring nonsense mutation elucidates a role of CPAMD8 in mammalian lens development. PLoS One 2017; 12:e0180665. [PMID: 28683140 PMCID: PMC5500361 DOI: 10.1371/journal.pone.0180665] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/19/2017] [Indexed: 11/23/2022] Open
Abstract
To investigate the genetic basis of hereditary lens opacities we analyzed 31 cases of bilateral congenital cataract in Red Holstein Friesian cattle. A genome-wide association study revealed a significant association on bovine chromosome 7 at positions 6,166,179 and 12,429,691. Whole genome re-sequencing of one case and four relatives showed a nonsense mutation (g.5995966C>T) in the PZP-like, alpha-2-macroglobulin domain containing 8 (CPAMD8) gene leading to a premature stop codon (CPAMD8 p.Gln74*) associated with cataract development in cattle. With immunohistochemistry we confirmed a physiological expression of CPAMD8 in the ciliary body epithelium of the eye in unaffected cattle, while the protein was not detectable in the ciliary body of cattle with cataracts. RNA expression of CPAMD8 was detected in healthy adult, fetal and cataractous lenses.
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Affiliation(s)
- Anne K. Hollmann
- University of Goettingen, Institute of Veterinary Medicine, Goettingen, Germany
| | - Insa Dammann
- University Medical Center Goettingen, Department of Neuropathology, Prion and Dementia Research Unit, Goettingen, Germany
| | - Wiebke M. Wemheuer
- University of the Saarland, Institute of Neuropathology, Homburg, Germany
| | - Wilhelm E. Wemheuer
- University of Goettingen, Institute of Veterinary Medicine, Goettingen, Germany
| | - Almuth Chilla
- University of Goettingen, Institute of Veterinary Medicine, Goettingen, Germany
| | - Andrea Tipold
- University of Veterinary Medicine Hannover, Foundation, Department of Small Animal Medicine and Surgery, Hannover, Germany
| | | | | | - Ekkehard Schütz
- University of Goettingen, Institute of Veterinary Medicine, Goettingen, Germany
| | - Bertram Brenig
- University of Goettingen, Institute of Veterinary Medicine, Goettingen, Germany
- * E-mail:
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Osinchuk S, Petrie L, Leis M, Schumann F, Bauer B, Sandmeyer L, Madder K, Buchanan F, Grahn B. Congenital nuclear cataracts in a Holstein dairy herd. THE CANADIAN VETERINARY JOURNAL = LA REVUE VETERINAIRE CANADIENNE 2017; 58:488-492. [PMID: 28507388 PMCID: PMC5394606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This report describes congenital nuclear cataracts and posterior lenticonus in a closed purebred Holstein dairy herd in Canada. Ophthalmic examinations were completed on 30 male and 249 female cattle aged newborn to 10 years old. Nutritional, infectious, and toxic etiologies were investigated. Necropsies of 3 affected calves were performed and eyes of 2 additional affected calves were examined with light microscopy. Bilateral nuclear cataracts were identified in 53/279 (19%) animals. Additional congenital anomalies observed included posterior lenticonus, iris to lens persistent pupillary membranes (n = 7), and lenticular colobomata (n = 1). Heifers did not give birth to calves with congenital nuclear cataracts (0/105), whereas the incidence of affected calves born to multiparous cows was 31% (53/171). The animals with nuclear cataracts ranged from newborn to 8 years old. The cataracts appeared to be non- or minimally progressive. Light microscopic examination of 10 affected globes confirmed nuclear cataract with posterior lenticonus (n = 10). Pedigree analysis was inconclusive. Polymerase chain reaction and sequence analysis for the NID1 gene deletion were negative. The etiology of the congenital lenticular anomalies was not determined.
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17
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A reverse genetic approach identifies an ancestral frameshift mutation in RP1 causing recessive progressive retinal degeneration in European cattle breeds. Genet Sel Evol 2016; 48:56. [PMID: 27510606 PMCID: PMC4980790 DOI: 10.1186/s12711-016-0232-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/26/2016] [Indexed: 01/17/2023] Open
Abstract
Background Domestication and artificial selection have resulted in strong genetic drift, relaxation of purifying selection and accumulation of deleterious mutations. As a consequence, bovine breeds experience regular outbreaks of recessive genetic defects which might represent only the tip of the iceberg since their detection depends on the observation of affected animals with distinctive symptoms. Thus, recessive mutations resulting in embryonic mortality or in non-specific symptoms are likely to be missed. The increasing availability of whole-genome sequences has opened new research avenues such as reverse genetics for their investigation. Our aim was to characterize the genetic load of 15 European breeds using data from the 1000 bull genomes consortium and prove that widespread harmful mutations remain to be detected. Results We listed 2489 putative deleterious variants (in 1923 genes) segregating at a minimal frequency of 5 % in at least one of the breeds studied. Gene enrichment analysis showed major enrichment for genes related to nervous, visual and auditory systems, and moderate enrichment for genes related to cardiovascular and musculoskeletal systems. For verification purposes, we investigated the phenotypic consequences of a frameshift variant in the retinitis pigmentosa-1 gene segregating in several breeds and at a high frequency (27 %) in Normande cattle. As described in certain human patients, clinical and histological examination revealed that this mutation causes progressive degeneration of photoreceptors leading to complete blindness in homozygotes. We established that the deleterious allele was even more frequent in the Normande breed before 1975 (>40 %) and has been progressively counter-selected likely because of its associated negative effect on udder morphology. Finally, using identity-by-descent analysis we demonstrated that this mutation resulted from a unique ancestral event that dates back to ~2800 to 4000 years. Conclusions We provide a list of mutations that likely represent a substantial part of the genetic load of domestication in European cattle. We demonstrate that they accumulated non-randomly and that genes related to cognition and sensory functions are particularly affected. Finally, we describe an ancestral deleterious variant segregating in different breeds causing progressive retinal degeneration and irreversible blindness in adult animals. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0232-y) contains supplementary material, which is available to authorized users.
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Pausch H, Venhoranta H, Wurmser C, Hakala K, Iso-Touru T, Sironen A, Vingborg RK, Lohi H, Söderquist L, Fries R, Andersson M. A frameshift mutation in ARMC3 is associated with a tail stump sperm defect in Swedish Red (Bos taurus) cattle. BMC Genet 2016; 17:49. [PMID: 26923438 PMCID: PMC4770540 DOI: 10.1186/s12863-016-0356-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/17/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Artificial insemination is widely used in many cattle breeding programs. Semen samples of breeding bulls are collected and closely examined immediately after collection at artificial insemination centers. Only ejaculates without anomalous findings are retained for artificial insemination. Although morphological aberrations of the spermatozoa are a frequent reason for discarding ejaculates, the genetic determinants underlying poor semen quality are scarcely understood. RESULTS A tail stump sperm defect was observed in three bulls of the Swedish Red cattle breed. The spermatozoa of affected bulls were immotile because of severely disorganized tails indicating disturbed spermatogenesis. We genotyped three affected bulls and 18 unaffected male half-sibs at 46,035 SNPs and performed homozygosity mapping to map the fertility disorder to an 8.42 Mb interval on bovine chromosome 13. The analysis of whole-genome re-sequencing data of an affected bull and 300 unaffected animals from eleven cattle breeds other than Swedish Red revealed a 1 bp deletion (Chr13: 24,301,425 bp, ss1815612719) in the eleventh exon of the armadillo repeat containing 3-encoding gene (ARMC3) that was compatible with the supposed recessive mode of inheritance. The deletion is expected to alter the reading frame and to induce premature translation termination (p.A451fs26). The mutated protein is shortened by 401 amino acids (46 %) and lacks domains that are likely essential for normal protein function. CONCLUSIONS We report the phenotypic and genetic characterization of a sterilizing tail stump sperm defect in the Swedish Red cattle breed. Exploiting high-density genotypes and massive re-sequencing data enabled us to identify the most likely causal mutation for the fertility disorder in bovine ARMC3. Our results provide the basis for monitoring the mutated variant in the Swedish Red cattle population and for the early identification of infertile animals.
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Affiliation(s)
- Hubert Pausch
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, 85354, Freising, Germany.
| | - Heli Venhoranta
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, 04920, Saarentaus, Finland.
| | - Christine Wurmser
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, 85354, Freising, Germany.
| | - Kalle Hakala
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, 04920, Saarentaus, Finland.
| | - Terhi Iso-Touru
- Natural Resources Institute Finland (Luke), Green Technology, 31600, Jokioinen, Finland.
| | - Anu Sironen
- Natural Resources Institute Finland (Luke), Green Technology, 31600, Jokioinen, Finland.
| | | | - Hannes Lohi
- Department of Veterinary Biosciences and Research Programs Unit, Molecular Neurology, University of Helsinki and Folkhälsan Research Center, 00290, Helsinki, Finland.
| | - Lennart Söderquist
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
| | - Ruedi Fries
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, 85354, Freising, Germany.
| | - Magnus Andersson
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, 04920, Saarentaus, Finland.
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Menzi F, Besuchet-Schmutz N, Fragnière M, Hofstetter S, Jagannathan V, Mock T, Raemy A, Studer E, Mehinagic K, Regenscheit N, Meylan M, Schmitz-Hsu F, Drögemüller C. A transposable element insertion in APOB causes cholesterol deficiency in Holstein cattle. Anim Genet 2016; 47:253-7. [PMID: 26763170 PMCID: PMC4849205 DOI: 10.1111/age.12410] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2015] [Indexed: 11/29/2022]
Abstract
Cholesterol deficiency, a new autosomal recessive inherited genetic defect in Holstein cattle, has been recently reported to have an influence on the rearing success of calves. The affected animals show unresponsive diarrhea accompanied by hypocholesterolemia and usually die within the first weeks or months of life. Here, we show that whole genome sequencing combined with the knowledge about the pedigree and inbreeding status of a livestock population facilitates the identification of the causative mutation. We resequenced the entire genomes of an affected calf and a healthy partially inbred male carrying one copy of the critical 2.24‐Mb chromosome 11 segment in its ancestral state and one copy of the same segment with the cholesterol deficiency mutation. We detected a single structural variant, homozygous in the affected case and heterozygous in the non‐affected carrier male. The genetic makeup of this key animal provides extremely strong support for the causality of this mutation. The mutation represents a 1.3kb insertion of a transposable LTR element (ERV2‐1) in the coding sequence of the APOB gene, which leads to truncated transcripts and aberrant splicing. This finding was further supported by RNA sequencing of the liver transcriptome of an affected calf. The encoded apolipoprotein B is an essential apolipoprotein on chylomicrons and low‐density lipoproteins, and therefore, the mutation represents a loss of function mutation similar to autosomal recessive inherited familial hypobetalipoproteinemia‐1 (FHBL1) in humans. Our findings provide a direct gene test to improve selection against this deleterious mutation in Holstein cattle.
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Affiliation(s)
- F Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - N Besuchet-Schmutz
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - M Fragnière
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - S Hofstetter
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - T Mock
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - A Raemy
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - E Studer
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - K Mehinagic
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122 CH-3001, Bern, Switzerland
| | - N Regenscheit
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122 CH-3001, Bern, Switzerland
| | - M Meylan
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - F Schmitz-Hsu
- Swissgenetics, Meielenfeldweg 12 CH-3052, Zollikofen, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
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Wiedemar N, Riedi AK, Jagannathan V, Drögemüller C, Meylan M. Genetic Abnormalities in a Calf with Congenital Increased Muscular Tonus. J Vet Intern Med 2015; 29:1418-21. [PMID: 26289121 PMCID: PMC4858041 DOI: 10.1111/jvim.13599] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 05/06/2015] [Accepted: 07/21/2015] [Indexed: 12/12/2022] Open
Affiliation(s)
- N Wiedemar
- Institute of Genetics, Vetsuisse Faculty, University of Berne, Berne, Switzerland
| | - A-K Riedi
- Clinic for Ruminants, Vetsuisse Faculty, University of Berne, Berne, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Berne, Berne, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Berne, Berne, Switzerland
| | - M Meylan
- Clinic for Ruminants, Vetsuisse Faculty, University of Berne, Berne, Switzerland
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21
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Murgiano L, Shirokova V, Welle MM, Jagannathan V, Plattet P, Oevermann A, Pienkowska-Schelling A, Gallo D, Gentile A, Mikkola M, Drögemüller C. Hairless Streaks in Cattle Implicate TSR2 in Early Hair Follicle Formation. PLoS Genet 2015. [PMID: 26203908 PMCID: PMC4512707 DOI: 10.1371/journal.pgen.1005427] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Four related cows showed hairless streaks on various parts of the body with no correlation to the pigmentation pattern. The stripes occurred in a consistent pattern resembling the lines of Blaschko. The non-syndromic hairlessness phenotype observed occurred across three generations of a single family and was compatible with an X-linked mode of inheritance. Linkage analysis and subsequent whole genome sequencing of one affected female identified two perfectly associated non-synonymous sequence variants in the critical interval on bovine chromosome X. Both variants occurred in complete linkage disequilibrium and were absent in more than 3900 controls. An ERCC6L missense mutation was predicted to cause an amino acid substitution of a non-conserved residue. Analysis in mice showed no specific Ercc6l expression pattern related to hair follicle development and therefore ERCC6L was not considered as causative gene. A point mutation at the 5'-splice junction of exon 5 of the TSR2, 20S rRNA accumulation, homolog (S. cerevisiae), gene led to the production of two mutant transcripts, both of which contain a frameshift and generate a premature stop codon predicted to truncate approximately 25% of the protein. Interestingly, in addition to the presence of both physiological TSR2 transcripts, the two mutant transcripts were predominantly detected in the hairless skin of the affected cows. Immunohistochemistry, using an antibody against the N-terminal part of the bovine protein demonstrated the specific expression of the TSR2 protein in the skin and the hair of the affected and the control cows as well as in bovine fetal skin and hair. The RNA hybridization in situ showed that Tsr2 was expressed in pre- and post-natal phases of hair follicle development in mice. Mammalian TSR2 proteins are highly conserved and are known to be broadly expressed, but their precise in vivo functions are poorly understood. Thus, by dissecting a naturally occurring mutation in a domestic animal species, we identified TSR2 as a regulator of hair follicle development. The identification of causal mutations of rare monogenic disorders provides an insight into the function of single genes. We herein report an example which demonstrates that the bovine species presents an excellent system for identifying these inherited phenotypes. The individual health status of modern dairy cows is well monitored, and emerging disorders are routinely recorded. An Italian breeder of ~500 Pezzata Rossa cattle reported a case of congenital streaked hairlessness. Three additional, closely related cows, showing similar hairless pattern following Blaschko’s lines were subsequently observed. A causative mutation was discovered in a previously uncharacterized rRNA processing gene. Cows possessing a single copy of this TSR2 mutation located on the X chromosome showed a mosaic skin pattern which is very likely due to the skewed inactivation of the X-chromosome, also known as lyonization. The expression of TSR2 was shown in skin and hair of cattle and mice. This study is the first to implicate an essential role for TSR2 during hair follicle development and reflects once more the potential of using rare diseases in cows to gain additional insights into mammalian biology.
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Affiliation(s)
- Leonardo Murgiano
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Vera Shirokova
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Monika Maria Welle
- DermFocus, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Philippe Plattet
- Division of Neurological Sciences, DCR-VPH, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Anna Oevermann
- Division of Neurological Sciences, DCR-VPH, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Daniele Gallo
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell’Emilia, Italy
| | - Arcangelo Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell’Emilia, Italy
| | - Marja Mikkola
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
- * E-mail:
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22
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Esmaeeli Nieh S, Madou MRZ, Sirajuddin M, Fregeau B, McKnight D, Lexa K, Strober J, Spaeth C, Hallinan BE, Smaoui N, Pappas JG, Burrow TA, McDonald MT, Latibashvili M, Leshinsky-Silver E, Lev D, Blumkin L, Vale RD, Barkovich AJ, Sherr EH. De novo mutations in KIF1A cause progressive encephalopathy and brain atrophy. Ann Clin Transl Neurol 2015; 2:623-35. [PMID: 26125038 PMCID: PMC4479523 DOI: 10.1002/acn3.198] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 12/30/2022] Open
Abstract
Objective To determine the cause and course of a novel syndrome with progressive encephalopathy and brain atrophy in children. Methods Clinical whole-exome sequencing was performed for global developmental delay and intellectual disability; some patients also had spastic paraparesis and evidence of clinical regression. Six patients were identified with de novo missense mutations in the kinesin gene KIF1A. The predicted functional disruption of these mutations was assessed in silico to compare the calculated conformational flexibility and estimated efficiency of ATP binding to kinesin motor domains of wild-type (WT) versus mutant alleles. Additionally, an in vitro microtubule gliding assay was performed to assess the effects of de novo dominant, inherited recessive, and polymorphic variants on KIF1A motor function. Results All six subjects had severe developmental delay, hypotonia, and varying degrees of hyperreflexia and spastic paraparesis. Microcephaly, cortical visual impairment, optic neuropathy, peripheral neuropathy, ataxia, epilepsy, and movement disorders were also observed. All six patients had a degenerative neurologic course with progressive cerebral and cerebellar atrophy seen on sequential magnetic resonance imaging scans. Computational modeling of mutant protein structures when compared to WT kinesin showed substantial differences in conformational flexibility and ATP-binding efficiency. The de novo KIF1A mutants were nonmotile in the microtubule gliding assay. Interpretation De novo mutations in KIF1A cause a degenerative neurologic syndrome with brain atrophy. Computational and in vitro assays differentiate the severity of dominant de novo heterozygous versus inherited recessive KIF1A mutations. The profound effect de novo mutations have on axonal transport is likely related to the cause of progressive neurologic impairment in these patients.
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Affiliation(s)
- Sahar Esmaeeli Nieh
- Department of Neurology, University of California San Francisco, California, 94158
| | - Maura R Z Madou
- Department of Neurology, University of California San Francisco, California, 94158
| | - Minhajuddin Sirajuddin
- Department of Cellular and Molecular Pharmacology and the Howard Hughes Medical Institute, University of California San Francisco, California ; Cardiovascular Biology and Diseases, Institute of Stem Cell Biology and Regenerative Medicine, NCBS-TIFR Bangalore, India
| | - Brieana Fregeau
- Department of Neurology, University of California San Francisco, California, 94158
| | | | - Katrina Lexa
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, California
| | - Jonathan Strober
- Department of Neurology, University of California San Francisco, California, 94158
| | - Christine Spaeth
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center Cincinnati, Ohio
| | - Barbara E Hallinan
- Division of Neurology, Cincinnati Children's Hospital Medical Center Cincinnati, Ohio
| | | | - John G Pappas
- Department of Pediatrics, Clinical Genetic Services, NYU School of Medicine New York, New York
| | - Thomas A Burrow
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center Cincinnati, Ohio ; Department of pediatrics, University of Cincinnati School of Medicine Cincinnati, Ohio
| | - Marie T McDonald
- Section of Medical Genetics, Department of Pediatrics, Duke University Durham, North Carolina
| | - Mariam Latibashvili
- Department of Neurology, University of California San Francisco, California, 94158 ; University of California San Diego, California
| | - Esther Leshinsky-Silver
- Molecular Genetics Laboratory, and Metabolic-Neurogenetic Service, Wolfson Medical Center and Sackler Medical School, Tel Aviv University Tel Aviv, Israel
| | - Dorit Lev
- Institute of Medical Genetics and Metabolic Neurogenetic Service, Wolfson Medical Center and Sackler Medical School, Tel Aviv University Tel Aviv, Israel
| | - Luba Blumkin
- Pediatric Neurology Unit and Metabolic Neurogenetic Service, Wolfson Medical Center, Holon and Sackler Medical School, Tel Aviv University Tel Aviv, Israel
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology and the Howard Hughes Medical Institute, University of California San Francisco, California
| | - Anthony James Barkovich
- Department of Radiology and Biomedical Imaging, University of California San Francisco, California
| | - Elliott H Sherr
- Department of Neurology, University of California San Francisco, California, 94158
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