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Zhou F, Wang S, Qin H, Zeng H, Ye J, Yang J, Cai G, Wu Z, Zhang Z. Genome-wide association analysis unveils candidate genes and loci associated with aplasia cutis congenita in pigs. BMC Genomics 2023; 24:701. [PMID: 37990155 PMCID: PMC10664689 DOI: 10.1186/s12864-023-09803-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/11/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Aplasia cutis congenita (ACC) is a rare genetic disorder characterized by the localized or widespread absence of skin in humans and animals. Individuals with ACC may experience developmental abnormalities in the skeletal and muscular systems, as well as potential complications. Localized and isolated cases of ACC can be treated through surgical and medical interventions, while extensive cases of ACC may result in neonatal mortality. The presence of ACC in pigs has implications for animal welfare. It contributes to an elevated mortality rate among piglets at birth, leading to substantial economic losses in the pig farming industry. In order to elucidate candidate genetic loci associated with ACC, we performed a Genome-Wide Association Study analysis on 216 Duroc pigs. The primary goal of this study was to identify candidate genes that associated with ACC. RESULTS This study identified nine significant SNPs associated with ACC. Further analysis revealed the presence of two quantitative trait loci, 483 kb (5:18,196,971-18,680,098) on SSC 5 and 159 kb (13:20,713,440-207294431 bp) on SSC13. By annotating candidate genes within a 1 Mb region surrounding the significant SNPs, a total of 11 candidate genes were identified on SSC5 and SSC13, including KRT71, KRT1, KRT4, ITGB7, CSAD, RARG, SP7, PFKL, TRPM2, SUMO3, and TSPEAR. CONCLUSIONS The results of this study further elucidate the potential mechanisms underlying and genetic architecture of ACC and identify reliable candidate genes. These results lay the foundation for treating and understanding ACC in humans.
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Affiliation(s)
- Fuchen Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Shenghui Wang
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Haojun Qin
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Haiyu Zeng
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Jian Ye
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China.
| | - Zebin Zhang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.
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Neutral sphingomyelinase 2 deficiency is associated with lung anomalies similar to emphysema. Mamm Genome 2012; 23:758-63. [PMID: 22945695 DOI: 10.1007/s00335-012-9419-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/23/2012] [Indexed: 01/05/2023]
Abstract
Neutral sphingomyelinase 2 (nSMase2) upregulation was recently demonstrated to serve as a molecular link between smoke inhalation and emphysematous changes in lungs. Here we report that nSMase2 deficit impairs lung development in mice. We have shown previously that fragilitas ossium (fro) mice carry a mutation in the Smpd3 gene, rendering nSMase2 catalytically inactive. Analysis of lung phenotype revealed that fro mice have abnormally enlarged alveoli and increased compliance of the respiratory system, similar to morphological and functional manifestations of emphysema. Analysis of sphingolipid content in fro lungs revealed a decreased level of C14:0 ceramide but no significant alterations in the levels of sphingosine or sphingosine-1-phosphate. Altogether, our data suggest that nSMase2 activity and ceramide level are critical for lung development and function. Based on our data, ceramide can no longer be viewed as a lipid solely detrimental to lung function.
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Gandolfi B, Outerbridge CA, Beresford LG, Myers JA, Pimentel M, Alhaddad H, Grahn JC, Grahn RA, Lyons LA. The naked truth: Sphynx and Devon Rex cat breed mutations in KRT71. Mamm Genome 2010; 21:509-15. [PMID: 20953787 PMCID: PMC2974189 DOI: 10.1007/s00335-010-9290-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 09/13/2010] [Indexed: 01/25/2023]
Abstract
Hair is a unique structure, characteristic of mammals, controlling body homeostasis, as well as cell and tissue integration. Previous studies in dog, mouse, and rat have identified polymorphisms in Keratin 71 (KRT71) as responsible for the curly/wavy phenotypes. The coding sequence and the 3′ UTR of KRT71 were directly sequenced in randomly bred and pedigreed domestic cats with different pelage mutations, including hairless varieties. A SNP altering a splice site was identified in the Sphynx breed and suggested to be the hairless (hr) allele, and a complex sequence alteration, also causing a splice variation, was identified in the Devon Rex breed and suggested to be the curly (re) allele. The polymorphisms were genotyped in approximately 200 cats. All the Devon Rex were homozygous for the complex alterations and most of the Sphynx were either homozygous for the hr allele or compound heterozygotes with the Devon-associated re allele, suggesting that the phenotypes are a result of the identified SNPs. Two Sphynx carrying the proposed hr mutation did not carry the Devon-associated alteration. No other causative mutations for eight different rexoid and hairless cat phenotypes were identified. The allelic series KRT71+ > KRT71hr > KRT71re is suggested.
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Affiliation(s)
- Barbara Gandolfi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California—Davis, 1114 Tupper Hall, Davis, CA 95616 USA
| | - Catherine A. Outerbridge
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California—Davis, Davis, CA 95616 USA
| | - Leslie G. Beresford
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California—Davis, 1114 Tupper Hall, Davis, CA 95616 USA
| | - Jeffrey A. Myers
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California—Davis, 1114 Tupper Hall, Davis, CA 95616 USA
| | - Monica Pimentel
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California—Davis, 1114 Tupper Hall, Davis, CA 95616 USA
| | - Hasan Alhaddad
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California—Davis, 1114 Tupper Hall, Davis, CA 95616 USA
| | - Jennifer C. Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California—Davis, 1114 Tupper Hall, Davis, CA 95616 USA
| | - Robert A. Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California—Davis, 1114 Tupper Hall, Davis, CA 95616 USA
| | - Leslie A. Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California—Davis, 1114 Tupper Hall, Davis, CA 95616 USA
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A novel hairless mouse model on an atopic dermatitis-prone genetic background generated by receptor-mediated transgenesis. Transgenic Res 2008; 17:1155-62. [DOI: 10.1007/s11248-008-9203-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Accepted: 07/08/2008] [Indexed: 10/21/2022]
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Nanashima N, Akita M, Yamada T, Shimizu T, Nakano H, Fan Y, Tsuchida S. The Hairless Phenotype of the Hirosaki Hairless Rat Is Due to the Deletion of an 80-kb Genomic DNA Containing Five Basic Keratin Genes. J Biol Chem 2008; 283:16868-75. [DOI: 10.1074/jbc.m802539200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Dominant suppression of repeat-induced point mutation in Neurospora crassa by a variant catalytic subunit of DNA polymerase zeta. Genetics 2008; 178:1169-76. [PMID: 18245848 DOI: 10.1534/genetics.107.079483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Crosses involving the Adiopodoumé strain of Neurospora crassa are defective for repeat-induced point mutation (RIP), a genome defense mechanism of fungi. We show here that the Adiopodoumé strain possesses an incompletely penetrant and variably expressive dominant suppressor of RIP (Srp) that maps to an approximately 34-kbp genome segment that is approximately 26 kbp proximal to mat on linkage group IL. Gene disruption experiments revealed that Srp is the upr-1 allele of Adiopodoumé (upr-1(Ad)) that is contained within this segment. The upr-1 gene codes for the catalytic subunit of the translesion DNA polymerase-zeta (Pol-zeta) and it is unusually polymorphic in Neurospora. That the upr-1 gene contains upstream ORFs that overlap with the main ORF is potentially relevant to the incomplete penetrance and variable expressivity of the suppressor. Crosses between heterokaryons that contain upr-1(Ad) and strains that prevent mating events involving nuclei that contain upr-1(Ad) yielded no progeny in which RIP had occurred, consistent with the idea that the suppressor encoded by upr-1(Ad) is diffusible. The potential involvement of the Pol-zeta subunit in two functions, translesion DNA synthesis and RIP regulation, might account for the rapid evolution of its gene in Neurospora.
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Wang Z, Wong P, Langbein L, Schweizer J, Coulombe PA. Type II epithelial keratin 6hf (K6hf) is expressed in the companion layer, matrix, and medulla in anagen-stage hair follicles. J Invest Dermatol 2004; 121:1276-82. [PMID: 14675170 DOI: 10.1111/j.1523-1747.2003.12644.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
More than half of the known keratin genes (n approximately 50) are expressed in the hair follicle. An in-depth knowledge of their differential expression in this organ will help us to understand the mechanisms of its formation and cycling, and the etiology of inherited hair disorders. Keratin 6hf is a type II keratin recently shown to occur in the companion layer. We cloned the mouse ortholog and characterized its expression in skin and oral mucosa. The mK6hf gene is 9.1 kb long and located in the cluster of type II keratin genes on mouse chromosome 15, between the keratin 6 (mK6alpha/mK6beta) and hair keratin genes. In situ hybridization and protein immunolocalization showed that, in addition to the companion layer, mK6hf is expressed in the upper matrix and medulla of the anagen-stage hair. This distribution is seen for all types of mouse hairs and medullated human hairs. The distribution of keratin 6hf protein in the hair shaft mirrors that of keratin 17, and the observation of reduced levels of keratin 6hf in keratin 17 null hair argues for a direct interaction between them. mK6hf is also expressed in the nail bed epithelium and fungiform papillae of dorsal tongue epithelium. Our findings provide an additional marker for the hair matrix and medulla, and suggest that the cellular precursors for the medulla, cortex, and cuticle compartments are already spatially segregated within the hair matrix. They also have obvious implications for the epithelial alterations associated with defects in keratin 6 genes.
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Affiliation(s)
- Zhiling Wang
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Kikkawa Y, Oyama A, Ishii R, Miura I, Amano T, Ishii Y, Yoshikawa Y, Masuya H, Wakana S, Shiroishi T, Taya C, Yonekawa H. A Small Deletion Hotspot in the Type II Keratin Gene mK6irs1/Krt2-6g on Mouse Chromosome 15, a Candidate for Causing the Wavy Hair of the Caracul (Ca) Mutation. Genetics 2003; 165:721-33. [PMID: 14573483 PMCID: PMC1462786 DOI: 10.1093/genetics/165.2.721] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
A new mutation has arisen in a colony of mice transgenic for human α-galactosidase. The mutation is independent of the transgenic insertion, autosomal dominant, and morphologically very similar to the classical wavy coat mutation, caracul (Ca), on chromosome 15. Therefore, we designated this locus the caracul Rinshoken (CaRin). Applying a positional cloning approach, we identified the mK6irs1/Krt2-6g gene as a strong candidate for CaRin because among five Ca alleles examined mutations always occurred in the highly conserved positions of the α-helical rod domain (1A and 2B subdomain) of this putative gene product. The most striking finding is that four independently discovered alleles, the three preexistent alleles CaJ, Ca9J, Ca10J, and our allele CaRin, all share one identical amino acid deletion (N 140 del) and the fifth, CamedJ, has an amino acid substitution (A 431 D). These findings indicate that a mutation hotspot exists in the Ca locus. Additionally, we describe a Ca mutant allele induced by ENU mutagenesis, which also possesses an amino acid substitution (L 424 W) in the mK6irs1/Krt2-6g gene. The identification of the Ca candidate gene enables us to further define the nature of the genetic pathway required for hair formation and provides an important new candidate that may be implicated in human hair and skin diseases.
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Affiliation(s)
- Yoshiaki Kikkawa
- Department of Laboratory Animal Science, The Tokyo Metropolitan Institute of Medical Science (Rinshoken), Tokyo 113-8613, Japan
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