- Email: [email protected]
Contribution of DNA copy number variants to equine cryptorchidism
Journal of Equine Veterinary Science 34 (2014) 29
Contents lists available at ScienceDirect
Journal of Equine Veterinary Science journal homepage: www.j-evs.com
Contribution of DNA copy number variants to equine cryptorchidism S. Ghosh 1, P.J. Das 1, C. Arnold 2, J. Jaxheimer 2, D.D. Varner 2, B.P. Chowdhary 2, T. Raudsepp 1, * 1 2
Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX77843, USA Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX77843, USA
Cryptorchidism, a failure of one or both testes to descend into the scrotum, affects about 2-8% of live male foals, with a significantly higher risk in the American Quarter Horse. The genetic component of cryptorchidism is largely unknown, although involvement of both single gene mutations and DNA copy number variants (CNVs), i.e., DNA sequence losses or gains, have been proposed for the condition in men. Here we investigated possible involvement of CNVs in equine isolated (nonsyndromic) bilateral abdominal cryptorchidism. Genomic DNA was obtained from 11 affected horses of various breeds: an Appaloosa, a Lipizzaner, a pony, and 8 purebred or mixed American Quarter Horses. Their genomes were interrogated for CNVs by array comparative genomic hybridization (aCGH) using our custom designed whole genome oligonucleotide tiling array comprising 417,377 probes of which 85,852 represent gene exons. Reference DNA for aCGH was from a male Thoroughbred. The data were analyzed with Agilent Genomics Workbench software and CNVs were called as +0.5 log2 -0.5, over 5 consecutive probes. The results were compared with the CNV dataset available for the horse genome, including our unpublished data for 16 diverse breeds. Altogether, we detected in cryptorchid horses 50 CNVs, the majority of which were shared with those known in normal equine populations, while 11 CNVs (9 gains, 2 losses) were uniquely found in
* Presenting author 0737-0806/$ – see front matter Ó 2014 Published by Elsevier Inc. http://dx.doi.org/10.1016/j.jevs.2013.10.015
bilateral cryptorchids. The most notable was a 106 kilobase-pair (kb) duplication in a homeobox (HOX) gene cluster in chromosome 18 because mutations in these genes have been associated with cryptorchidism in men and mice. Furthermore, our previous functional studies in stallions show that HOX genes are significantly overexpressed in cryptorchid testes compared to normal testes. In addition to ‘cryptorchid-specific’ CNVs, a common CNV of functional interest was found in chromosome 29. The region contains the AKR1C gene cluster known to be involved in testicular androgen biosynthesis and sex determination in humans, and has been associated with cryptorchidism and other disorders of sexual development in men. While the region is also variable in the general horse population, a homozygous 300 kb deletion of all AKR1C genes was found only in a cryptorchid horse. The findings were confirmed by qPCR and fluorescence in situ hybridization in the study population and will be examined further in a cohort of over 60 uni-and bilateral cryptorchid horses. We conclude that, like in other mammals, the genetic component of equine cryptorchidism is complex and heterogeneous, and likely involves CNVs. Our results indicate that CNVs in morphogenetic genes and genes involved in sex steroidal signaling pathways might contribute to the phenotype. This research was supported by the American Quarter Horse Association.
Contents lists available at ScienceDirect
Journal of Equine Veterinary Science journal homepage: www.j-evs.com
Contribution of DNA copy number variants to equine cryptorchidism S. Ghosh 1, P.J. Das 1, C. Arnold 2, J. Jaxheimer 2, D.D. Varner 2, B.P. Chowdhary 2, T. Raudsepp 1, * 1 2
Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX77843, USA Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX77843, USA
Cryptorchidism, a failure of one or both testes to descend into the scrotum, affects about 2-8% of live male foals, with a significantly higher risk in the American Quarter Horse. The genetic component of cryptorchidism is largely unknown, although involvement of both single gene mutations and DNA copy number variants (CNVs), i.e., DNA sequence losses or gains, have been proposed for the condition in men. Here we investigated possible involvement of CNVs in equine isolated (nonsyndromic) bilateral abdominal cryptorchidism. Genomic DNA was obtained from 11 affected horses of various breeds: an Appaloosa, a Lipizzaner, a pony, and 8 purebred or mixed American Quarter Horses. Their genomes were interrogated for CNVs by array comparative genomic hybridization (aCGH) using our custom designed whole genome oligonucleotide tiling array comprising 417,377 probes of which 85,852 represent gene exons. Reference DNA for aCGH was from a male Thoroughbred. The data were analyzed with Agilent Genomics Workbench software and CNVs were called as +0.5 log2 -0.5, over 5 consecutive probes. The results were compared with the CNV dataset available for the horse genome, including our unpublished data for 16 diverse breeds. Altogether, we detected in cryptorchid horses 50 CNVs, the majority of which were shared with those known in normal equine populations, while 11 CNVs (9 gains, 2 losses) were uniquely found in
* Presenting author 0737-0806/$ – see front matter Ó 2014 Published by Elsevier Inc. http://dx.doi.org/10.1016/j.jevs.2013.10.015
bilateral cryptorchids. The most notable was a 106 kilobase-pair (kb) duplication in a homeobox (HOX) gene cluster in chromosome 18 because mutations in these genes have been associated with cryptorchidism in men and mice. Furthermore, our previous functional studies in stallions show that HOX genes are significantly overexpressed in cryptorchid testes compared to normal testes. In addition to ‘cryptorchid-specific’ CNVs, a common CNV of functional interest was found in chromosome 29. The region contains the AKR1C gene cluster known to be involved in testicular androgen biosynthesis and sex determination in humans, and has been associated with cryptorchidism and other disorders of sexual development in men. While the region is also variable in the general horse population, a homozygous 300 kb deletion of all AKR1C genes was found only in a cryptorchid horse. The findings were confirmed by qPCR and fluorescence in situ hybridization in the study population and will be examined further in a cohort of over 60 uni-and bilateral cryptorchid horses. We conclude that, like in other mammals, the genetic component of equine cryptorchidism is complex and heterogeneous, and likely involves CNVs. Our results indicate that CNVs in morphogenetic genes and genes involved in sex steroidal signaling pathways might contribute to the phenotype. This research was supported by the American Quarter Horse Association.