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Peart CR, Williams C, Pophaly SD, Neely BA, Gulland FMD, Adams DJ, Ng BL, Cheng W, Goebel ME, Fedrigo O, Haase B, Mountcastle J, Fungtammasan A, Formenti G, Collins J, Wood J, Sims Y, Torrance J, Tracey A, Howe K, Rhie A, Hoffman JI, Johnson J, Jarvis ED, Breen M, Wolf JBW. Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution. Mol Ecol Resour 2021; 21:2455-2470. [PMID: 34097816 PMCID: PMC9732816 DOI: 10.1111/1755-0998.13443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/06/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022]
Abstract
With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome assemblies of an emerging wild animal model for carcinogenesis, the California sea lion (Zalophus californianus). Short-read assemblies were scaffolded with two independent chromatin interaction mapping data sets (Hi-C and Chicago), and long-read assemblies with three data types (Hi-C, optical maps and 10X linked reads) following the "Vertebrate Genomes Project (VGP)" pipeline. In both approaches, 18 major scaffolds recovered the karyotype (2n = 36), with scaffold N50s of 138 and 147 Mb, respectively. Synteny relationships at the chromosome level with other pinniped genomes (2n = 32-36), ferret (2n = 34), red panda (2n = 36) and domestic dog (2n = 78) were consistent across approaches and recovered known fissions and fusions. Comparative chromosome painting and multicolour chromosome tiling with a panel of 264 genome-integrated single-locus canine bacterial artificial chromosome probes provided independent evaluation of genome organization. Broad-scale discrepancies between the approaches were observed within chromosomes, most commonly in translocations centred around centromeres and telomeres, which were better resolved in the VGP assembly. Genomic and cytological approaches agreed on near-perfect synteny of the X chromosome, and in combination allowed detailed investigation of autosomal rearrangements between dog and sea lion. This study presents high-quality genomes of an emerging cancer model and highlights that even highly fragmented short-read assemblies scaffolded with Hi-C can yield reliable chromosome-level scaffolds suitable for comparative genomic analyses.
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Affiliation(s)
- Claire R. Peart
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munchen, Germany
| | - Christina Williams
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Saurabh D. Pophaly
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munchen, Germany,Max Planck institute for Plant Breeding Research, Cologne, Germany
| | - Benjamin A. Neely
- National Institute of Standards and Technology, NIST Charleston, Charleston, South Carolina, USA
| | - Frances M. D. Gulland
- Karen Dryer Wildlife Health Center, University of California Davis, Davis, California, USA
| | - David J. Adams
- Cytometry Core Facility, Wellcome Sanger Institute, Cambridge, UK
| | - Bee Ling Ng
- Cytometry Core Facility, Wellcome Sanger Institute, Cambridge, UK
| | - William Cheng
- Cytometry Core Facility, Wellcome Sanger Institute, Cambridge, UK
| | - Michael E. Goebel
- Institute of Marine Science, University of California Santa Cruz, Santa Cruz, California, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA
| | - Bettina Haase
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA
| | | | | | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA,Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, New York, USA
| | - Joanna Collins
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Jonathan Wood
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Ying Sims
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - James Torrance
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Alan Tracey
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Kerstin Howe
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Joseph I. Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany,British Antarctic Survey, Cambridge, UK
| | - Jeremy Johnson
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
| | - Erich D. Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA,Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Jochen B. W. Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munchen, Germany
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2
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Szczerbal I, Switonski M. Clinical Cytogenetics of the Dog: A Review. Animals (Basel) 2021; 11:947. [PMID: 33801756 PMCID: PMC8066086 DOI: 10.3390/ani11040947] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/15/2022] Open
Abstract
The dog is an important companion animal and has been recognized as a model in biomedical research. Its karyotype is characterized by a high chromosome number (2n = 78) and by the presence of one-arm autosomes, which are mostly small in size. This makes the dog a difficult subject for cytogenetic studies. However, there are some chromosome abnormalities that can be easily identified, such as sex chromosome aneuploidies, XX/XY leukocyte chimerism, and centric fusions (Robertsonian translocations). Fluorescence in situ hybridization (FISH) with the use of whole-chromosome painting or locus-specific probes has improved our ability to identify and characterize chromosomal abnormalities, including reciprocal translocations. The evaluation of sex chromosome complement is an important diagnostic step in dogs with disorders of sex development (DSD). In such cases, FISH can detect the copy number variants (CNVs) associated with the DSD phenotype. Since cancers are frequently diagnosed in dogs, cytogenetic evaluation of tumors has also been undertaken and specific chromosome mutations for some cancers have been reported. However, the study of meiotic, gamete, and embryo chromosomes is not very advanced. Knowledge of canine genome organization and new molecular tools, such as aCGH (array comparative genome hybridization), SNP (single nucleotide polymorphism) microarray, and ddPCR (droplet digital PCR) allow the identification of chromosomal rearrangements. It is anticipated that the comprehensive use of chromosome banding, FISH, and molecular techniques will substantially improve the diagnosis of chromosome abnormalities in dogs.
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Affiliation(s)
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637 Poznan, Poland;
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Vozdova M, Kubickova S, Cernohorska H, Fröhlich J, Vodicka R, Rubes J. Comparative Study of the Bush Dog (Speothos venaticus) Karyotype and Analysis of Satellite DNA Sequences and Their Chromosome Distribution in Six Species of Canidae. Cytogenet Genome Res 2019; 159:88-96. [DOI: 10.1159/000503082] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2019] [Indexed: 12/18/2022] Open
Abstract
The bush dog (Speothos venaticus, 2n = 74) is a near threatened species taxonomically classified among South American canids. We revised the bush dog karyotype and performed a comparative sequence analysis of satellite and satellite-like DNAs in 6 canids: the bush dog, domestic dog (Canis familiaris, 2n = 78), grey wolf (C. lupus, 2n = 78), Chinese raccoon dog (Nyctereutes procyonoides procyonoides, 2n = 54+B), red fox (Vulpes vulpes, 2n = 34+B), and arctic fox (V. lagopus, 2n = 48-50) to specify the species position among Canidae. Using FISH with painting and BAC probes, we found that the distribution of canid evolutionarily conserved chromosome segments in the bush dog karyotype is similar to that of the domestic dog and grey wolf. The bush dog karyotype differs by 2 acrocentric chromosome pairs formed by tandem fusions of the canine (29;34) and (26;35) orthologues. An interstitial signal of the telomeric probe was observed in the (26;35) fusion site in the bush dog indicating a recent evolutionary origin of this rearrangement. Sequences and hybridisation patterns of satellite DNAs were compared, and a phylogenetic tree of the 6 canid species was constructed which confirmed the bush dog position close to the wolf-like canids, and apart from the raccoon dog and foxes.
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4
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Structural and copy number chromosome abnormalities in canine cutaneous mast cell tumours. J Appl Genet 2018; 60:63-70. [DOI: 10.1007/s13353-018-0471-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/25/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022]
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Doronina L, Churakov G, Kuritzin A, Shi J, Baertsch R, Clawson H, Schmitz J. Speciation network in Laurasiatheria: retrophylogenomic signals. Genome Res 2017; 27:997-1003. [PMID: 28298429 PMCID: PMC5453332 DOI: 10.1101/gr.210948.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 02/23/2017] [Indexed: 11/24/2022]
Abstract
Rapid species radiation due to adaptive changes or occupation of new ecospaces challenges our understanding of ancestral speciation and the relationships of modern species. At the molecular level, rapid radiation with successive speciations over short time periods-too short to fix polymorphic alleles-is described as incomplete lineage sorting. Incomplete lineage sorting leads to random fixation of genetic markers and hence, random signals of relationships in phylogenetic reconstructions. The situation is further complicated when you consider that the genome is a mosaic of ancestral and modern incompletely sorted sequence blocks that leads to reconstructed affiliations to one or the other relative, depending on the fixation of their shared ancestral polymorphic alleles. The laurasiatherian relationships among Chiroptera, Perissodactyla, Cetartiodactyla, and Carnivora present a prime example for such enigmatic affiliations. We performed whole-genome screenings for phylogenetically diagnostic retrotransposon insertions involving the representatives bat (Chiroptera), horse (Perissodactyla), cow (Cetartiodactyla), and dog (Carnivora), and extracted among 162,000 preselected cases 102 virtually homoplasy-free, phylogenetically informative retroelements to draw a complete picture of the highly complex evolutionary relations within Laurasiatheria. All possible evolutionary scenarios received considerable retrotransposon support, leaving us with a network of affiliations. However, the Cetartiodactyla-Carnivora relationship as well as the basal position of Chiroptera and an ancestral laurasiatherian hybridization process did exhibit some very clear, distinct signals. The significant accordance of retrotransposon presence/absence patterns and flanking nucleotide changes suggest an important influence of mosaic genome structures in the reconstruction of species histories.
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
| | - Gennady Churakov
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Andrej Kuritzin
- Department of System Analysis, Saint Petersburg State Institute of Technology, 190013 St. Petersburg, Russia
| | - Jingjing Shi
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
| | - Robert Baertsch
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Hiram Clawson
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Jürgen Schmitz
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
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6
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Hensley MT, Tang J, Woodruff K, Defrancesco T, Tou S, Williams CM, Breen M, Meurs K, Keene B, Cheng K. Intracoronary allogeneic cardiosphere-derived stem cells are safe for use in dogs with dilated cardiomyopathy. J Cell Mol Med 2017; 21:1503-1512. [PMID: 28296006 PMCID: PMC5543505 DOI: 10.1111/jcmm.13077] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/21/2016] [Indexed: 12/18/2022] Open
Abstract
Cardiosphere‐derived cells (CDCs) have been shown to reduce scar size and increase viable myocardium in human patients with mild/moderate myocardial infarction. Studies in rodent models suggest that CDC therapy may confer therapeutic benefits in patients with non‐ischaemic dilated cardiomyopathy (DCM). We sought to determine the safety and efficacy of allogeneic CDC in a large animal (canine) model of spontaneous DCM. Canine CDCs (cCDCs) were grown from a donor dog heart. Similar to human CDCs, cCDCs express CD105 and are slightly positive for c‐kit and CD90. Thirty million of allogeneic cCDCs was infused into the coronary vessels of Doberman pinscher dogs with spontaneous DCM. Adverse events were closely monitored, and cardiac functions were measured by echocardiography. No adverse events occurred during and after cell infusion. Histology on dog hearts (after natural death) revealed no sign of immune rejection from the transplanted cells.
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Affiliation(s)
- Michael Taylor Hensley
- Department of Molecular Biomedical Sciences and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
| | - Junnan Tang
- Department of Molecular Biomedical Sciences and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.,Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Kathleen Woodruff
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Teresa Defrancesco
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Sandra Tou
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Christina M Williams
- Department of Molecular Biomedical Sciences and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
| | - Mathew Breen
- Department of Molecular Biomedical Sciences and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Kathryn Meurs
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Bruce Keene
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Ke Cheng
- Department of Molecular Biomedical Sciences and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.,Joint Department of Biomedical Engineering, University of North Carolina Chapel Hill and North Carolina State University, Raleigh and Chapel Hill, NC, USA.,Eshelman School of Pharmacy, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
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7
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Ramsey SA, Xu T, Goodall C, Rhodes AC, Kashyap A, He J, Bracha S. Cross-species analysis of the canine and human bladder cancer transcriptome and exome. Genes Chromosomes Cancer 2017; 56:328-343. [DOI: 10.1002/gcc.22441] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/27/2016] [Accepted: 12/29/2016] [Indexed: 02/06/2023] Open
Affiliation(s)
- Stephen A. Ramsey
- Department of Biomedical Sciences; Oregon State University; Corvallis Oregon USA
- School of Electrical Engineering and Computer Science; Oregon State University; Corvallis Oregon USA
| | - Tanjin Xu
- Department of Biomedical Sciences; Oregon State University; Corvallis Oregon USA
- School of Electrical Engineering and Computer Science; Oregon State University; Corvallis Oregon USA
| | - Cheri Goodall
- Department of Clinical Sciences; Oregon State University; Corvallis Oregon USA
| | - Adelaide C. Rhodes
- Department of Biomedical Sciences; Oregon State University; Corvallis Oregon USA
- Center for Genome Research and Biocomputing, Oregon State University; Corvallis Oregon USA
| | - Amita Kashyap
- Department of Biomedical Sciences; Oregon State University; Corvallis Oregon USA
| | - Jun He
- Department of Biomedical Sciences; Oregon State University; Corvallis Oregon USA
- School of Electrical Engineering and Computer Science; Oregon State University; Corvallis Oregon USA
| | - Shay Bracha
- Department of Clinical Sciences; Oregon State University; Corvallis Oregon USA
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8
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Abstract
The association between chromosomal abnormalities and reduced fertility in domestic animals is well recorded and has been studied for decades. Chromosome aberrations directly affect meiosis, gametogenesis, and the viability of zygotes and embryos. In some instances, balanced structural rearrangements can be transmitted, causing fertility problems in subsequent generations. Here, we aim to give a comprehensive overview of the current status and future prospects of clinical cytogenetics of animal reproduction by focusing on the advances in molecular cytogenetics during the genomics era. We describe how advancing knowledge about animal genomes has improved our understanding of connections between gross structural or molecular chromosome variations and reproductive disorders. Further, we expand on a key area of reproduction genetics: cytogenetics of animal gametes and embryos. Finally, we describe how traditional cytogenetics is interfacing with advanced genomics approaches, such as array technologies and next-generation sequencing, and speculate about the future prospects.
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Affiliation(s)
- Terje Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458;
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9
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Ansari HA, Ellison NW, Bassett SA, Hussain SW, Bryan GT, Williams WM. Fluorescence chromosome banding and FISH mapping in perennial ryegrass, Lolium perenne L. BMC Genomics 2016; 17:977. [PMID: 27887567 PMCID: PMC5124321 DOI: 10.1186/s12864-016-3231-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 11/01/2016] [Indexed: 11/29/2022] Open
Abstract
Background The unambiguous identification of individual chromosomes is a key part of the genomic characterization of any species. In this respect, the development and application of chromosome banding techniques has revolutionised mammalian and especially, human genomics. However, partly because of the traditional use of chromosome squash preparations, consistent fluorescence banding has rarely been achieved in plants. Here, successful fluorescence chromosome banding has been achieved for the first time in perennial ryegrass (Lolium perenne), a forage and turf grass with a large genome and a symmetrical karyotype with chromosomes that are difficult to distinguish. Results Based on flame-dried chromosome preparations instead of squashes, a simple fluorescence Q-banding technique using quinacrine mustard, unambiguously identified each chromosome and enabled the development of a banded karyotype and ideogram of the species. This Q-banding technique was also shown to be compatible with sequential FISH mapping enabling labelled genes and molecular markers to be precisely assigned to specific cytogenetic bands. A technique for DAPI-banding, which gave a similar pattern to Q-banding, was also introduced. This was compatible with FISH mapping and was used to anchor a single copy gene from an earlier mapped linkage group of L. perenne, thus providing a step towards integration of the genetic and cytogenetic maps. Conclusions By enabling the allocation of genes mapped by other methods to physically identified chromosome positions, this work will contribute to a better understanding of genomic structures and functions in grasses.
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Affiliation(s)
- Helal A Ansari
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand.
| | - Nicholas W Ellison
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand.,, Present address: 16 Moerangi St., Palmerston North, 4410, New Zealand
| | - Shalome A Bassett
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Syed W Hussain
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Gregory T Bryan
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Warren M Williams
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand
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10
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Poorman K, Borst L, Moroff S, Roy S, Labelle P, Motsinger-Reif A, Breen M. Comparative cytogenetic characterization of primary canine melanocytic lesions using array CGH and fluorescence in situ hybridization. Chromosome Res 2015; 23:171-86. [PMID: 25511566 PMCID: PMC5462112 DOI: 10.1007/s10577-014-9444-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/07/2014] [Accepted: 10/14/2014] [Indexed: 02/03/2023]
Abstract
Melanocytic lesions originating from the oral mucosa or cutaneous epithelium are common in the general dog population, with up to 100,000 diagnoses each year in the USA. Oral melanoma is the most frequent canine neoplasm of the oral cavity, exhibiting a highly aggressive course. Cutaneous melanocytomas occur frequently, but rarely develop into a malignant form. Despite the differential prognosis, it has been assumed that subtypes of melanocytic lesions represent the same disease. To address the relative paucity of information about their genomic status, molecular cytogenetic analysis was performed on the three recognized subtypes of canine melanocytic lesions. Using array comparative genomic hybridization (aCGH) analysis, highly aberrant distinct copy number status across the tumor genome for both of the malignant melanoma subtypes was revealed. The most frequent aberrations included gain of dog chromosome (CFA) 13 and 17 and loss of CFA 22. Melanocytomas possessed fewer genome wide aberrations, yet showed a recurrent gain of CFA 20q15.3-17. A distinctive copy number profile, evident only in oral melanomas, displayed a sigmoidal pattern of copy number loss followed immediately by a gain, around CFA 30q14. Moreover, when assessed by fluorescence in situ hybridization (FISH), copy number aberrations of targeted genes, such as gain of c-MYC (80 % of cases) and loss of CDKN2A (68 % of cases), were observed. This study suggests that in concordance with what is known for human melanomas, canine melanomas of the oral mucosa and cutaneous epithelium are discrete and initiated by different molecular pathways.
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Affiliation(s)
- Kelsey Poorman
- Department of Molecular Biomedical Science, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
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11
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Omeir R, Thomas R, Teferedegne B, Williams C, Foseh G, Macauley J, Brinster L, Beren J, Peden K, Breen M, Lewis AM. A novel canine kidney cell line model for the evaluation of neoplastic development: karyotype evolution associated with spontaneous immortalization and tumorigenicity. Chromosome Res 2015; 23:663-80. [PMID: 25957863 PMCID: PMC4666904 DOI: 10.1007/s10577-015-9474-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/12/2015] [Accepted: 04/14/2015] [Indexed: 01/01/2023]
Abstract
The molecular mechanisms underlying spontaneous neoplastic transformation in cultured mammalian cells remain poorly understood, confounding recognition of parallels with the biology of naturally occurring cancer. The broad use of tumorigenic canine cell lines as research tools, coupled with the accumulation of cytogenomic data from naturally occurring canine cancers, makes the domestic dog an ideal system in which to investigate these relationships. We developed a canine kidney cell line, CKB1-3T7, which allows prospective examination of the onset of spontaneous immortalization and tumorigenicity. We documented the accumulation of cytogenomic aberrations in CKB1-3T7 over 24 months in continuous culture. The majority of aberrations emerged in parallel with key phenotypic changes in cell morphology, growth kinetics, and tumor incidence and latency. Focal deletion of CDKN2A/B emerged first, preceding the onset and progression of tumorigenic potential, and progressed to a homozygous deletion across the cell population during extended culture. Interestingly, CKB1-3T7 demonstrated a tumorigenic phenotype in vivo prior to exhibiting loss of contact inhibition in vitro. We also performed the first genome-wide characterization of the canine tumorigenic cell line MDCK, which also exhibited CDKN2A/B deletion. MDCK and CKB1-3T7 cells shared several additional aberrations that we have reported previously as being highly recurrent in spontaneous canine cancers, many of which, as with CDKN2A/B deletion, are evolutionarily conserved in their human counterparts. The conservation of these molecular events across multiple species, in vitro and in vivo, despite their contrasting karyotypic architecture, is a powerful indicator of a common mechanism underlying emerging neoplastic activity. Through integrated cytogenomic and phenotypic characterization of serial passages of CKB1-3T7 from initiation to development of a tumorigenic phenotype, we present a robust and readily accessible model (to be made available through the American Type Culture Collection) of spontaneous neoplastic transformation that overcomes many of the limitations of earlier studies.
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Affiliation(s)
- R Omeir
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - R Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, 27607, USA
| | - B Teferedegne
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - C Williams
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - G Foseh
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - J Macauley
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - L Brinster
- Division of Veterinary Resources, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J Beren
- Office of Counter-Terrorism and Emergency Coordination, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - K Peden
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - M Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA. .,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, 27607, USA. .,Cancer Genetics Program, University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, 27599, USA. .,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27607, USA.
| | - A M Lewis
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA.
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12
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Simmons JK, Dirksen WP, Hildreth BE, Dorr C, Williams C, Thomas R, Breen M, Toribio RE, Rosol TJ. Canine prostate cancer cell line (Probasco) produces osteoblastic metastases in vivo. Prostate 2014; 74:1251-65. [PMID: 25043424 PMCID: PMC4216720 DOI: 10.1002/pros.22838] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 05/28/2014] [Indexed: 01/07/2023]
Abstract
BACKGROUND In 2012, over 240,000 men were diagnosed with prostate cancer and over 28,000 died from the disease. Animal models of prostate cancer are vital to understanding its pathogenesis and developing therapeutics. Canine models in particular are useful due to their similarities to late-stage, castration-resistant human disease with osteoblastic bone metastases. This study established and characterized a novel canine prostate cancer cell line that will contribute to the understanding of prostate cancer pathogenesis. METHODS A novel cell line (Probasco) was derived from a mixed breed dog that had spontaneous prostate cancer. Cell proliferation and motility were analyzed in vitro. Tumor growth in vivo was studied by subcutaneous, intratibial, and intracardiac injection of Probasco cells into nude mice. Tumors were evaluated by bioluminescent imaging, Faxitron radiography, µCT, and histology. RT-PCR and genome-wide DNA copy number profiling were used to characterize the cell line. RESULTS The Probasco cells grew in vitro (over 75 passages) and were tumorigenic in nude mice. Probasco cells expressed high levels of BMP2, CDH1, MYOF, FOLH1, RUNX2, and SMAD5 modest CXCL12, SLUG, and BMP, and no PTHrP mRNA. Following intracardiac injection, Probasco cells metastasized primarily to the appendicular skeleton, and both intratibial and intracardiac injections produced osteoblastic tumors in bone. Comparative genomic hybridization demonstrated numerous DNA copy number aberrations throughout the genome, including large losses and gains in multiple chromosomes. CONCLUSIONS The Probasco prostate cancer cell line will be a valuable model to investigate the mechanisms of prostate cancer pathogenesis and osteoblastic bone metastases.
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Affiliation(s)
- Jessica K. Simmons
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio
| | - Wessel P. Dirksen
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio
| | - Blake E. Hildreth
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio
| | - Carlee Dorr
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina
| | - Christina Williams
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina
| | - Rachael Thomas
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina
- Cancer Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Ramiro E. Toribio
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio
| | - Thomas J. Rosol
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio
- Correspondence to: Dr. Thomas J. Rosol, Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210.
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Filioli Uranio M, Dell'Aquila ME, Caira M, Guaricci AC, Ventura M, Catacchio CR, Martino NA, Valentini L. Characterization and in vitro differentiation potency of early-passage canine amnion- and umbilical cord-derived mesenchymal stem cells as related to gestational age. Mol Reprod Dev 2014; 81:539-51. [PMID: 24659564 DOI: 10.1002/mrd.22322] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 03/15/2014] [Indexed: 12/20/2022]
Abstract
Fetal adnexa are a non-controversial source of mesenchymal stem cells (MSCs) that have high plasticity, a high proliferation rate, and the ability to differentiate towards multiple lineages. MSC populations have been characterized for their stemness and differentiation capabilities; more recent work has focused on MSC selection and on establishing predictable elements to discriminate the cells with the most potential for regenerative medicine. In this study, we cytogenetically and molecularly characterized and followed the in vitro proliferation and differentiation potential of early-passage canine amniotic membrane MSCs (AM-MSCs) and umbilical cord matrix MSCs (UCM-MSCs) isolated from fetuses at early (35-40 days) and late (45-55 days) gestational ages. We found that cells from both fetal gestational ages showed similar features. In all examined cell lines, the morphology of proliferating cells typically appeared fibroblast-like. Population doublings, passaged up to 10 times, increased significantly with passage number. In both cell types, cell viability and chromosomal number and structure were not affected by gestational age at early passages. Passage-3 AM- and UCM-MSCs from both gestational phases also expressed embryonic (POU5F1) and mesenchymal (CD29, CD44) stemness markers, whereas hematopoietic and histocompatibility markers were never found in any sample. Passage-3 cell populations of each cell type were also multipotential as they could differentiate into neurocytes and osteocytes, based on cell morphology, specific stains, and molecular analysis. These results indicated that MSCs retrieved from the UCM and AM in the early and late fetal phases of gestation could be used for canine regenerative medicine.
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Affiliation(s)
- Manuel Filioli Uranio
- Veterinary Clinics and Animal Productions Section, Department for Emergency and Organ Transplantation, University of Bari Aldo Moro, Valenzano, Italy
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Avila F, Das PJ, Kutzler M, Owens E, Perelman P, Rubes J, Hornak M, Johnson WE, Raudsepp T. Development and application of camelid molecular cytogenetic tools. J Hered 2012; 105:858-69. [PMID: 23109720 DOI: 10.1093/jhered/ess067] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cytogenetic chromosome maps offer molecular tools for genome analysis and clinical cytogenetics and are of particular importance for species with difficult karyotypes, such as camelids (2n = 74). Building on the available human-camel zoo-fluorescence in situ hybridization (FISH) data, we developed the first cytogenetic map for the alpaca (Lama pacos, LPA) genome by isolating and identifying 151 alpaca bacterial artificial chromosome (BAC) clones corresponding to 44 specific genes. The genes were mapped by FISH to 31 alpaca autosomes and the sex chromosomes; 11 chromosomes had 2 markers, which were ordered by dual-color FISH. The STS gene mapped to Xpter/Ypter, demarcating the pseudoautosomal region, whereas no markers were assigned to chromosomes 14, 21, 22, 28, and 36. The chromosome-specific markers were applied in clinical cytogenetics to identify LPA20, the major histocompatibility complex (MHC)-carrying chromosome, as a part of an autosomal translocation in a sterile male llama (Lama glama, LGL; 2n = 73,XY). FISH with LPAX BACs and LPA36 paints, as well as comparative genomic hybridization, were also used to investigate the origin of the minute chromosome, an abnormally small LPA36 in infertile female alpacas. This collection of cytogenetically mapped markers represents a new tool for camelid clinical cytogenetics and has applications for the improvement of the alpaca genome map and sequence assembly.
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Affiliation(s)
- Felipe Avila
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Pranab J Das
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Michelle Kutzler
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Elaine Owens
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Polina Perelman
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Jiri Rubes
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Miroslav Hornak
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Warren E Johnson
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Terje Raudsepp
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak).
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15
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Maeda J, Yurkon CR, Fujisawa H, Kaneko M, Genet SC, Roybal EJ, Rota GW, Saffer ER, Rose BJ, Hanneman WH, Thamm DH, Kato TA. Genomic instability and telomere fusion of canine osteosarcoma cells. PLoS One 2012; 7:e43355. [PMID: 22916246 PMCID: PMC3420908 DOI: 10.1371/journal.pone.0043355] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 07/23/2012] [Indexed: 12/29/2022] Open
Abstract
Canine osteosarcoma (OSA) is known to present with highly variable and chaotic karyotypes, including hypodiploidy, hyperdiploidy, and increased numbers of metacentric chromosomes. The spectrum of genomic instabilities in canine OSA has significantly augmented the difficulty in clearly defining the biological and clinical significance of the observed cytogenetic abnormalities. In this study, eight canine OSA cell lines were used to investigate telomere fusions by fluorescence in situ hybridization (FISH) using a peptide nucleotide acid probe. We characterized each cell line by classical cytogenetic studies and cellular phenotypes including telomere associated factors and then evaluated correlations from this data. All eight canine OSA cell lines displayed increased abnormal metacentric chromosomes and exhibited numerous telomere fusions and interstitial telomeric signals. Also, as evidence of unstable telomeres, colocalization of γ-H2AX and telomere signals in interphase cells was observed. Each cell line was characterized by a combination of data representing cellular doubling time, DNA content, chromosome number, metacentric chromosome frequency, telomere signal level, cellular radiosensitivity, and DNA-PKcs protein expression level. We have also studied primary cultures from 10 spontaneous canine OSAs. Based on the observation of telomere aberrations in those primary cell cultures, we are reasonably certain that our observations in cell lines are not an artifact of prolonged culture. A correlation between telomere fusions and the other characteristics analyzed in our study could not be identified. However, it is important to note that all of the canine OSA samples exhibiting telomere fusion utilized in our study were telomerase positive. Pending further research regarding telomerase negative canine OSA cell lines, our findings may suggest telomere fusions can potentially serve as a novel marker for canine OSA.
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Affiliation(s)
- Junko Maeda
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Charles R. Yurkon
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Hiroshi Fujisawa
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Masami Kaneko
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Stefan C. Genet
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Erica J. Roybal
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Garrett W. Rota
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Ethan R. Saffer
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Barbara J. Rose
- Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - William H. Hanneman
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Douglas H. Thamm
- Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Takamitsu A. Kato
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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16
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Seiser EL, Thomas R, Richards KL, Kelley MK, Moore P, Suter SE, Breen M. Reading between the lines: molecular characterization of five widely used canine lymphoid tumour cell lines. Vet Comp Oncol 2011; 11:30-50. [PMID: 22236332 DOI: 10.1111/j.1476-5829.2011.00299.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Molecular characterization of tumour cell lines is increasingly regarded as a prerequisite for defining their validity as models of in vivo neoplasia. We present the first comprehensive catalogue of genomic and transcriptional characteristics of five widely used canine lymphoid tumour cell lines. High-resolution microarray-based comparative genomic hybridization defined their unique profiles of genomic DNA copy number imbalance. Multicolour fluorescence in situ hybridization identified aberrant gains of MYC, KIT and FLT3 and deletions of PTEN and CDKN2 in individual cell lines, and also revealed examples of extensive structural chromosome reorganization. Gene expression profiling and RT-PCR analyses defined the relationship between genomic imbalance and transcriptional dysregulation in each cell line, clarifying their relevance as models of discrete functional pathways with biological and therapeutic significance. In combination, these data provide an extensive resource of molecular data for directing the appropriate use of these cell lines as tools for studying canine lymphoid neoplasia.
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Affiliation(s)
- E L Seiser
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
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17
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Nie W, Wang J, Su W, Wang D, Tanomtong A, Perelman PL, Graphodatsky AS, Yang F. Chromosomal rearrangements and karyotype evolution in carnivores revealed by chromosome painting. Heredity (Edinb) 2011; 108:17-27. [PMID: 22086079 PMCID: PMC3238119 DOI: 10.1038/hdy.2011.107] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Chromosomal evolution in carnivores has been revisited extensively using cross-species chromosome painting. Painting probes derived from flow-sorted chromosomes of the domestic dog, which has one of the most rearranged karyotypes in mammals and the highest dipoid number (2n=78) in carnivores, are a powerful tool in detecting both evolutionary intra- and inter-chromosomal rearrangements. However, only a few comparative maps have been established between dog and other non-Canidae species. Here, we extended cross-species painting with dog probes to seven more species representing six carnivore families: Eurasian lynx (Lynx lynx), the stone marten (Martes foina), the small Indian civet (Viverricula indica), the Asian palm civet (Paradoxurus hermaphrodites), Javan mongoose (Hepestes javanicas), the raccoon (Procyon lotor) and the giant panda (Ailuropoda melanoleuca). The numbers and positions of intra-chromosomal rearrangements were found to differ among these carnivore species. A comparative map between human and stone marten, and a map among the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis), stone marten and human were also established to facilitate outgroup comparison and to integrate comparative maps between stone marten and other carnivores with such maps between human and other species. These comparative maps give further insight into genome evolution and karyotype phylogenetic relationships among carnivores, and will facilitate the transfer of gene mapping data from human, domestic dog and cat to other species.
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Affiliation(s)
- W Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan, PR
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18
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Anchoring the dog to its relatives reveals new evolutionary breakpoints across 11 species of the Canidae and provides new clues for the role of B chromosomes. Chromosome Res 2011; 19:685-708. [DOI: 10.1007/s10577-011-9233-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 08/15/2011] [Accepted: 08/16/2011] [Indexed: 12/27/2022]
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19
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Thudi NK, Shu ST, Martin CK, Lanigan LG, Nadella MV, Van Bokhoven A, Werbeck JL, Simmons JK, Murahari S, Kisseberth WC, Breen M, Williams C, Chen CS, McCauley LK, Keller ET, Rosol TJ. Development of a brain metastatic canine prostate cancer cell line. Prostate 2011; 71:1251-63. [PMID: 21321976 PMCID: PMC3139788 DOI: 10.1002/pros.21341] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 12/16/2010] [Indexed: 12/27/2022]
Abstract
BACKGROUND Prostate cancer in men has a high mortality and morbidity due to metastatic disease. The pathobiology of prostate cancer metastasis is not well understood and cell lines and animal models that recapitulate the complex nature of the disease are needed. Therefore, the goal of the study was to establish and characterize a new prostate cancer line derived from a dog with spontaneous prostate cancer. METHODS A new cell line (Leo) was derived from a dog with spontaneous prostate cancer. Immunohistochemistry and PCR were used to characterize the primary prostate cancer and xenografts in nude mice. Subcutaneous tumor growth and metastases in nude mice were evaluated by bioluminescent imaging, radiography and histopathology. In vitro chemosensitivity of Leo cells to therapeutic agents was measured. RESULTS Leo cells expressed the secretory epithelial cytokeratins (CK)8, 18, and ductal cell marker, CK7. The cell line grew in vitro (over 75 passages) and was tumorigenic in the subcutis of nude mice. Following intracardiac injection, Leo cells metastasized to the brain, spinal cord, bone, and adrenal gland. The incidence of metastases was greatest to the central nervous system (80%) with a lower incidence to bone (20%) and the adrenal glands (16%). In vitro chemosensitivity assays demonstrated that Leo cells were sensitive to Velcade and an HDAC-42 inhibitor with IC(50) concentrations of 1.9 nm and 0.95 µm, respectively. CONCLUSION The new prostate cancer cell line (Leo) will be a valuable model to investigate the mechanisms of the brain and bone metastases.
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Affiliation(s)
- Nanda K. Thudi
- Department of Radiation Oncology, University of Alabama, Birmingham, Alabama, 35233
| | - Sherry T. Shu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, 43210
| | - Chelsea K. Martin
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, 43210
| | - Lisa G. Lanigan
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, 43210
| | - Murali V.P. Nadella
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, 43210
| | - Adrie Van Bokhoven
- Department of Pathology, University of Colorado Health Sciences Center, Aurora, Colorado
| | - Jillian L. Werbeck
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, 43210
| | - Jessica K. Simmons
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, 43210
| | - Sridhar Murahari
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, 43210
| | - William C. Kisseberth
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, 43210
| | - Matthew Breen
- Dept. of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh NC 27606
| | - Christina Williams
- Dept. of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh NC 27606
| | - Ching-Shih Chen
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, 43210
| | - Laurie K. McCauley
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109
| | - Evan T. Keller
- Departments of Urology and Pathology, School of Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Thomas J. Rosol
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, 43210
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20
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Grzes M, Szczerbal I, Fijak-Nowak H, Szydlowski M, Switonski M. Two Candidate Genes (FTO and INSIG2) for Fat Accumulation in Four Canids: Chromosome Mapping, Gene Polymorphisms and Association Studies of Body and Skin Weight of Red Foxes. Cytogenet Genome Res 2011; 135:25-32. [DOI: 10.1159/000330457] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2011] [Indexed: 11/19/2022] Open
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21
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Hedan B, Thomas R, Motsinger-Reif A, Abadie J, Andre C, Cullen J, Breen M. Molecular cytogenetic characterization of canine histiocytic sarcoma: A spontaneous model for human histiocytic cancer identifies deletion of tumor suppressor genes and highlights influence of genetic background on tumor behavior. BMC Cancer 2011; 11:201. [PMID: 21615919 PMCID: PMC3121728 DOI: 10.1186/1471-2407-11-201] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 05/26/2011] [Indexed: 01/20/2023] Open
Abstract
Background Histiocytic malignancies in both humans and dogs are rare and poorly understood. While canine histiocytic sarcoma (HS) is uncommon in the general domestic dog population, there is a strikingly high incidence in a subset of breeds, suggesting heritable predisposition. Molecular cytogenetic profiling of canine HS in these breeds would serve to reveal recurrent DNA copy number aberrations (CNAs) that are breed and/or tumor associated, as well as defining those shared with human HS. This process would identify evolutionarily conserved cytogenetic changes to highlight regions of particular importance to HS biology. Methods Using genome wide array comparative genomic hybridization we assessed CNAs in 104 spontaneously occurring HS from two breeds of dog exhibiting a particularly elevated incidence of this tumor, the Bernese Mountain Dog and Flat-Coated Retriever. Recurrent CNAs were evaluated further by multicolor fluorescence in situ hybridization and loss of heterozygosity analyses. Statistical analyses were performed to identify CNAs associated with tumor location and breed. Results Almost all recurrent CNAs identified in this study were shared between the two breeds, suggesting that they are associated more with the cancer phenotype than with breed. A subset of recurrent genomic imbalances suggested involvement of known cancer associated genes in HS pathogenesis, including deletions of the tumor suppressor genes CDKN2A/B, RB1 and PTEN. A small number of aberrations were unique to each breed, implying that they may contribute to the major differences in tumor location evident in these two breeds. The most highly recurrent canine CNAs revealed in this study are evolutionarily conserved with those reported in human histiocytic proliferations, suggesting that human and dog HS share a conserved pathogenesis. Conclusions The breed associated clinical features and DNA copy number aberrations exhibited by canine HS offer a valuable model for the human counterpart, providing additional evidence towards elucidation of the pathophysiological and genetic mechanisms associated with histiocytic malignancies. Extrapolation of data derived from canine histiocytic disorders to human histiocytic proliferation may help to further our understanding of the propagation and cancerization of histiocytic cells, contributing to development of new and effective therapeutic modalities for both species.
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Affiliation(s)
- Benoit Hedan
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
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22
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Filioli Uranio M, Valentini L, Lange-Consiglio A, Caira M, Guaricci AC, L'Abbate A, Catacchio CR, Ventura M, Cremonesi F, Dell'Aquila ME. Isolation, proliferation, cytogenetic, and molecular characterization and in vitro differentiation potency of canine stem cells from foetal adnexa: a comparative study of amniotic fluid, amnion, and umbilical cord matrix. Mol Reprod Dev 2011; 78:361-73. [PMID: 21491540 DOI: 10.1002/mrd.21311] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 03/11/2011] [Indexed: 12/17/2022]
Abstract
The possibility to isolate canine mesenchymal stem cells (MSCs) from foetal adnexa is interesting since several canine genetic disorders are reported to resemble similar dysfunctions in humans. In this study, we successfully isolated, cytogenetically and molecularly characterized, and followed the differentiation potency of canine MSCs from foetal adnexa, such as amniotic fluid (AF), amniotic membrane (AM), and umbilical cord matrix (UCM). In the three types of cell lines, the morphology of proliferating cells typically appeared fibroblast-like, and the population doubling time (DT) significantly increased with passage number. For AF- and AM-MSCs, cell viability did not change with passages. In UCM-MSCs, cell viability remained at approximately constant levels up to P6 and significantly decreased from P7 (P < 0.05). Amnion and UCM-MSCs expressed embryonic and MSC markers, such as Oct-4 CD44, CD184, and CD29, whereas AF-MSCs expressed Oct-4, CD44. Expression of the hematopoietic markers CD34 and CD45 was not found. Dog leucocyte antigens (DLA-DRA1 and DLA-79) were expressed only in AF-MSCs at P1. Isolated cells of the three cell lines at P3 showed multipotent capacity, and differentiated in vitro into neurocyte, adipocyte, osteocyte, and chondrocyte, as demonstrated by specific stains and expression of molecular markers. Cells at P4 showed normal chromosomal number, structure, and telomerase activity. These results demonstrate that, in dog, MSCs can be successfully isolated from foetal adnexa and grown in vitro. Their proven stemness and chromosomal stability indicated that MSCs could be used as a model to study stem cell biology and have an application in therapeutic programs.
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Affiliation(s)
- M Filioli Uranio
- Department of Animal Production, University of Bari Aldo Moro, Bari, Italy.
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Switonski M, Szczerbal I, Nizanski W, Kociucka B, Bartz M, Dzimira S, Mikolajewska N. Robertsonian Translocation in a Sex Reversal Dog (XX, SRY negative) May Indicate that the Causative Mutation for This Intersexuality Syndrome Resides on Canine Chromosome 23 (CFA23). Sex Dev 2011; 5:141-6. [DOI: 10.1159/000324689] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2010] [Indexed: 11/19/2022] Open
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Thomas R, Duke SE, Wang HJ, Breen TE, Higgins RJ, Linder KE, Ellis P, Langford CF, Dickinson PJ, Olby NJ, Breen M. 'Putting our heads together': insights into genomic conservation between human and canine intracranial tumors. J Neurooncol 2009; 94:333-49. [PMID: 19333554 PMCID: PMC3225023 DOI: 10.1007/s11060-009-9877-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 03/19/2009] [Indexed: 11/30/2022]
Abstract
Numerous attributes render the domestic dog a highly pertinent model for cancer-associated gene discovery. We performed microarray-based comparative genomic hybridization analysis of 60 spontaneous canine intracranial tumors to examine the degree to which dog and human patients exhibit aberrations of ancestrally related chromosome regions, consistent with a shared pathogenesis. Canine gliomas and meningiomas both demonstrated chromosome copy number aberrations (CNAs) that share evolutionarily conserved synteny with those previously reported in their human counterpart. Interestingly, however, genomic imbalances orthologous to some of the hallmark aberrations of human intracranial tumors, including chromosome 22/NF2 deletions in meningiomas and chromosome 1p/19q deletions in oligodendrogliomas, were not major events in the dog. Furthermore, and perhaps most significantly, we identified highly recurrent CNAs in canine intracranial tumors for which the human orthologue has been reported previously at low frequency but which have not, thus far, been associated intimately with the pathogenesis of the tumor. The presence of orthologous CNAs in canine and human intracranial cancers is strongly suggestive of their biological significance in tumor development and/or progression. Moreover, the limited genetic heterogenity within purebred dog populations, coupled with the contrasting organization of the dog and human karyotypes, offers tremendous opportunities for refining evolutionarily conserved regions of tumor-associated genomic imbalance that may harbor novel candidate genes involved in their pathogenesis. A comparative approach to the study of canine and human intracranial tumors may therefore provide new insights into their genetic etiology, towards development of more sophisticated molecular subclassification and tailored therapies in both species.
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Affiliation(s)
- Rachael Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
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Thomas R, Wang HJ, Tsai PC, Langford CF, Fosmire SP, Jubala CM, Getzy DM, Cutter GR, Modiano JF, Breen M. Influence of genetic background on tumor karyotypes: evidence for breed-associated cytogenetic aberrations in canine appendicular osteosarcoma. Chromosome Res 2009; 17:365-377. [PMID: 19337847 PMCID: PMC3758998 DOI: 10.1007/s10577-009-9028-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Revised: 12/15/2008] [Accepted: 12/15/2008] [Indexed: 12/23/2022]
Abstract
Recurrent chromosomal aberrations in solid tumors can reveal the genetic pathways involved in the evolution of a malignancy and in some cases predict biological behavior. However, the role of individual genetic backgrounds in shaping karyotypes of sporadic tumors is unknown. The genetic structure of purebred dog breeds, coupled with their susceptibility to spontaneous cancers, provides a robust model with which to address this question. We tested the hypothesis that there is an association between breed and the distribution of genomic copy number imbalances in naturally occurring canine tumors through assessment of a cohort of Golden Retrievers and Rottweilers diagnosed with spontaneous appendicular osteosarcoma. Our findings reveal significant correlations between breed and tumor karyotypes that are independent of gender, age at diagnosis, and histological classification. These data indicate for the first time that individual genetic backgrounds, as defined by breed in dogs, influence tumor karyotypes in a cancer with extensive genomic instability.
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Affiliation(s)
- Rachael Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27606, USA
| | - Huixia J. Wang
- Department of Statistics, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Pei-Chien Tsai
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
| | - Cordelia F. Langford
- Microarray Facility, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Susan P. Fosmire
- Integrated Department of Immunology, University of Colorado, Denver, CO 80214, USA
| | - Cristan M. Jubala
- Integrated Department of Immunology, University of Colorado, Denver, CO 80214, USA
| | | | - Gary R. Cutter
- Department of Biostatistics, University of Alabama Birmingham, Birmingham, AL 35294, USA
| | - Jaime F. Modiano
- Integrated Department of Immunology, University of Colorado, Denver, CO 80214, USA
- University of Colorado Cancer Center, Aurora, CO 80045, USA
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27606, USA
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Thomas R, Duke SE, Karlsson EK, Evans A, Ellis P, Lindblad-Toh K, Langford CF, Breen M. A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis. Cytogenet Genome Res 2008; 122:110-21. [PMID: 19096206 PMCID: PMC2874680 DOI: 10.1159/000163088] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2008] [Indexed: 12/17/2022] Open
Abstract
Molecular cytogenetic studies have been instrumental in defining the nature of numerical and structural chromosome changes in human cancers, but their significance remains to be fully understood. The emergence of high quality genome assemblies for several model organisms provides exciting opportunities to develop novel genome-integrated molecular cytogenetic resources that now permit a comparative approach to evaluating the relevance of tumor-associated chromosome aberrations, both within and between species. We have used the dog genome sequence assembly to identify a framework panel of 2,097 bacterial artificial chromosome (BAC) clones, selected at intervals of approximately one megabase. Each clone has been evaluated by multicolor fluorescence in situ hybridization (FISH) to confirm its unique cytogenetic location in concordance with its reported position in the genome assembly, providing new information on the organization of the dog genome. This panel of BAC clones also represents a powerful cytogenetic resource with numerous potential applications. We have used the clone set to develop a genome-wide microarray for comparative genomic hybridization (aCGH) analysis, and demonstrate its application in detection of tumor-associated DNA copy number aberrations (CNAs) including single copy deletions and amplifications, regional aneuploidy and whole chromosome aneuploidy. We also show how individual clones selected from the BAC panel can be used as FISH probes in direct evaluation of tumor karyotypes, to verify and explore CNAs detected using aCGH analysis. This cytogenetically validated, genome integrated BAC clone panel has enormous potential for aiding gene discovery through a comparative approach to molecular oncology.
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Affiliation(s)
- R Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, Raleigh, NC 27606, USA
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Usher SG, Radford AD, Villiers EJ, Blackwood L. RAS, FLT3, and C-KIT mutations in immunophenotyped canine leukemias. Exp Hematol 2008; 37:65-77. [PMID: 18977066 DOI: 10.1016/j.exphem.2008.09.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 09/08/2008] [Accepted: 09/08/2008] [Indexed: 12/30/2022]
Abstract
OBJECTIVE To determine the frequency of FLT3, C-KIT, and RAS mutations in canine leukemia patients. MATERIALS AND METHODS Ethylenediamine tetra-acetic acid blood samples were recruited from dogs with suspected leukemia, categorized by quantitative and cytological evaluation and immunophenotyping. Flow cytometry was carried out using antibodies against CD3; CD3e; CD4; CD5; CD8; CD11a, b, c, and d; CD14; CD21; CD34; CD45 and 45RA; CD79a; CD90 (THY-1); major histocompatibility complex II; myeloperoxidase; MAC387; and neutrophil-specific antibody. Genomic DNA was extracted from whole blood and analyzed for mutations in N, H, and K-RAS, FLT3, and C-KIT genes by polymerase chain reaction and sequencing. RESULTS Fifty-seven (77.0%) of 74 samples submitted from dogs with suspected leukemia had cytologically and immunophenotypically confirmed leukemia. There were 36 (63.2%) acute leukemias, 16 (28.1%) chronic, 3 (5.3%) prolymphocytic, 1 natural killer cell, and 1 chronic leukemia undergoing blast transformation. N-RAS mis-sense mutations were identified in 14 (25%) dogs with acute myeloid (AML) or lymphoid (ALL) leukemia, and also in one dog in the leukemic phase of lymphoma. Mutations in K-RAS were found in two dogs with AML. There were no H-RAS mutations. FLT3 internal tandem duplications were identified in three dogs with ALL, and a mis-sense mutation was found in one dog with ALL. C-KIT mutations were identified in three dogs with AML. Sixty-one percent of dogs with acute leukemia harbored mutations in N/K-RAS, FLT3, or C-KIT. CONCLUSION RAS, FLT3, and C-KIT mutations, analogous to those found in human leukemia, occur commonly in acute canine leukemia.
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Affiliation(s)
- Suzanne G Usher
- Small Animal Teaching Hospital, University of Liverpool, The Leahurst Campus, Neston, Wirral, UK
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Courtay-Cahen C, Platt SR, De Risio L, Starkey MP. Preliminary analysis of genomic abnormalities in canine meningiomas. Vet Comp Oncol 2008; 6:182-92. [DOI: 10.1111/j.1476-5829.2008.00159.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Beuing C, Soller JT, Muth M, Wagner S, Dolf G, Schelling C, Richter A, Willenbrock S, Reimann-Berg N, Winkler S, Nolte I, Bullerdiek J, Escobar HM. Genomic characterisation, chromosomal assignment and in vivo localisation of the canine high mobility group A1 (HMGA1) gene. BMC Genet 2008; 9:49. [PMID: 18651940 PMCID: PMC2500044 DOI: 10.1186/1471-2156-9-49] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 07/23/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The high mobility group A1 proteins (HMGA1a/HMGA1b) are highly conserved between mammalian species and widely described as participating in various cellular processes. By inducing DNA conformation changes the HMGA1 proteins indirectly influence the binding of various transcription factors and therefore effect the transcription regulation. In humans chromosomal aberrations affecting the HMGA1 gene locus on HSA 6p21 were described to be the cause for various benign mesenchymal tumours while high titres of HMGA1 proteins were shown to be associated with the neoplastic potential of various types of cancer. Interestingly, the absence of HMGA1 proteins was shown to cause insulin resistance and diabetes in humans and mice. Due to the various similarities in biology and presentation of human and canine cancers the dog has joined the common rodent animal model for therapeutic and preclinical studies. Accordingly, the canine genome was sequenced completely twice but unfortunately this could not solve the structure of canine HMGA1 gene. RESULTS Herein we report the characterisation of the genomic structure of the canine HMGA1 gene consisting of 7 exons and 6 introns spanning in total 9524 bp, the in vivo localisation of the HMGA1 protein to the nucleus, and a chromosomal assignment of the gene by FISH to CFA12q11. Additionally, we evaluated a described canine HMGA1 exon 6 SNP in 55 Dachshunds. CONCLUSION The performed characterisations will make comparative analyses of aberrations affecting the human and canine gene and proteins possible, thereby providing a basis for revealing mechanisms involved in HMGA1 related pathogenesis in both species.
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Affiliation(s)
- Claudia Beuing
- Clinic for Small Animals and Research Cluster of Excellence "REBIRTH", University of Veterinary Medicine Hanover, Bischofsholer Damm 15, 30173 Hanover, Germany
| | - Jan T Soller
- Clinic for Small Animals and Research Cluster of Excellence "REBIRTH", University of Veterinary Medicine Hanover, Bischofsholer Damm 15, 30173 Hanover, Germany
- Centre for Human Genetics, University of Bremen, Leobener Str ZHG, 28359 Bremen, Germany
| | - Michaela Muth
- Centre for Human Genetics, University of Bremen, Leobener Str ZHG, 28359 Bremen, Germany
| | - Sigfried Wagner
- Centre for Human Genetics, University of Bremen, Leobener Str ZHG, 28359 Bremen, Germany
| | - Gaudenz Dolf
- Institute of Animal Genetics, Nutrition and Housing, University of Berne, Berne, Switzerland
| | - Claude Schelling
- Department of Animal Sciences, Swiss Federal Institute of Technology Zurich and Vetsuisse Faculty Zurich, University of Zurich, Zurich, Switzerland
| | - Andreas Richter
- Centre for Human Genetics, University of Bremen, Leobener Str ZHG, 28359 Bremen, Germany
| | - Saskia Willenbrock
- Clinic for Small Animals and Research Cluster of Excellence "REBIRTH", University of Veterinary Medicine Hanover, Bischofsholer Damm 15, 30173 Hanover, Germany
- Centre for Human Genetics, University of Bremen, Leobener Str ZHG, 28359 Bremen, Germany
| | - Nicola Reimann-Berg
- Clinic for Small Animals and Research Cluster of Excellence "REBIRTH", University of Veterinary Medicine Hanover, Bischofsholer Damm 15, 30173 Hanover, Germany
- Centre for Human Genetics, University of Bremen, Leobener Str ZHG, 28359 Bremen, Germany
| | - Susanne Winkler
- Centre for Human Genetics, University of Bremen, Leobener Str ZHG, 28359 Bremen, Germany
| | - Ingo Nolte
- Clinic for Small Animals and Research Cluster of Excellence "REBIRTH", University of Veterinary Medicine Hanover, Bischofsholer Damm 15, 30173 Hanover, Germany
| | - Jorn Bullerdiek
- Clinic for Small Animals and Research Cluster of Excellence "REBIRTH", University of Veterinary Medicine Hanover, Bischofsholer Damm 15, 30173 Hanover, Germany
- Centre for Human Genetics, University of Bremen, Leobener Str ZHG, 28359 Bremen, Germany
| | - Hugo Murua Escobar
- Clinic for Small Animals and Research Cluster of Excellence "REBIRTH", University of Veterinary Medicine Hanover, Bischofsholer Damm 15, 30173 Hanover, Germany
- Centre for Human Genetics, University of Bremen, Leobener Str ZHG, 28359 Bremen, Germany
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Breen M. Canine cytogenetics--from band to basepair. Cytogenet Genome Res 2008; 120:50-60. [PMID: 18467825 DOI: 10.1159/000118740] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2008] [Indexed: 12/22/2022] Open
Abstract
Humans and dogs have coexisted for thousands of years, during which time we have developed a unique bond, centered on companionship. Along the way, we have developed purebred dog breeds in a manner that has resulted unfortunately in many of them being affected by serious genetic disorders, including cancers. With serendipity and irony the unique genetic architecture of the 21st century genome of Man's best friend may ultimately provide many of the keys to unlock some of nature's most intriguing biological puzzles. Canine cytogenetics has advanced significantly over the past 10 years, spurred on largely by the surge of interest in the dog as a biomedical model for genetic disease and the availability of advanced genomics resources. As such the role of canine cytogenetics has moved rapidly from one that served initially to define the gross genomic organization of the canine genome and provide a reliable means to determine the chromosomal location of individual genes, to one that enabled the assembled sequence of the canine genome to be anchored to the karyotype. Canine cytogenetics now presents the biomedical research community with a means to assist in our search for a greater understanding of how genome architectures altered during speciation and in our search for genes associated with cancers that affect both dogs and humans. The cytogenetics 'toolbox' for the dog is now loaded. This review aims to provide a summary of some of the recent advancements in canine cytogenetics.
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Affiliation(s)
- M Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, and Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA.
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31
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Hitte C, Kirkness EF, Ostrander EA, Galibert F. Survey sequencing and radiation hybrid mapping to construct comparative maps. Methods Mol Biol 2008; 422:65-77. [PMID: 18629661 PMCID: PMC2661178 DOI: 10.1007/978-1-59745-581-7_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Radiation hybrid (RH) mapping has become one of the most well-established techniques for economically and efficiently navigating genomes of interest. The success of the technique relies on random chromosome breakage of a target genome, which is then captured by recipient cells missing a preselected marker. Selection for hybrid cells that have DNA fragments bearing the marker of choice, plus a random set of DNA fragments from the initial irradiation, generates a set of cell lines that recapitulates the genome of the target organism several-fold. Markers or genes of interest are analyzed by PCR using DNA isolated from each cell line. Statistical tools are applied to determine both the linear order of markers on each chromosome, and the confidence of each placement. The resolution of the resulting map relies on many factors, most notably the degree of breakage from the initial radiation as well as the number of hybrid clones and mean retention value.A high-resolution RH map of a genome derived from low pass or survey sequencing (coverage from 1 to 2 times) can provide essentially the same comparative data on gene order that is derived from high-coverage (greater than x7) genome sequencing. When combined with fluorescence in situ hybridization, RH maps are complete and ordered blueprints for each chromosome. They give information about the relative order and spacing of genes and markers, and allow investigators to move between target and reference genomes, such as those of mouse or human, with ease although the approach is not limited to mammal genomes.
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Affiliation(s)
- Christophe Hitte
- IGDR, Institut de Génétique et Développement de Rennes
CNRS : UMR6061Université Rennes IIFR140Faculté de Médecine - CS 34317
2 Av du Professeur Léon Bernard
35043 RENNES CEDEX,FR
| | - Ewen F. Kirkness
- TIGR, The Institute for Genomic Research
JCVI J. Craig Venter InstituteRockville, MD,FR
| | | | - Francis Galibert
- IGDR, Institut de Génétique et Développement de Rennes
CNRS : UMR6061Université Rennes IIFR140Faculté de Médecine - CS 34317
2 Av du Professeur Léon Bernard
35043 RENNES CEDEX,FR
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Standard DAPI karyotype of the common shrew Sorex araneus L. (Soricidae, Eulipotyphla). RUSSIAN JOURNAL OF THERIOLOGY 2007. [DOI: 10.15298/rusjtheriol.06.1.02] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Thomas R, Duke SE, Bloom SK, Breen TE, Young AC, Feiste E, Seiser EL, Tsai PC, Langford CF, Ellis P, Karlsson EK, Lindblad-Toh K, Breen M. A Cytogenetically Characterized, Genome-Anchored 10-Mb BAC Set and CGH Array for the Domestic Dog. J Hered 2007; 98:474-84. [PMID: 17702974 DOI: 10.1093/jhered/esm053] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The generation of a 7.5x dog genome assembly provides exciting new opportunities to interpret tumor-associated chromosome aberrations at the biological level. We present a genomic microarray for array comparative genomic hybridization (aCGH) analysis in the dog, comprising 275 bacterial artificial chromosome (BAC) clones spaced at intervals of approximately 10 Mb. Each clone has been positioned accurately within the genome assembly and assigned to a unique chromosome location by fluorescence in situ hybridization (FISH) analysis, both individually and as chromosome-specific BAC pools. The microarray also contains clones representing the dog orthologues of 31 genes implicated in human cancers. FISH analysis of the 10-Mb BAC clone set indicated excellent coverage of each dog chromosome by the genome assembly. The order of clones was consistent with the assembly, but the cytogenetic intervals between clones were variable. We demonstrate the application of the BAC array for aCGH analysis to identify both whole and partial chromosome imbalances using a canine histiocytic sarcoma case. Using BAC clones selected from the array as probes, multicolor FISH analysis was used to further characterize these imbalances, revealing numerous structural chromosome rearrangements. We outline the value of a combined aCGH/FISH approach, together with a well-annotated dog genome assembly, in canine and comparative cancer studies.
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Affiliation(s)
- Rachael Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
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Islam-Faridi MN, Nelson CD, Kubisiak TL. Reference karyotype and cytomolecular map for loblolly pine (Pinus taeda L.). Genome 2007; 50:241-51. [PMID: 17546089 DOI: 10.1139/g06-153] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A reference karyotype is presented for loblolly pine (Pinus taeda L., subgenus Pinus, section Pinus, subsection Australes), based on fluorescent in situ hybridization (FISH), using 18S-28S rDNA, 5S rDNA, and an Arabidopsis-type telomere repeat sequence (A-type TRS). Well separated somatic chromosomes were prepared from colchicine-treated root meristems, using an enzymatic digestion technique. Statistical analyses performed on chromosome-arm lengths, centromeric indices, and interstitial rDNA and telomeric positions were based on observations from 6 well-separated metaphase cells from each of 3 unrelated trees. Statistically, 7 of the 12 loblolly pine chromosomes could be distinguished by their relative lengths. Centromeric indices were unable to distinguish additional chromosomes. However, the position and relative strength of the rDNA and telomeric sites made it possible to uniquely identify all of the chromosomes, providing a reference karyotype for use in comparative genome analyses. A dichotomous key was developed to aid in the identification of loblolly pine chromosomes and their comparison to chromosomes of other Pinus spp. A cytomolecular map was developed using the interstitial 18S-28S rDNA and A-type TRS signals. A total of 54 bins were assigned, ranging from 3 to 5 bins per chromosome. This is the first report of a chromosome-anchored physical map for a conifer that includes a dichotomous key for accurate and consistent identification of the P. taeda chromosomes.
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Affiliation(s)
- M Nurul Islam-Faridi
- Forest Tree Molecular Cytogenetics Laboratory, Southern Institute of Forest Genetics, Southern Research Station, USDA Forest Service, Texas A&M University, 2585-TAMU, College Station, TX 77843-2585, USA.
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Galibert F, André C. The dog: A powerful model for studying genotype-phenotype relationships. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2007; 3:67-77. [PMID: 20483208 DOI: 10.1016/j.cbd.2007.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 05/31/2007] [Accepted: 06/01/2007] [Indexed: 12/11/2022]
Abstract
Within the last two years, series of studies have focused on the structure of the dog genome (Canis familiaris) and the characteristics of the dog population as it evolved since being domesticated from wolves about 14,000 years ago. In this review, we explain why the dog is a unique and promising model for determining genotype/phenotype relationships and why it should be easier with this model to identify the genes responsible for many genetic diseases. We also revisit the last ten years of developments in canine molecular genetics that culminated in the release of the entire genome sequence.
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Affiliation(s)
- Francis Galibert
- Laboratoire de Génétique et Développement, UMR 6061, CNRS/Université de Rennes 1, IFR 140 Génomique Fonctionnelle et Santé, 2 avenue Léon Bernard, Rennes Cedex 35043, France
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Kisseberth WC, Nadella MVP, Breen M, Thomas R, Duke SE, Murahari S, Kosarek CE, Vernau W, Avery AC, Burkhard MJ, Rosol TJ. A novel canine lymphoma cell line: a translational and comparative model for lymphoma research. Leuk Res 2007; 31:1709-20. [PMID: 17532464 DOI: 10.1016/j.leukres.2007.04.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2006] [Revised: 03/14/2007] [Accepted: 04/02/2007] [Indexed: 11/29/2022]
Abstract
A novel canine lymphoma cell line, OSW, was established from the malignant pleural effusion of a dog with peripheral T-cell lymphoma. The immunoprofile as determined by flow cytometry was as follows: positive for CD45, CD49d, CD18, CD11a; weakly positive for CD11b, CD11c, CD11d; and negative for CD45RA, CD1a, CD1c, CD3, TCRalphabeta, TCRgammadelta, CD4, CD5, CD8a, CD8b, CD90(Thy1), CD21, MHCII, CD14(TUK4), CD34, and MPO. Immunocytochemistry of cytospin preparations was negative for cytoplasmic CD3, CD79a, and MPO, but was positive for CD20. The cell line had an oligoclonal T-cell receptor gamma (TCRgamma) gene rearrangement. Array comparative genomic hybridization (aCGH) and single locus probe (SLP) analysis showed that there were copy number increases of loci on dog chromosome 13 (CFA 13), and copy number decreases were evident for regions of CFA 11, 22, 26, 30 and 32, which include several of the more common chromosomal aberrations reported previously in canine lymphoma. The OSW cell line grows rapidly in vitro and is tumorigenic as a xenograft in SCID/NOD mice. OSW represents one of only a few reported canine lymphoma cell lines and is the most thoroughly characterized. This cell line and xenograft represent significant in vitro and in vivo models, respectively, for comparative and translational lymphoma research.
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Affiliation(s)
- William C Kisseberth
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA.
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37
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Courtay-Cahen C, Griffiths LA, Hudson R, Starkey M. Extensive coloured identification of dog chromosomes to support karyotype studies: the colour code. Cytogenet Genome Res 2007; 116:198-204. [PMID: 17317960 DOI: 10.1159/000098187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Accepted: 10/05/2006] [Indexed: 01/21/2023] Open
Abstract
The identification of individual dog chromosomes is problematic because the 38 pairs of autosomes are small and acrocentric. Here we describe the design and application of a FISH tool that enables definitive identification of each dog autosome in a normal karyotype, without relying on subjective interpretation of DAPI banding patterns. From a high-resolution physical map of the canine genome, we have chosen a panel of 80 canine chromosome-specific BAC clones. DNA from each clone is labeled with one of five different fluorochrome-conjugated nucleotides. By selecting one to three spatially separated BACs per chromosome, and labelling them with a distinctive combination of colours, each autosome can be identified objectively and orientated accurately, irrespective of the quality of DAPI chromosome banding. This tool, or part of it, can be used for any purpose where accurate identification of canine autosomes in a normal karyotype is essential. In this study, we demonstrate use of the 'colour code' for chromosome identification following CGH analysis of unbalanced genomic aberrations in a canine brain tumour. Our method is an improvement of an earlier procedure, featuring chromosome-specific BACs and sequential FISH hybridisations, as it enables simultaneous identification of all chromosomes in a single hybridisation.
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Affiliation(s)
- C Courtay-Cahen
- Molecular Cytogenetics Group, Oncology Research Section, Animal Health Trust, Newmarket, Suffolk, UK.
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38
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Parker HG, Meurs KM, Ostrander EA. Finding cardiovascular disease genes in the dog. J Vet Cardiol 2006; 8:115-27. [PMID: 19083345 PMCID: PMC3559124 DOI: 10.1016/j.jvc.2006.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2006] [Revised: 04/10/2006] [Accepted: 04/13/2006] [Indexed: 11/20/2022]
Abstract
Recent advances in canine genomics are changing the landscape of veterinary biology, and by default, veterinary medicine. No longer are clinicians locked into traditional methods of diagnoses and therapy. Rather, major advances in canine genetics and genomics from the past five years are now changing the way the veterinarian of the 21st century practices medicine. First, the availability of a dense genome map gives canine genetics a much-needed foothold in comparative medicine, allowing advances made in human and mouse genetics to be applied to companion animals. Second, the recently released 7.5x whole genome sequence of the dog is facilitating the identification of hereditary disease genes. Finally, development of genetic tools for rapid screening of families and populations at risk for inherited disease means that the cost of identifying and testing for disease loci will significantly decrease in coming years. Out of these advances will come major changes in companion animal diagnostics and therapy. Clinicians will be able to offer their clients genetic testing and counseling for a myriad of disorders. In this review we summarize recent findings in canine genomics and discuss their application to the study of canine cardiac health.
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Affiliation(s)
- Heidi G. Parker
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, MSC 8000, Building 50, Room 5334, Bethesda MD 20892-8000, Phone: 301-594-5284; FAX: 301-480-0472
| | - Kathryn M. Meurs
- Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman WA 99164-7010, Phone: 509-335-0711 Fax: 509-335-0880
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, MSC 8000, Building 50, Room 5334, Bethesda MD 20892-8000, Phone: 301-594-5284; FAX: 301-480-0472
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39
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Abstract
The domestication of the dog from its wolf ancestors is perhaps the most complex genetic experiment in history, and certainly the most extensive. Beginning with the wolf, man has created dog breeds that are hunters or herders, big or small, lean or squat, and independent or loyal. Most breeds were established in the 1800s by dog fanciers, using a small number of founders that featured traits of particular interest. Popular sire effects, population bottlenecks, and strict breeding programs designed to expand populations with desirable traits led to the development of what are now closed breeding populations, with limited phenotypic and genetic heterogeneity, but which are ideal for genetic dissection of complex traits. In this review, we first discuss the advances in mapping and sequencing that accelerated the field in recent years. We then highlight findings of interest related to disease gene mapping and population structure. Finally, we summarize novel results on the genetics of morphologic variation.
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40
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Stabej P, Leegwater PAJ, Imholz S, Versteeg SA, Zijlstra C, Stokhof AA, Domanjko-Petriè A, van Oost BA. The canine sarcoglycan delta gene: BAC clone contig assembly, chromosome assignment and interrogation as a candidate gene for dilated cardiomyopathy in Dobermann dogs. Cytogenet Genome Res 2006; 111:140-6. [PMID: 16103655 DOI: 10.1159/000086383] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2004] [Accepted: 12/29/2004] [Indexed: 11/19/2022] Open
Abstract
Dilated cardiomyopathy (DCM) is a common disease of the myocardium recognized in human, dog and experimental animals. Genetic factors are responsible for a large proportion of cases in humans, and 17 genes with DCM causing mutations have been identified. The genetic origin of DCM in the Dobermann dogs has been suggested, but no disease genes have been identified to date. In this paper, we describe the characterization and evaluation of the canine sarcoglycan delta (SGCD), a gene implicated in DCM in human and hamster. Bacterial artificial chromosomes (BACs) containing the canine SGCD gene were isolated with probes for exon 3 and exons 4-8 and were characterized by Southern blot analysis. BAC end sequences were obtained for four BACs. Three of the BACs overlapped and could be ordered relative to each other and the end sequences of all four BACs could be anchored on the preliminary assembly of the dog genome sequence (www. ensembl.org). One of the BACs of the partial contig was localized by fluorescent in situ hybridization to canine chromosome 4q22, in agreement with the dog genome sequence. Two highly informative polymorphic microsatellite markers in intron 7 of the SGCD gene were identified. In 25 DCM-affected and 13 non DCM-affected dogs seven different haplotypes could be distinguished. However, no association between any of the SGCD variants and the disease locus was apparent.
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Affiliation(s)
- P Stabej
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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41
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Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SMJ, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O'Neill B, O'Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 2005; 438:803-19. [PMID: 16341006 DOI: 10.1038/nature04338] [Citation(s) in RCA: 1698] [Impact Index Per Article: 89.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 10/11/2005] [Indexed: 12/12/2022]
Abstract
Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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Affiliation(s)
- Kerstin Lindblad-Toh
- Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA.
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42
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Kuiper H, Drögemüller C, Evanno G, Guyon R, André C, Distl O. Assignment of the calcium channel, voltage-dependent, P/Q type, alpha 1A subunit gene (CACNA1A), and the ataxin 7 gene (ATXN7) to canine chromosome 20 by fluorescence in situ hybridization and confirmation by radiation hybrid mapping. Cytogenet Genome Res 2005; 111:96. [PMID: 16097083 DOI: 10.1159/000085678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- H Kuiper
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany.
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43
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Klukowska-Rötzler J, Szczerbal I, Braunschweig M, Switonski M, Schelling C, Dolf G. Mapping and development of four microsatellite markers for the canine 5'-hydroxytryptamine serotonin receptor 2A (HTR2A). Anim Genet 2005; 36:173-5. [PMID: 15771737 DOI: 10.1111/j.1365-2052.2005.01248.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- J Klukowska-Rötzler
- Institute of Animal Genetics, Nutrition and Housing, University of Berne, Berne, Switzerland.
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44
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Klukowska J, Szczerbal I, Wengi-Piasecka A, Switonski M, Schelling C, Gmür A, Dolf G. Characterization and mapping of canine microsatellites isolated from BAC clones harbouring DNA sequences homologous to seven human genes. Anim Genet 2004; 35:404-7. [PMID: 15373746 DOI: 10.1111/j.1365-2052.2004.01183.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Human primers specific for the genes LEP, HBB, PAX3, ESR2, TPH1, ABCA4 and ATP2A2 were used to identify clones in a canine BAC library. Subcloning of the positive BACs in plasmids, screening with microsatellite motifs and subsequent sequencing allowed for the identification of eight novel microsatellites. The presence of the gene of interest was confirmed by sequencing the polymerase chain reaction (PCR) products amplified in the positive BACs. Fluorescent in situ hybridization (FISH) using the positive BACs as probes allowed for the chromosomal localization of the insert DNAs in two canid species, dog (Canis familiaris) and red fox (Vulpes vulpes). The use of gene-associated microsatellites may accelerate the identification of candidate genes for phenotypic traits in linkage studies.
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Affiliation(s)
- J Klukowska
- Institute of Animal Genetics, Nutrition and Housing, University of Berne, Vetsuisse-Faculty Bern, Switzerland.
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45
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Abstract
Purebred dogs are providing invaluable information about morphology, behaviour and complex diseases, both of themselves and humans, by supplying tractable populations in which to map genes that control those processes. The diversification of dog breeds has led to the development of breeds enriched for particular genetic disorders, the mapping and cloning of which have been facilitated by the availability of the canine genome map and sequence. These tools have aided our understanding of canine population genetics, linkage disequilibrium and haplotype sharing in the dog, and have informed ongoing efforts of the need to identify quantitative trait loci that are important in complex traits.
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Affiliation(s)
- Nathan B Sutter
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, MSC8002, Building 50, Room 5222, Bethesda, Maryland 20892, USA
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46
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Stabej P, Imholz S, Versteeg SA, Zijlstra C, Stokhof AA, Domanjko-Petric A, Leegwater PAJ, van Oost BA. Characterization of the canine desmin (DES) gene and evaluation as a candidate gene for dilated cardiomyopathy in the Dobermann. Gene 2004; 340:241-9. [PMID: 15475165 DOI: 10.1016/j.gene.2004.06.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2004] [Revised: 06/15/2004] [Accepted: 06/29/2004] [Indexed: 10/26/2022]
Abstract
Canine-dilated cardiomyopathy (DCM) in dogs is a disease of the myocardium associated with dilatation and impaired contraction of the ventricles and is suspected to have a genetic cause. A missense mutation in the desmin gene (DES) causes DCM in a human family. Human DCM closely resembles the canine disease. In the present study, we evaluated whether DES gene mutations are responsible for DCM in Dobermann dogs. We have isolated bacterial artificial chromosome clones (BACs) containing the canine DES gene and determined the chromosomal location by fluorescence in situ hybridization (FISH). Using data deposited in the NCBI trace archive and GenBank, the canine DES gene DNA sequence was assembled and seven single nucleotide polymorphisms (SNPs) were identified. From the canine DES gene BAC clones, a polymorphic microsatellite marker was isolated. The microsatellite marker and four informative desmin SNPs were typed in a Dobermann family with frequent DCM occurrence, but the disease phenotype did not associate with a desmin haplotype. We concluded that mutations in the DES gene do not play a role in Dobermann DCM. Availability of the microsatellite marker, SNPs and DNA sequence reported in this study enable fast evaluation of the DES gene as a DCM candidate gene in other dog breeds with DCM occurrence.
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Affiliation(s)
- Polona Stabej
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 8, 3584 CM Utrecht, The Netherlands.
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47
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Milne BS, Hoather T, O'Brien PCM, Yang F, Ferguson-Smith MA, Dobson J, Sargan D. Karyotype of canine soft tissue sarcomas: a multi-colour, multi-species approach to canine chromosome painting. Chromosome Res 2004; 12:825-35. [PMID: 15702421 DOI: 10.1007/s10577-005-5542-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Accepted: 10/14/2004] [Indexed: 11/25/2022]
Abstract
Many canine tumour types represent useful models for tumours also found in humans. Studies of chromosomal abnormalities in canine tumours have been impeded by the complexity of the canine karyotype (2n = 78), which has made accurate identification of rearranged chromosomes difficult and laborious. To overcome this difficulty we have developed a seven-colour paint system for canine chromosomes, with six sets of chromosome paints covering all chromosomes except Y. Several pairs of canine autosomes co-locate in the flow karyotype. To distinguish these autosomes from each other, paint sets were supplemented with chromosomes of red fox and Japanese raccoon dog. Paints were used in fluorescence in-situ hybridization to analyse karyotypes in fourteen canine soft tissue sarcomas. Rearranged karyotypes were observed in seven tumours, but there was evidence for loss of rearrangement during tissue culture. Five tumours had rearrangements involving four chromosomes or fewer; one, a chondrosarcoma, had lost seven chromosomes whilst the last, a spindle cell sarcoma, had rearrangements involving eighteen chromosome pairs. The paint sets described here facilitate the complete cytogenetic analysis of balanced translocations and other inter-chromosomal rearrangements in canine tumours. We believe that this is the first canine tumour series to be subjected to this level of analysis.
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Affiliation(s)
- Bruce S Milne
- Centre for Veterinary Science, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
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48
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Breen M, Hitte C, Lorentzen TD, Thomas R, Cadieu E, Sabacan L, Scott A, Evanno G, Parker HG, Kirkness EF, Hudson R, Guyon R, Mahairas GG, Gelfenbeyn B, Fraser CM, André C, Galibert F, Ostrander EA. An integrated 4249 marker FISH/RH map of the canine genome. BMC Genomics 2004; 5:65. [PMID: 15363096 PMCID: PMC520820 DOI: 10.1186/1471-2164-5-65] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Accepted: 09/13/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The 156 breeds of dog recognized by the American Kennel Club offer a unique opportunity to map genes important in genetic variation. Each breed features a defining constellation of morphological and behavioral traits, often generated by deliberate crossing of closely related individuals, leading to a high rate of genetic disease in many breeds. Understanding the genetic basis of both phenotypic variation and disease susceptibility in the dog provides new ways in which to dissect the genetics of human health and biology. RESULTS To facilitate both genetic mapping and cloning efforts, we have constructed an integrated canine genome map that is both dense and accurate. The resulting resource encompasses 4249 markers, and was constructed using the RHDF5000-2 whole genome radiation hybrid panel. The radiation hybrid (RH) map features a density of one marker every 900 Kb and contains 1760 bacterial artificial chromosome clones (BACs) localized to 1423 unique positions, 851 of which have also been mapped by fluorescence in situ hybridization (FISH). The two data sets show excellent concordance. Excluding the Y chromosome, the map features an RH/FISH mapped BAC every 3.5 Mb and an RH mapped BAC-end, on average, every 2 Mb. For 2233 markers, the orthologous human genes have been established, allowing the identification of 79 conserved segments (CS) between the dog and human genomes, dramatically extending the length of most previously described CS. CONCLUSIONS These results provide a necessary resource for the canine genome mapping community to undertake positional cloning experiments and provide new insights into the comparative canine-human genome maps.
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Affiliation(s)
- Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA.
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49
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Szczerbal I, Rogalska-Niznik N, Klukowska J, Schelling C, Dolf G, Switonski M. Comparative chromosomal localization of the canine-derived BAC clones containing LEP and IGF1 genes in four species of the family Canidae. Cytogenet Genome Res 2004; 102:264-6. [PMID: 14970714 DOI: 10.1159/000075760] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2003] [Accepted: 07/28/2003] [Indexed: 11/19/2022] Open
Abstract
In the present report we show the chromosomal localization of two BAC clones, carrying the leptin (LEP) and insuline-like growth factor 1 (IGF1) genes, respectively, in four species belonging to the family Canidae: the dog, red fox, arctic fox and the Chinese raccoon dog. The assignments are in agreement with earlier data obtained from comparative chromosome painting for the dog, red fox and arctic fox.
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Affiliation(s)
- I Szczerbal
- Department of Genetics and Animal Breeding, August Cieszkowski Agricultural University of Poznan, Poznan, Poland
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50
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Szczerbal I, Rogalska-Niznik N, Schelling C, Schläpfer J, Dolf G, Switonski M. Development of a cytogenetic map for the Chinese raccoon dog (Nyctereutes procyonoides procyonoides) and the arctic fox (Alopex lagopus) genomes, using canine-derived microsatellite probes. Cytogenet Genome Res 2004; 102:267-71. [PMID: 14970715 DOI: 10.1159/000075761] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2003] [Accepted: 07/28/2003] [Indexed: 11/19/2022] Open
Abstract
New chromosomal assignments of canine-derived cosmid clones containing microsatellites to the Chinese raccoon dog and arctic fox genomes are presented in the study. The localizations are in agreement with data obtained from comparative chromosome painting experiments between the dog and arctic fox genomes. However, paracentric inversions have been detected by comparing the loci order in canid karyotypes. The number of physically mapped loci increased to thirty-five both in the Chinese raccoon dog and in the arctic fox. Furthermore, the present status of the cytogenetic map of the Chinese raccoon dog and arctic fox is presented in this study.
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Affiliation(s)
- I Szczerbal
- Department of Genetics and Animal Breeding, August Cieszkowski Agricultural University of Poznan, Poznan, Poland
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