Genomic landscape of copy number variation and copy neutral loss of heterozygosity events in equine sarcoids reveals increased instability of the sarcoid genome.
Abstract: Although they are the most common neoplasms in equids, sarcoids are not fully characterized at the molecular level. Therefore, the objective of this study was to characterize the landscape of structural rearrangements, such as copy number variation (CNV) and copy neutral loss of heterozygosity (cnLOH), in the genomes of sarcoid tumor cells. This information will not only broaden our understanding of the characteristics of this genome but will also improve the general knowledge of this tumor and the mechanisms involved in its generation. To this end, Equine SNP64K Illumina microarrays were applied along with bioinformatics tools dedicated for signal intensity analysis. The analysis revealed increased instability of the genome of sarcoid cells compared with unaltered skin tissue samples, which was manifested by the prevalence of CNV and cnLOH events. Many of the identified CNVs overlapped with the other research results, but the simultaneously observed variability in the number and sizes of detected aberrations indicated a need for further studies and the development of more reliable bioinformatics algorithms. The functional analysis of genes co-localized with the identified aberrations revealed that these genes are engaged in vital cellular processes. In addition, a number of these genes directly contribute to neoplastic transformation. Furthermore, large numbers of cnLOH events identified in the sarcoids suggested that they may play no less significant roles than CNVs in the carcinogenesis of this tumor. Thus, our results indicate the importance of cnLOH and CNV in equine sarcoid oncogenesis and present a direction of future research.
Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.
Publication Date: 2017-07-23 PubMed ID: 28743673DOI: 10.1016/j.biochi.2017.07.006Google Scholar: Lookup
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- Journal Article
Summary
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The study aims to understand the genetic alterations that occur in sarcoids, which are the most common types of tumours in horses. The genome of sarcoid cells show more instability than normal skin tissue, revealed by prevalent copy number variation (CNV) and copy-neutral loss of heterozygosity (cnLOH) events, suggesting these may play a significant role in the formation and growth of these tumours.
Study Objectives
- The main objective of this research was to map out the patterns of structural changes such as CNVs (where parts of the genome are duplicated or deleted) and cnLOHs (where both copies of a gene come from one parent) in the genome of sarcoid tumor cells in horses.
- The aim was not just to understand the characteristics of these tumour genomes better, but also to add to the overall understanding of these tumours and their formation process.
Methods
- To achieve these objectives, Equine SNP64K Illumina microarrays were used alongside bioinformatics tools for signal intensity analysis.
- This gave a comprehensive overview of the structural rearrangements in the cells of these tumours.
Findings
- Results from the analysis suggested that the genome of sarcoid cells is significantly more unstable than unaltered skin tissue samples.
- This was indicated by the prevalence of CNV and cnLOH events in these cells, showing that they are likely to have a significant role in the carcinogenesis of this tumour.
- The research also found that many of the identified CNVs overlapped with results from other research, but the variability in the number and sizes of identified aberrations highlighted the need for further study and more reliable bioinformatics algorithms.
Functional Analysis
- The genes found within the identified CNV and cnLOH regions were evaluated, revealing that these genes are involved in crucial cellular processes, including several that contribute to tumour formation.
Implications
- The findings underscore the importance of cnLOH and CNV in equine sarcoid oncogenesis.
- This knowledge presents new directions for future research into these tumours, potentially paving the way for more effective treatments.
Cite This Article
APA
Pawlina-Tyszko K, Gurgul A, Szmatoła T, Ropka-Molik K, Semik-Gurgul E, Klukowska-Rötzler J, Koch C, Mählmann K, Bugno-Poniewierska M.
(2017).
Genomic landscape of copy number variation and copy neutral loss of heterozygosity events in equine sarcoids reveals increased instability of the sarcoid genome.
Biochimie, 140, 122-132.
https://doi.org/10.1016/j.biochi.2017.07.006 Publication
Researcher Affiliations
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland. Electronic address: klaudia.pawlina@izoo.krakow.pl.
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland. Electronic address: artur.gurgul@izoo.krakow.pl.
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland. Electronic address: tomasz.szmatola@izoo.krakow.pl.
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland. Electronic address: katarzyna.ropka@izoo.krakow.pl.
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland. Electronic address: ewelina.semik@izoo.krakow.pl.
- Division of Pedriatric Hematology/Oncology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3008, Bern, Switzerland; Department of Emergency Medicine, University Hospital Bern, Inselspital, 3010, Bern, Switzerland. Electronic address: jolanta.klukowska-roetzler@insel.ch.
- Swiss Institute of Equine Medicine ISME, Faculty of Veterinary Medicine, University of Bern and Agroscope, Länggassstrasse 124c, Postfach 8466, CH-3001, Bern, Switzerland. Electronic address: christoph.koch@vetsuisse.unibe.ch.
- Swiss Institute of Equine Medicine ISME, Faculty of Veterinary Medicine, University of Bern and Agroscope, Länggassstrasse 124c, Postfach 8466, CH-3001, Bern, Switzerland; Equine Clinic: Surgery and Radiology, Department of Veterinary Medicine, Free University of Berlin, Oertzenweg 19b, 14163, Berlin, Germany. Electronic address: Kathrin.Maehlmann@fu-berlin.de.
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland. Electronic address: monika.bugno@izoo.krakow.pl.
MeSH Terms
- Animals
- Gene Dosage
- Genes, Neoplasm
- Genome
- Genomic Instability
- Horse Diseases / genetics
- Horses
- Loss of Heterozygosity
- Skin Neoplasms / genetics
- Skin Neoplasms / veterinary
Citations
This article has been cited 3 times.- Laseca N, Molina A, Valera M, Antonini A, Demyda-Peyrás S. Copy Number Variation (CNV): A New Genomic Insight in Horses.. Animals (Basel) 2022 Jun 2;12(11).
- Podstawski P, Witarski W, Szmatoła T, Bugno-Poniewierska M, Ropka-Molik K. Mobility and Invasion Related Gene Expression Patterns in Equine Sarcoid.. Animals (Basel) 2020 May 19;10(5).
- Schurink A, da Silva VH, Velie BD, Dibbits BW, Crooijmans RPMA, Franҫois L, Janssens S, Stinckens A, Blott S, Buys N, Lindgren G, Ducro BJ. Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity.. BMC Genet 2018 Jul 30;19(1):49.
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