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Pawlina-Tyszko K, Gurgul A, Szmatoła T, Ropka-Molik K, Semik-Gurgul E, Klukowska-Rötzler J, Koch C, Mählmann K, Bugno-Poniewierska M. Genomic landscape of copy number variation and copy neutral loss of heterozygosity events in equine sarcoids reveals increased instability of the sarcoid genome. Biochimie 2017; 140:122-132. [PMID: 28743673 DOI: 10.1016/j.biochi.2017.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/20/2017] [Indexed: 12/20/2022]
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.
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Affiliation(s)
- Klaudia Pawlina-Tyszko
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Artur Gurgul
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Tomasz Szmatoła
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Katarzyna Ropka-Molik
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Ewelina Semik-Gurgul
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Jolanta Klukowska-Rötzler
- 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.
| | - Christoph Koch
- Swiss Institute of Equine Medicine ISME, Faculty of Veterinary Medicine, University of Bern and Agroscope, Länggassstrasse 124c, Postfach 8466, CH-3001, Bern, Switzerland.
| | - Kathrin Mählmann
- 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.
| | - Monika Bugno-Poniewierska
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
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Holst F. Estrogen receptor alpha gene amplification in breast cancer: 25 years of debate. World J Clin Oncol 2016; 7:160-173. [PMID: 27081639 PMCID: PMC4826962 DOI: 10.5306/wjco.v7.i2.160] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 01/05/2016] [Accepted: 02/16/2016] [Indexed: 02/06/2023] Open
Abstract
Twenty-five years ago, Nembrot and colleagues reported amplification of the estrogen receptor alpha gene (ESR1) in breast cancer, initiating a broad and still ongoing scientific debate on the prevalence and clinical significance of this genetic aberration, which affects one of the most important genes in breast cancer. Since then, a multitude of studies on this topic has been published, covering a wide range of divergent results and arguments. The reported prevalence of this alteration in breast cancer ranges from 0% to 75%, suggesting that ESR1 copy number analysis is hampered by technical and interpreter issues. To date, two major issues related to ESR1 amplification remain to be conclusively addressed: (1) The extent to which abundant amounts of messenger RNA can mimic amplification in standard fluorescence in situ hybridization assays in the analysis of strongly expressed genes like ESR1, and (2) the clinical relevance of ESR1 amplification: Such relevance is strongly disputed, with data showing predictive value for response as well as for resistance of the cancer to anti-estrogen therapies, or for subsequent development of cancers in the case of precursor lesions that display amplification of ESR1. This review provides a comprehensive summary of the various views on ESR1 amplification, and highlights explanations for the contradictions and conflicting data that could inform future ESR1 research.
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Ferroni L, Della Puppa A, D'Avella D, Isola M, Scienza R, Gardin C, Zavan B. Tissue Engineering Strategies as Tools for Personalized Meningioma Treatment. Artif Organs 2015; 39:E114-26. [DOI: 10.1111/aor.12483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Letizia Ferroni
- Department of Biomedical Sciences; University of Padova; Padova Italy
| | | | | | - Maurizio Isola
- Department of Animal Medicine, Production and Health (MAPS); University of Padova; Padova Italy
| | - Renato Scienza
- Department of Neurosciences; University of Padova; Padova Italy
| | - Chiara Gardin
- Department of Biomedical Sciences; University of Padova; Padova Italy
| | - Barbara Zavan
- Department of Biomedical Sciences; University of Padova; Padova Italy
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Park CH, Rha SY, Ahn JB, Shin SJ, Kwon WS, Kim TS, An S, Kim NK, Yang WI, Chung HC. PINCH-2 presents functional copy number variation and suppresses migration of colon cancer cells by paracrine activity. Int J Cancer 2014; 136:2273-83. [PMID: 25346044 DOI: 10.1002/ijc.29273] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/30/2014] [Indexed: 01/15/2023]
Abstract
In recent years, characterization of cancer and its environment has become necessary. However, studies of the cancer microenvironment remain insufficient. Copy number variations (CNVs) occur in 40% of cancer-related genes, but few studies have reported the correlation between CNVs in morphologically normal tissues adjacent to cancer and cancer progression. In this study, we evaluated cancer cell migration and invasion according to the genetic differences between cancer tissues and their surrounding normal tissues. To study the field cancerization effect, we screened 89 systemic metastasis-related CNVs from morphologically normal tissues adjacent to colon cancers. Among these CNVs, LIM and senescent cell antigen-like domain 2 (PINCH-2) showed copy number amplification and upregulation of mRNA in the nonrelapsed group compared to the systemic relapse group. PINCH-2 expression in colon cancer cells was lower than that in normal epithelial colon cells at both the protein and mRNA levels. Suppression of PINCH-2 resulted in decreased formation of the PINCH-2-IPP (PINCH-2, integrin-linked kinase and α-parvin) complex and reciprocally increased formation of the PINCH-1-IPP complex. Although PINCH-2 expression of survival pathway-related proteins (Akt and phospho-Akt) did not change upon suppression of PINCH-2 expression, cell migration-related proteins [matrix-metalloproteinase (MMP)-9 and -11] were upregulated through autocrine and paracrine activation. Thus, PINCH-2 participates in decreased systemic recurrence by competitively regulating IPP complex formation with PINCH-1, thereby suppressing autocrine and paracrine effects on motility in colon cancer. This genetic change in morphologically normal tissue suggests a field cancerization effect of the tumor microenvironment in cancer progression.
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Affiliation(s)
- Chan Hee Park
- National Biochip Research Center, Yonsei University College of Medicine, Yonsei University Health System, Seoul, Korea; Cancer Metastasis Research Center, Yonsei University College of Medicine, Yonsei University Health System, Seoul, Korea; Yonsei Cancer Research Institute, Yonsei University College of Medicine, Yonsei University Health System, Seoul, Korea
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Moelans CB, Holst F, Hellwinkel O, Simon R, van Diest PJ. ESR1 amplification in breast cancer by optimized RNase FISH: frequent but low-level and heterogeneous. PLoS One 2013; 8:e84189. [PMID: 24367641 PMCID: PMC3867473 DOI: 10.1371/journal.pone.0084189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/13/2013] [Indexed: 01/09/2023] Open
Abstract
Prevalence of ESR1 amplification in breast cancer is highly disputed and discrepancies have been related to different technical protocols and different scoring approaches. In addition, pre-mRNA artifacts have been proposed to influence outcome of ESR1 FISH analysis. We analyzed ESR1 gene copy number status combining an improved RNase FISH protocol with multiplex ligation-dependent probe amplification (MLPA) after laser microdissection. FISH showed a high prevalence of ESR1 gains and amplifications despite RNase treatment but MLPA did not confirm ESR1 copy number increases detected by FISH in more than half of cases. We suggest that the combination of the ESR1-specific intra-tumor heterogeneity and low-level copy number increase accounts for these discrepancies.
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Affiliation(s)
- Cathy B. Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Frederik Holst
- Section of Gynecology and Obstetrics, Department of Clinical Science, Haukeland University Hospital, Bergen, Norway
- Department of Pathology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Olaf Hellwinkel
- Department of Legal Medicine, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Ronald Simon
- Department of Pathology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Paul J. van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
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Lopes AM, Aston KI, Thompson E, Carvalho F, Gonçalves J, Huang N, Matthiesen R, Noordam MJ, Quintela I, Ramu A, Seabra C, Wilfert AB, Dai J, Downie JM, Fernandes S, Guo X, Sha J, Amorim A, Barros A, Carracedo A, Hu Z, Hurles ME, Moskovtsev S, Ober C, Paduch DA, Schiffman JD, Schlegel PN, Sousa M, Carrell DT, Conrad DF. Human spermatogenic failure purges deleterious mutation load from the autosomes and both sex chromosomes, including the gene DMRT1. PLoS Genet 2013; 9:e1003349. [PMID: 23555275 PMCID: PMC3605256 DOI: 10.1371/journal.pgen.1003349] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 01/17/2013] [Indexed: 01/17/2023] Open
Abstract
Gonadal failure, along with early pregnancy loss and perinatal death, may be an important filter that limits the propagation of harmful mutations in the human population. We hypothesized that men with spermatogenic impairment, a disease with unknown genetic architecture and a common cause of male infertility, are enriched for rare deleterious mutations compared to men with normal spermatogenesis. After assaying genomewide SNPs and CNVs in 323 Caucasian men with idiopathic spermatogenic impairment and more than 1,100 controls, we estimate that each rare autosomal deletion detected in our study multiplicatively changes a man's risk of disease by 10% (OR 1.10 [1.04–1.16], p<2×10−3), rare X-linked CNVs by 29%, (OR 1.29 [1.11–1.50], p<1×10−3), and rare Y-linked duplications by 88% (OR 1.88 [1.13–3.13], p<0.03). By contrasting the properties of our case-specific CNVs with those of CNV callsets from cases of autism, schizophrenia, bipolar disorder, and intellectual disability, we propose that the CNV burden in spermatogenic impairment is distinct from the burden of large, dominant mutations described for neurodevelopmental disorders. We identified two patients with deletions of DMRT1, a gene on chromosome 9p24.3 orthologous to the putative sex determination locus of the avian ZW chromosome system. In an independent sample of Han Chinese men, we identified 3 more DMRT1 deletions in 979 cases of idiopathic azoospermia and none in 1,734 controls, and found none in an additional 4,519 controls from public databases. The combined results indicate that DMRT1 loss-of-function mutations are a risk factor and potential genetic cause of human spermatogenic failure (frequency of 0.38% in 1306 cases and 0% in 7,754 controls, p = 6.2×10−5). Our study identifies other recurrent CNVs as potential causes of idiopathic azoospermia and generates hypotheses for directing future studies on the genetic basis of male infertility and IVF outcomes. Infertility is a disease that prevents the transmission of DNA from one generation to the next, and consequently it has been difficult to study the genetics of infertility using classical human genetics methods. Now, new technologies for screening entire genomes for rare and patient-specific mutations are revolutionizing our understanding of reproductively lethal diseases. Here, we apply techniques for variation discovery to study a condition called azoospermia, the failure to produce sperm. Large deletions of the Y chromosome are the primary known genetic risk factor for azoospermia, and genetic testing for these deletions is part of the standard treatment for this condition. We have screened over 300 men with azoospermia for rare deletions and duplications, and find an enrichment of these mutations throughout the genome compared to unaffected men. Our results indicate that sperm production is affected by mutations beyond the Y chromosome and will motivate whole-genome analyses of larger numbers of men with impaired spermatogenesis. Our finding of an enrichment of rare deleterious mutations in men with poor sperm production also raises the possibility that the slightly increased rate of birth defects reported in children conceived by in vitro fertilization may have a genetic basis.
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Affiliation(s)
- Alexandra M. Lopes
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- * E-mail: (AML); (DFC)
| | - Kenneth I. Aston
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Emma Thompson
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Filipa Carvalho
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
| | - João Gonçalves
- Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Ni Huang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rune Matthiesen
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Michiel J. Noordam
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Inés Quintela
- Genomics Medicine Group, National Genotyping Center, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Avinash Ramu
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Catarina Seabra
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Amy B. Wilfert
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jonathan M. Downie
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Susana Fernandes
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - António Amorim
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Alberto Barros
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
- Centre for Reproductive Genetics Alberto Barros, Porto, Portugal
| | - Angel Carracedo
- Genomics Medicine Group, National Genotyping Center, University of Santiago de Compostela, Santiago de Compostela, Spain
- Galician Foundation of Genomic Medicine and University of Santiago de Compostela, CIBERER, Santiago de Compostela, Spain
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Matthew E. Hurles
- Genome Mutation and Genetic Disease Group, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Sergey Moskovtsev
- CReATe Fertility Center, University of Toronto, Toronto, Canada
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Canada
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, Illinois, United States of America
| | - Darius A. Paduch
- Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, New York, New York, United States of America
| | - Joshua D. Schiffman
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Center for Children's Cancer Research (C3R), Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Division of Pediatric Hematology/Oncology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Peter N. Schlegel
- Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, New York, New York, United States of America
| | - Mário Sousa
- Laboratory of Cell Biology, UMIB, ICBAS, University of Porto, Porto, Portugal
| | - Douglas T. Carrell
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Physiology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Donald F. Conrad
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail: (AML); (DFC)
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Chiara M, Pesole G, Horner DS. SVM²: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data. Nucleic Acids Res 2012; 40:e145. [PMID: 22735696 PMCID: PMC3467043 DOI: 10.1093/nar/gks606] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Several bioinformatics methods have been proposed for the detection and characterization of genomic structural variation (SV) from ultra high-throughput genome resequencing data. Recent surveys show that comprehensive detection of SV events of different types between an individual resequenced genome and a reference sequence is best achieved through the combination of methods based on different principles (split mapping, reassembly, read depth, insert size, etc.). The improvement of individual predictors is thus an important objective. In this study, we propose a new method that combines deviations from expected library insert sizes and additional information from local patterns of read mapping and uses supervised learning to predict the position and nature of structural variants. We show that our approach provides greatly increased sensitivity with respect to other tools based on paired end read mapping at no cost in specificity, and it makes reliable predictions of very short insertions and deletions in repetitive and low-complexity genomic contexts that can confound tools based on split mapping of reads.
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Affiliation(s)
- Matteo Chiara
- Department of Biomolecular Sciences and Biotechnology, University of Milan, Milan 20133, Italy.
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Yoshimoto M, Ludkovski O, DeGrace D, Williams JL, Evans A, Sircar K, Bismar TA, Nuin P, Squire JA. PTEN genomic deletions that characterize aggressive prostate cancer originate close to segmental duplications. Genes Chromosomes Cancer 2011; 51:149-60. [DOI: 10.1002/gcc.20939] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 09/19/2011] [Indexed: 12/30/2022] Open
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Talseth-Palmer BA, Scott RJ. Genetic variation and its role in malignancy. INTERNATIONAL JOURNAL OF BIOMEDICAL SCIENCE : IJBS 2011; 7:158-71. [PMID: 23675233 PMCID: PMC3614837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 02/16/2011] [Indexed: 11/21/2022]
Abstract
Genetic variation has long been thought associated with common complex disease and has therefore been widely studied. Genetic variation in the human genome is present in many forms and have been summarised in this review. The potential role of DNA damage, DNA repair and environmental influence on genetic variation in the development of cancer will be discussed, before significant genome projects are reviewed. All the various forms of genetic variation have been associated with malignancies and have been extensively studied and this is a review of the state of the field. We also discuss the road ahead in fulfilling the ultimate goal in all cancer genetic studies, which is decreasing deaths caused by cancer.
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Affiliation(s)
- Bente A. Talseth-Palmer
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Australia;,Hunter Medical Research Institute, John Hunter Hospital, Newcastle, Australia;
| | - Rodney J. Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Australia;,Hunter Medical Research Institute, John Hunter Hospital, Newcastle, Australia;,Hunter Area Pathology Service, Hunter New England Area Health, Newcastle, Australia
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Zechel JL, MacLennan GT, Heaney JD, Nadeau JH. Spontaneous metastasis in mouse models of testicular germ-cell tumours. ACTA ACUST UNITED AC 2011; 34:e278-87. [PMID: 21651572 DOI: 10.1111/j.1365-2605.2011.01160.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Testicular germ-cell tumours (TGCTs) are the most common cancer in young men; the incidence is increasing worldwide and they have an unusually high rate of metastasis. Despite significant work on TGCTs and their metastases in humans, absence of a mouse model of spontaneous metastasis has greatly limited our understanding of the mechanisms by which metastatic potential is acquired and on their modes of dissemination. We report a new model of spontaneous TGCT metastasis in the 129 family of mice and provide evidence that these are true metastases derived directly from primary testicular cancers rather than independently from ectopic stem cells. These putative metastases (pMETs) occur at similar frequencies among TGCT-affected males in six genetically distinct TGCT-susceptible strains and were largely found in anatomical sites that are consistent with patterns of TGCT metastasis in humans. Various lines of evidence support their pluripotency and germ-cell origin, including presence of multiple endodermal, mesodermal and ectodermal derivatives as well as cells showing OCT4 and SSEA-1 pluripotency markers. In addition, pMETs were never found in males that did not have a TGCT, suggesting that metastases are derived from primary tumours. Finally, pMETS and primary TGCTs shared several DNA copy number variants suggesting a common cellular and developmental origin. Together, these results provide the first evidence for spontaneous TGCT metastasis in mice and show that these metastases originate from primary TGCTs rather than independently from ectopic stem cells.
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Affiliation(s)
- J L Zechel
- Department of Genetics, Case Western Reserve University School of Medicine, University Hospitals Case Medical Center, Institute of Pathology, Cleveland OH, USA
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11
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Jeon JP, Shim SM, Nam HY, Ryu GM, Hong EJ, Kim HL, Han BG. Copy number variation at leptin receptor gene locus associated with metabolic traits and the risk of type 2 diabetes mellitus. BMC Genomics 2010; 11:426. [PMID: 20624279 PMCID: PMC2996954 DOI: 10.1186/1471-2164-11-426] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 07/12/2010] [Indexed: 12/26/2022] Open
Abstract
Background Recent efforts have been made to link complex human traits and disease susceptibility to DNA copy numbers. The leptin receptor (LEPR) has been implicated in obesity and diabetes. Mutations and genetic variations of LEPR gene have been discovered in rodents and humans. However, the association of DNA copy number variations at the LEPR gene locus with human complex diseases has not been reported. In an attempt to study DNA copy number variations associated with metabolic traits and type 2 diabetes mellitus (T2DM), we targeted the LEPR gene locus in DNA copy number analyses. Results We identified DNA copy number variations at the LEPR gene locus among a Korean population using genome-wide SNP chip data, and then quantified copy numbers of the E2 DNA sequence in the first two exons overlapped between LEPR and LEPROT genes by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method. Among the non-diabetic subjects (n = 1,067), lower E2 DNA copy numbers were associated with higher fasting glucose levels in men (p = 1.24 × 10-7) and women (p = 9.45 × 10-5), as well as higher total cholesterol levels in men (p = 9.96 × 10-7). In addition, the significant association between lower E2 DNA copy numbers and lower level of postprandial 2hr insulin was evident only in non-diabetic women, whereas some obesity-related phenotypes and total cholesterol level exhibited significant associations only in non-diabetic men. Logistic regression analysis indicated that lower E2 DNA copy numbers were associated with T2DM (odds ratio, 1.92; 95% CI, 1.26~2.96; p < 0.003) in our nested case-control study. Interestingly, the E2 DNA copy number exhibited a negative correlation with LEPR gene expression, but a positive correlation with LEPROT gene expression. Conclusions This work suggests that a structural variation at the LEPR gene locus is functionally associated with complex metabolic traits and the risk of T2DM.
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Affiliation(s)
- Jae-Pil Jeon
- Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, 194 Tongil Ro, Seoul, 122-701, Korea.
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12
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Jeon JP, Shim SM, Jung JS, Nam HY, Lee HJ, Oh BS, Kim K, Kim HL, Han BG. A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans. Exp Mol Med 2010; 41:618-28. [PMID: 19478558 DOI: 10.3858/emm.2009.41.9.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P<0.01) and standard deviation of copy numbers (SD>or= 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n=643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P<0.001 and SD>or=0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations.
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Affiliation(s)
- Jae Pil Jeon
- Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea
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13
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Genomic deletions correlate with underexpression of novel candidate genes at six loci in pediatric pilocytic astrocytoma. Neoplasia 2008; 10:757-72. [PMID: 18670637 DOI: 10.1593/neo.07914] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 05/09/2008] [Accepted: 05/11/2008] [Indexed: 01/24/2023] Open
Abstract
The molecular pathogenesis of pediatric pilocytic astrocytoma (PA) is not well defined. Previous cytogenetic and molecular studies have not identified nonrandom genetic aberrations. To correlate differential gene expression and genomic copy number aberrations (CNAs) in PA, we have used Affymetrix GeneChip HG_U133A to generate gene expression profiles of 19 pediatric patients and the SpectralChip 2600 to investigate CNAs in 11 of these tumors. Hierarchical clustering according to expression profile similarity grouped tumors and controls separately. We identified 1844 genes that showed significant differential expression between tumor and normal controls, with a large number clearly influencing phosphatidylinositol and mitogen-activated protein kinase signaling in PA. Most CNAs identified in this study were single-clone alterations. However, a small region of loss involving up to seven adjacent clones at 7q11.23 was observed in seven tumors and correlated with the underexpression of BCL7B. Loss of four individual clones was also associated with reduced gene expression including SH3GL2 at 9p21.2-p23, BCL7A (which shares 90% sequence homology with BCL7B) at 12q24.33, DRD1IP at 10q26.3, and TUBG2 and CNTNAP1 at 17q21.31. Moreover, the down-regulation of FOXG1B at 14q12 correlated with loss within the gene promoter region in most tumors. This is the first study to correlate differential gene expression with CNAs in PA.
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14
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Matsuda D, Khoo SK, Massie A, Iwamura M, Chen J, Petillo D, Wondergem B, Avallone M, Kloostra SJ, Tan MH, Koeman J, Zhang Z, Kahnoski RJ, Baba S, Teh BT. Identification of copy number alterations and its association with pathological features in clear cell and papillary RCC. Cancer Lett 2008; 272:260-7. [PMID: 18682315 DOI: 10.1016/j.canlet.2008.06.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 04/30/2008] [Accepted: 06/30/2008] [Indexed: 01/08/2023]
Abstract
We report and characterize the copy number alterations (CNAs) in 35 clear cell and 12 papillary renal cell carcinomas (RCC) using Affymetrix 100K SNP arrays. Novel gain and loss regions are identified in both subtypes. In addition, statistically significant CNA are detected and associated with the pathological features: VHL mutation status, tumor grades, and sarcomatoid component in clear cell RCC and in types 1 and 2 of papillary RCC. Florescence in situ hybridization confirmed the copy number gain in the transforming growth factor, beta-induced gene (TGFBI), which is a possible oncogene for clear cell RCC.
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Affiliation(s)
- Daisuke Matsuda
- Laboratory of Cancer Genetics/Sequencing, Van Andel Research Institute, 333 Bostwick Avenue N.E., Grand Rapids, MI 49503, USA
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15
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Abstract
Genome-wide association studies provide a new and powerful approach to investigate the effect of inherited genetic variation on the risk of human disease. These studies rely on high throughput DNA microarray technology to genotype hundreds of thousands of genetic variants across the human genome. The first genome-wide association studies have identified previously unknown genetic risk factors that influence a range of diseases, including prostate cancer, breast cancer, myocardial infarction, age-related macular degeneration, diabetes, Crohn's disease and obesity. Many more studies are currently underway, including a number that will focus on other cancers (e.g., colorectal). Here we discuss the major issues involved in conducting genome-wide association studies and how these studies can be used to examine cancer phenotypes.
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Affiliation(s)
- Eric Jorgenson
- University of California, Department of Epidemiology & Biostatistics , San Francisco, CA 94143-0794, USA.
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16
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Adelson DL. Insights and applications from sequencing the bovine genome. Reprod Fertil Dev 2008; 20:54-60. [DOI: 10.1071/rd07157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Humans have sought to improve/tailor cattle since their domestication a few thousand years ago. Up until the last 40–50 years, consistent genetic improvement of cattle was a hit or miss proposition. Recent progress has been more rapid, thanks to applications of quantitative genetics to breeding schemes. With the availability of the bovine genome sequence, genetic selection and on-farm management are likely to be revolutionised yet again. Genetic association studies that were previously impossible to carry out due to a lack of markers are now possible. In addition to improved genetic mapping of economic traits, the bovine genome sequence allows us to create a common context for genetic and physiological data, which will provide novel insights into gene regulation and function.
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17
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Brazma D, Grace C, Howard J, Melo JV, Holyoke T, Apperley JF, Nacheva EP. Genomic profile of chronic myelogenous leukemia: Imbalances associated with disease progression. Genes Chromosomes Cancer 2007; 46:1039-50. [PMID: 17696194 DOI: 10.1002/gcc.20487] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The expression of the chimeric BCR/ABL1 fusion gene resulting from t(9;22)(q34;q11) in chronic myelogenous leukemia (CML) is necessary for malignant transformation, but not sufficient to maintain disease progression. The appearance of various chromosomal and molecular alterations in the accelerated and terminal phase of CML is well documented, but evidence for causal relationship is largely lacking. We carried out a genome wide screening at a resolution of 1 Mb of 54 samples at different stages of CML together with 12 CML cell lines and found that disease progression is accompanied by a spectrum of recurrent genome imbalances. Among the most frequent are losses at 1p36, 5q21, 9p21, and 9q34 and gains at 1q, 8q24, 9q34, 16p, and 22q11, all of which were located with higher precision within the genome than previously possible. These genome imbalances are unique to CML cases with clinically manifested or suspected accelerated/blast stage alike, but not seen in chronic phase samples. Previously unrecognized cryptic imbalances occurring within the Ph-chromosome were also detected, although further scrutiny is required to pin-point gene involvement and seek association with disease features. Importantly, some of these imbalances were seen in the CD34(+) cells but not in the whole BM samples of patients in accelerated phase. Taken together, these findings highlight the potential of screening CD34(+) cells for genome wide imbalances associated with disease progression. Finally, the numerous single copy number variations recorded, many unique to this cohort of patients, raise the possible association of genome polymorphism and CML.
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Affiliation(s)
- D Brazma
- Royal Free and UCL Medical School, Academic Haematology, Molecular Cytogenetics, Rowland Hill Street, Hampstead, and Hammersmith Hospital, London NW3 2PF, UK
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18
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Trevino V, Falciani F, Barrera-Saldaña HA. DNA microarrays: a powerful genomic tool for biomedical and clinical research. Mol Med 2007; 13:527-41. [PMID: 17660860 PMCID: PMC1933257 DOI: 10.2119/2006-00107.trevino] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Accepted: 07/02/2007] [Indexed: 12/11/2022] Open
Abstract
Among the many benefits of the Human Genome Project are new and powerful tools such as the genome-wide hybridization devices referred to as microarrays. Initially designed to measure gene transcriptional levels, microarray technologies are now used for comparing other genome features among individuals and their tissues and cells. Results provide valuable information on disease subcategories, disease prognosis, and treatment outcome. Likewise, they reveal differences in genetic makeup, regulatory mechanisms, and subtle variations and move us closer to the era of personalized medicine. To understand this powerful tool, its versatility, and how dramatically it is changing the molecular approach to biomedical and clinical research, this review describes the technology, its applications, a didactic step-by-step review of a typical microarray protocol, and a real experiment. Finally, it calls the attention of the medical community to the importance of integrating multidisciplinary teams to take advantage of this technology and its expanding applications that, in a slide, reveals our genetic inheritance and destiny.
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Affiliation(s)
- Victor Trevino
- Institute Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Nuevo León, México
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Francesco Falciani
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Hugo A. Barrera-Saldaña
- Laboratorio de Genómica y Bioinformática del ULIEG. Departamento de Bioquímica, Facultad de Medicina de la Universidad Autónoma de Nuevo León. Monterrey, N.L. México
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19
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Etienne A, Carbuccia N, Adélaïde J, Bekhouche I, Rémy V, Sohn C, Sainty D, Gastaut JA, Olschwang S, Birnbaum D, Mozziconacci MJ, Chaffanet M. Rearrangements involving 12q in myeloproliferative disorders: possible role of HMGA2 and SOCS2 genes. ACTA ACUST UNITED AC 2007; 176:80-8. [PMID: 17574970 DOI: 10.1016/j.cancergencyto.2007.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 03/13/2007] [Accepted: 03/19/2007] [Indexed: 10/23/2022]
Abstract
We report two cases of translocation associated with deletion on derivative chromosomes in atypical myeloproliferative disorder (MPD). In a MPD with t(3;12)(q29;q14), the rearrangement targeted the HMGA2 locus at 12q14 and deleted a region of about 1.5 megabases (Mb) at 3q29. In an MPD with t(9;12)(q13 approximately q21;q22) and JAK2 V617F mutation, array comparative genomic hybridization delineated a deletion of about 3 Mb at 9q13 approximately q21 and a deletion of about 2 Mb at 12q22 containing SOCS2. These results show that close examination of translocations in hematopoietic diseases may reveal associated microdeletions. The role of these deletions is discussed.
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Affiliation(s)
- Anne Etienne
- UMR599 INSERM, Institut Paoli-Calmettes, Laboratoire d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille, 232 Bd. de Sainte-Marguerite, 13009 Marseille, France
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20
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Coe BP, Ylstra B, Carvalho B, Meijer GA, Macaulay C, Lam WL. Resolving the resolution of array CGH. Genomics 2007; 89:647-53. [PMID: 17276656 DOI: 10.1016/j.ygeno.2006.12.012] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Revised: 12/19/2006] [Accepted: 12/30/2006] [Indexed: 11/30/2022]
Abstract
Many recent technologies have been designed to supplant conventional metaphase CGH technology with the goal of refining the description of segmental copy number status throughout the genome. However, the emergence of new technologies has led to confusion as to how to describe adequately the capabilities of each array platform. The design of a CGH array can incorporate a uniform or a highly variable element distribution. This can lead to bias in the reporting of average or median resolutions, making it difficult to provide a fair comparison of platforms. In this report, we propose a new definition of resolution for array CGH technology, termed "functional resolution," that incorporates the uniformity of element spacing on the array, as well as the sensitivity of each platform to single-copy alterations. Calculation of these metrics is automated through the development of a Java-based application, "ResCalc," which is applicable to any array CGH platform.
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Affiliation(s)
- Bradley P Coe
- British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, Canada V5Z 1L3.
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21
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Cho EK, Tchinda J, Freeman JL, Chung YJ, Cai WW, Lee C. Array-based comparative genomic hybridization and copy number variation in cancer research. Cytogenet Genome Res 2006; 115:262-72. [PMID: 17124409 DOI: 10.1159/000095923] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 07/16/2006] [Indexed: 12/31/2022] Open
Abstract
Array-based comparative genomic hybridization (aCGH) is a molecular cytogenetic technique used in detecting and mapping DNA copy number alterations. aCGH is able to interrogate the entire genome at a previously unattainable, high resolution and has directly led to the recent appreciation of a novel class of genomic variation: copy number variation (CNV) in mammalian genomes. All forms of DNA variation/polymorphism are important for studying the basis of phenotypic diversity among individuals. CNV research is still at its infancy, requiring careful collation and annotation of accumulating CNV data that will undoubtedly be useful for accurate interpretation of genomic imbalances identified during cancer research.
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Affiliation(s)
- E K Cho
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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22
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Bayani J, Selvarajah S, Maire G, Vukovic B, Al-Romaih K, Zielenska M, Squire JA. Genomic mechanisms and measurement of structural and numerical instability in cancer cells. Semin Cancer Biol 2006; 17:5-18. [PMID: 17126026 DOI: 10.1016/j.semcancer.2006.10.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2006] [Accepted: 10/17/2006] [Indexed: 12/15/2022]
Abstract
The progression to cancer is often associated with instability and the acquisition of genomic heterogeneity, generating both clonal and non-clonal populations. Chromosomal instability (CIN) describes the excessive rate of numerical and structural genomic change in tumors. Mitotic segregation errors strongly influences copy number, while structural aberrations can occur at unstable genomic regions, or through aberrant DNA repair or methylation. Combined molecular cytogenetic analyses can evaluate cell-to-cell variation, and define the complexity of numerical and structural alterations. Because structural change may occur independently of numerical alteration, we propose the term structural chromosomal instability [(S)-CIN] to distinguish numerical from structural CIN.
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Affiliation(s)
- Jane Bayani
- Division of Applied Molecular Oncology, Princess Margaret Hospital, University Health Network, 610 University Avenue, Room 9-717, Toronto, Ontario, Canada M5G 2M9.
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