1
|
Kozmin SG, Dominska M, Zheng DQ, Petes TD. Splitting the yeast centromere by recombination. Nucleic Acids Res 2024; 52:690-707. [PMID: 37994724 PMCID: PMC10810202 DOI: 10.1093/nar/gkad1110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023] Open
Abstract
Although fusions between the centromeres of different human chromosomes have been observed cytologically in cancer cells, since the centromeres are long arrays of satellite sequences, the details of these fusions have been difficult to investigate. We developed methods of detecting recombination within the centromeres of the yeast Saccharomyces cerevisiae (intercentromere recombination). These events occur at similar rates (about 10-8/cell division) between two active or two inactive centromeres. We mapped the breakpoints of most of the recombination events to a region of 43 base pairs of uninterrupted homology between the two centromeres. By whole-genome DNA sequencing, we showed that most (>90%) of the events occur by non-reciprocal recombination (gene conversion/break-induced replication). We also found that intercentromere recombination can involve non-homologous chromosome, generating whole-arm translocations. In addition, intercentromere recombination is associated with very frequent chromosome missegregation. These observations support the conclusion that intercentromere recombination generally has negative genetic consequences.
Collapse
Affiliation(s)
- Stanislav G Kozmin
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | | | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| |
Collapse
|
2
|
Guin K, Chen Y, Mishra R, Muzaki SRBM, Thimmappa BC, O'Brien CE, Butler G, Sanyal A, Sanyal K. Spatial inter-centromeric interactions facilitated the emergence of evolutionary new centromeres. eLife 2020; 9:e58556. [PMID: 32469306 PMCID: PMC7292649 DOI: 10.7554/elife.58556] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Centromeres of Candida albicans form on unique and different DNA sequences but a closely related species, Candida tropicalis, possesses homogenized inverted repeat (HIR)-associated centromeres. To investigate the mechanism of centromere type transition, we improved the fragmented genome assembly and constructed a chromosome-level genome assembly of C. tropicalis by employing PacBio sequencing, chromosome conformation capture sequencing (3C-seq), chromoblot, and genetic analysis of engineered aneuploid strains. Further, we analyzed the 3D genome organization using 3C-seq data, which revealed spatial proximity among the centromeres as well as telomeres of seven chromosomes in C. tropicalis. Intriguingly, we observed evidence of inter-centromeric translocations in the common ancestor of C. albicans and C. tropicalis. Identification of putative centromeres in closely related Candida sojae, Candida viswanathii and Candida parapsilosis indicates loss of ancestral HIR-associated centromeres and establishment of evolutionary new centromeres (ENCs) in C. albicans. We propose that spatial proximity of the homologous centromere DNA sequences facilitated karyotype rearrangements and centromere type transitions in human pathogenic yeasts of the CUG-Ser1 clade.
Collapse
Affiliation(s)
- Krishnendu Guin
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | - Yao Chen
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Radha Mishra
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | | | - Bhagya C Thimmappa
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | - Caoimhe E O'Brien
- School Of Biomolecular & Biomed Science, Conway Institute of Biomolecular and Biomedical Research, University College DublinDublinIreland
| | - Geraldine Butler
- School Of Biomolecular & Biomed Science, Conway Institute of Biomolecular and Biomedical Research, University College DublinDublinIreland
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| |
Collapse
|
3
|
Barra V, Fachinetti D. The dark side of centromeres: types, causes and consequences of structural abnormalities implicating centromeric DNA. Nat Commun 2018; 9:4340. [PMID: 30337534 PMCID: PMC6194107 DOI: 10.1038/s41467-018-06545-y] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/06/2018] [Indexed: 12/18/2022] Open
Abstract
Centromeres are the chromosomal domains required to ensure faithful transmission of the genome during cell division. They have a central role in preventing aneuploidy, by orchestrating the assembly of several components required for chromosome separation. However, centromeres also adopt a complex structure that makes them susceptible to being sites of chromosome rearrangements. Therefore, preservation of centromere integrity is a difficult, but important task for the cell. In this review, we discuss how centromeres could potentially be a source of genome instability and how centromere aberrations and rearrangements are linked with human diseases such as cancer.
Collapse
Affiliation(s)
- V Barra
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005, Paris, France
| | - D Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005, Paris, France.
| |
Collapse
|
4
|
Wise SS, Aboueissa AEM, Martino J, Wise JP. Hexavalent Chromium-Induced Chromosome Instability Drives Permanent and Heritable Numerical and Structural Changes and a DNA Repair-Deficient Phenotype. Cancer Res 2018; 78:4203-4214. [PMID: 29880483 PMCID: PMC6072558 DOI: 10.1158/0008-5472.can-18-0531] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/03/2018] [Accepted: 06/04/2018] [Indexed: 11/16/2022]
Abstract
A key hypothesis for how hexavalent chromium [Cr(VI)] causes cancer is that it drives chromosome instability (CIN), which leads to neoplastic transformation. Studies show chronic Cr(VI) can affect DNA repair and induce centrosome amplification, which can lead to structural and numerical CIN. However, no studies have considered whether these outcomes are transient or permanent. In this study, we exposed human lung cells to particulate Cr(VI) for three sequential 24-hour periods, each separated by about a month. After each treatment, cells were seeded at colony-forming density, cloned, expanded, and retreated, creating three generations of clonal cell lines. Each generation of clones was tested for chromium sensitivity, chromosome complement, DNA repair capacity, centrosome amplification, and the ability to grow in soft agar. After the first treatment, Cr(VI)-treated clones exhibited a normal chromosome complement, but some clones showed a repair-deficient phenotype and amplified centrosomes. After the second exposure, more than half of the treated clones acquired an abnormal karyotype including numerical and structural alterations, with many exhibiting deficient DNA double-strand break repair and amplified centrosomes. The third treatment produced new abnormal clones, with previously abnormal clones acquiring additional abnormalities and most clones exhibiting repair deficiency. CIN, repair deficiency, and amplified centrosomes were all permanent and heritable phenotypes of repeated Cr(VI) exposure. These outcomes support the hypothesis that CIN is a key mechanism of Cr(VI)-induced carcinogenesis.Significance: Chromium, a major public health concern and human lung carcinogen, causes fundamental changes in chromosomes and DNA repair in human lung cells. Cancer Res; 78(15); 4203-14. ©2018 AACR.
Collapse
Affiliation(s)
- Sandra S Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky
| | | | - Julieta Martino
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky
| | - John Pierce Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky.
| |
Collapse
|
5
|
van den Broek E, van Lieshout S, Rausch C, Ylstra B, van de Wiel MA, Meijer GA, Fijneman RJ, Abeln S. GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes. F1000Res 2016; 5:2340. [PMID: 28713543 PMCID: PMC5500957 DOI: 10.12688/f1000research.9259.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/05/2017] [Indexed: 01/23/2023] Open
Abstract
Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of chromosomal segments in tumor genomes. However, there is lack of computational methods that systematically detect structural chromosomal aberrations by virtue of the genomic location of CNA-associated chromosomal breaks and identify genes that appear non-randomly affected by chromosomal breakpoints across (large) series of tumor samples. 'GeneBreak' is developed to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach, which can be applied to DNA copy number data obtained by array-Comparative Genomic Hybridization (CGH) or by (low-pass) whole genome sequencing (WGS). First, 'GeneBreak' collects the genomic locations of chromosomal CNA-associated breaks that were previously pinpointed by the segmentation algorithm that was applied to obtain CNA profiles. Next, a tailored annotation approach for breakpoint-to-gene mapping is implemented. Finally, dedicated cohort-based statistics is incorporated with correction for covariates that influence the probability to be a breakpoint gene. In addition, multiple testing correction is integrated to reveal recurrent breakpoint events. This easy-to-use algorithm, 'GeneBreak', is implemented in R ( www.cran.r-project.org) and is available from Bioconductor ( www.bioconductor.org/packages/release/bioc/html/GeneBreak.html).
Collapse
Affiliation(s)
- Evert van den Broek
- Department of Pathology, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, 1066CX, Netherlands
| | - Stef van Lieshout
- Department of Pathology, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
| | - Christian Rausch
- Department of Pathology, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, 1066CX, Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
| | - Mark A. van de Wiel
- Department of Epidemiology & Biostatistics, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
- Department of Mathematics, VU University Medical Center, Amsterdam, Amsterdam, 1081 HV, Netherlands
| | - Gerrit A. Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, 1066CX, Netherlands
| | - Remond J.A. Fijneman
- Department of Pathology, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, 1066CX, Netherlands
| | - Sanne Abeln
- Department of Computer Science, VU University Medical Center, Amsterdam, 1081 HV, Netherlands
| |
Collapse
|
6
|
van den Broek E, van Lieshout S, Rausch C, Ylstra B, van de Wiel MA, Meijer GA, Fijneman RJ, Abeln S. GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes. F1000Res 2016; 5:2340. [PMID: 28713543 PMCID: PMC5500957 DOI: 10.12688/f1000research.9259.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/14/2016] [Indexed: 06/02/2024] Open
Abstract
Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of chromosomal segments in tumor genomes. However, there is lack of computational methods that systematically detect structural chromosomal aberrations by virtue of the genomic location of CNA-associated chromosomal breaks and identify genes that appear non-randomly affected by chromosomal breakpoints across (large) series of tumor samples. 'GeneBreak' is developed to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach, which can be applied to DNA copy number data obtained by array-Comparative Genomic Hybridization (CGH) or by (low-pass) whole genome sequencing (WGS). First, 'GeneBreak' collects the genomic locations of chromosomal CNA-associated breaks that were previously pinpointed by the segmentation algorithm that was applied to obtain CNA profiles. Next, a tailored annotation approach for breakpoint-to-gene mapping is implemented. Finally, dedicated cohort-based statistics is incorporated with correction for covariates that influence the probability to be a breakpoint gene. In addition, multiple testing correction is integrated to reveal recurrent breakpoint events. This easy-to-use algorithm, 'GeneBreak', is implemented in R ( www.cran.r-project.org) and is available from Bioconductor ( www.bioconductor.org/packages/release/bioc/html/GeneBreak.html).
Collapse
Affiliation(s)
- Evert van den Broek
- Department of Pathology, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, 1066CX, Netherlands
| | - Stef van Lieshout
- Department of Pathology, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
| | - Christian Rausch
- Department of Pathology, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, 1066CX, Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
| | - Mark A. van de Wiel
- Department of Epidemiology & Biostatistics, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
- Department of Mathematics, VU University Medical Center, Amsterdam, Amsterdam, 1081 HV, Netherlands
| | - Gerrit A. Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, 1066CX, Netherlands
| | - Remond J.A. Fijneman
- Department of Pathology, VU University Medical Center, Amsterdam, 1081 HZ, Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, 1066CX, Netherlands
| | - Sanne Abeln
- Department of Computer Science, VU University Medical Center, Amsterdam, 1081 HV, Netherlands
| |
Collapse
|
7
|
Bosch LJW, Luo Y, Lao VV, Snaebjornsson P, Trooskens G, Vlassenbroeck I, Mongera S, Tang W, Welcsh P, Herman JG, Koopman M, Nagtegaal ID, Punt CJA, van Criekinge W, Meijer GA, Monnat RJ, Carvalho B, Grady WM. WRN Promoter CpG Island Hypermethylation Does Not Predict More Favorable Outcomes for Patients with Metastatic Colorectal Cancer Treated with Irinotecan-Based Therapy. Clin Cancer Res 2016; 22:4612-22. [PMID: 27121793 DOI: 10.1158/1078-0432.ccr-15-2703] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/26/2016] [Indexed: 01/28/2023]
Abstract
PURPOSE WRN promoter CpG island hypermethylation in colorectal cancer has been reported to increase sensitivity to irinotecan-based therapies. We aimed to characterize methylation of the WRN promoter, determine the effect of WRN promoter hypermethylation upon expression, and validate a previous report that WRN promoter hypermethylation predicts improved outcomes for patients with metastatic colorectal cancer (mCRC) treated with irinotecan-based therapy. EXPERIMENTAL DESIGN WRN methylation status was assessed using methylation-specific PCR and bisulfite sequencing assays. WRN expression was determined using qRT-PCR and Western blotting. WRN methylation status was correlated with overall survival (OS) and progression-free survival (PFS) in 183 patients with mCRC. Among these patients, 90 received capecitabine monotherapy as first-line therapy, and 93 received capecitabine plus irinotecan (CAPIRI) therapy as part of the CAIRO phase III clinical trial. RESULTS WRN mRNA and WRN protein expression levels were low in colorectal cancer cell lines and in primary colorectal cancer and were largely independent of WRN methylation status. Patients with methylated WRN colorectal cancer had a shorter OS compared with patients who had unmethylated WRN colorectal cancer (HR = 1.6; 95% confidence interval [CI], 1.2-2.2; P = 0.003). Patients with unmethylated WRN showed a significantly longer PFS when treated with CAPIRI compared with capecitabine alone (HR = 0.48; 95% CI, 0.32-0.70; P = 0.0001). In contrast, patients did not benefit from adding irinotecan to capecitabine when WRN was methylated (HR = 1.1; 95% CI, 0.69-1.77; P = 0.7). CONCLUSIONS WRN expression is largely independent of WRN promoter hypermethylation in colorectal cancer. Moreover, we could not validate the previous finding that WRN promoter hypermethylation predicts improved clinical outcomes of mCRC treated with irinotecan-based therapy and found instead the opposite result. Clin Cancer Res; 22(18); 4612-22. ©2016 AACR.
Collapse
Affiliation(s)
- Linda J W Bosch
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands. Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Yanxin Luo
- Clinical Research Division, Department of Medicine, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington. Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Victoria V Lao
- Clinical Research Division, Department of Medicine, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
| | - Petur Snaebjornsson
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands. Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Sandra Mongera
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Weiliang Tang
- Department of Pathology, University of Washington, Seattle Washington
| | - Piri Welcsh
- Department of Pathology, University of Washington, Seattle Washington
| | - James G Herman
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cornelis J A Punt
- Department of Medical Oncology, Academic Medical Center, Amsterdam, the Netherlands
| | - Wim van Criekinge
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands. Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands. Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium. MDxHealth SA, Liège, Belgium
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands. Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Raymond J Monnat
- Department of Pathology, University of Washington, Seattle Washington. Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Beatriz Carvalho
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands. Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - William M Grady
- Clinical Research Division, Department of Medicine, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington.
| |
Collapse
|
8
|
Gollin SM. Cytogenetic alterations and their molecular genetic correlates in head and neck squamous cell carcinoma: a next generation window to the biology of disease. Genes Chromosomes Cancer 2014; 53:972-90. [PMID: 25183546 DOI: 10.1002/gcc.22214] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 08/15/2014] [Indexed: 01/14/2023] Open
Abstract
Cytogenetic alterations underlie the development of head and neck squamous cell carcinoma (HNSCC), whether tobacco and alcohol use, betel nut chewing, snuff or human papillomavirus (HPV) causes the disease. Many of the molecular genetic aberrations in HNSCC result from these cytogenetic alterations. This review presents a brief introduction to the epidemiology of HNSCC, and discusses the role of HPV in the disease, cytogenetic alterations and their frequencies in HNSCC, their molecular genetic and The Cancer Genome Atlas (TCGA) correlates, prognostic implications, and possible therapeutic considerations. The most frequent cytogenetic alterations in HNSCC are gains of 5p14-15, 8q11-12, and 20q12-13, gains or amplifications of 3q26, 7p11, 8q24, and 11q13, and losses of 3p, 4q35, 5q12, 8p23, 9p21-24, 11q14-23, 13q12-14, 18q23, and 21q22. To understand their effects on tumor cell biology and response to therapy, the cytogenetic findings in HNSCC are increasingly being examined in the context of the biochemical pathways they disrupt. The goal is to minimize morbidity and mortality from HNSCC using cytogenetic abnormalities to identify valuable diagnostic biomarkers for HNSCC, prognostic biomarkers of tumor behavior, recurrence risk, and outcome, and predictive biomarkers of therapeutic response to identify the most efficacious treatment for each individual patient's tumor, all based on a detailed understanding of the next generation biology of HNSCC.
Collapse
Affiliation(s)
- Susanne M Gollin
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA; Departments of Otolaryngology and Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA; University of Pittsburgh Cancer Institute, Pittsburgh, PA
| |
Collapse
|
9
|
García Martínez J, García-Inclán C, Suárez C, Llorente JL, Hermsen MA. DNA aneuploidy-specific therapy for head and neck squamous cell carcinoma. Head Neck 2014; 37:884-8. [DOI: 10.1002/hed.23687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 11/22/2013] [Accepted: 03/08/2014] [Indexed: 11/09/2022] Open
Affiliation(s)
- Jorge García Martínez
- Department of Otolaryngology; Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias; Oviedo Asturias Spain
| | - Cristina García-Inclán
- Department of Otolaryngology; Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias; Oviedo Asturias Spain
| | - Carlos Suárez
- Department of Otolaryngology; Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias; Oviedo Asturias Spain
| | - José L. Llorente
- Department of Otolaryngology; Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias; Oviedo Asturias Spain
| | - Mario A. Hermsen
- Department of Otolaryngology; Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias; Oviedo Asturias Spain
| |
Collapse
|
10
|
Localization of centromeric breaks in head and neck squamous cell carcinoma. Cancer Genet 2012; 205:622-9. [DOI: 10.1016/j.cancergen.2012.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 10/01/2012] [Accepted: 10/02/2012] [Indexed: 11/20/2022]
|
11
|
Voorham QJ, Carvalho B, Spiertz AJ, van Grieken NC, Mongera S, Rondagh EJ, van de Wiel MA, Jordanova ES, Ylstra B, Kliment M, Grabsch H, Rembacken BJ, Arai T, de Bruïne AP, Sanduleanu S, Quirke P, Mulder CJ, van Engeland M, Meijer GA. Chromosome 5q Loss in Colorectal Flat Adenomas. Clin Cancer Res 2012; 18:4560-9. [DOI: 10.1158/1078-0432.ccr-11-2385] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
12
|
Hypomethylation of LINE-1, and not centromeric SAT-α, is associated with centromeric instability in head and neck squamous cell carcinoma. Cell Oncol (Dordr) 2012; 35:259-67. [DOI: 10.1007/s13402-012-0085-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2012] [Indexed: 10/28/2022] Open
|
13
|
Leone PE, González MB, Elosua C, Gómez-Moreta JA, Lumbreras E, Robledo C, Santos-Briz A, Valero JM, de la Guardia RD, Gutiérrez NC, Hernández JM, García JL. Integration of Global Spectral Karyotyping, CGH Arrays, and Expression Arrays Reveals Important Genes in the Pathogenesis of Glioblastoma Multiforme. Ann Surg Oncol 2012; 19:2367-79. [DOI: 10.1245/s10434-011-2202-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Indexed: 12/17/2022]
|
14
|
Coca-Pelaz A, Llorente-Pendás JL, García-Martínez J, Vivanco-Allende B, Balbín M, Suárez C, Hermsen M. Medullary thyroid carcinoma and 2q37 deletion in a patient with nevoid basal cell carcinoma syndrome: clinical description and genetic analysis. Head Neck 2012; 35:E147-52. [PMID: 22319002 DOI: 10.1002/hed.22000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2011] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Nevoid basal cell carcinoma syndrome (NBCCS) is a rare, inheritable, multisystem disorder characterized by numerous basal cell carcinomas (BCCs), maxillary keratocyst, and musculoskeletal malformations. Occasionally, it is associated with malignancies like rhabdomyoma, melanoma, and sinonasal undifferentiated carcinoma, to name a few. METHODS A patient presented with NBCCS with a medullary thyroid carcinoma. Clinical, surgical details, and germline genetic analysis are herein described. RESULTS A 32-year-old woman was referred to our department with suspicion of medullary thyroid carcinoma, which was confirmed by histopathological examination. The patient was diagnosed as also having NBCCS. Germline mutation analysis indicated wild-type genes PTCH1 and RET. DNA copy number analysis by high resolution microarray comparative genomic hybridization (CGH) revealed a small interstitial loss at chromosomal band 2q37.3. CONCLUSION To our knowledge, this is the first described patient with NBCCS carrying a medullary thyroid carcinoma and a 2q37 deletion, which confirms that this syndrome can be associated with many different malignancies.
Collapse
Affiliation(s)
- Andrés Coca-Pelaz
- Department of Otolaryngology, Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Spain.
| | | | | | | | | | | | | |
Collapse
|
15
|
Backsch C, Pauly B, Liesenfeld M, Scheungraber C, Gajda M, Mrasek K, Liehr T, Clad A, Schrock E, Runnebaum IB, Dürst M. Two novel unbalanced whole arm translocations are frequently detected in cervical squamous cell carcinoma. Cancer Genet 2011; 204:646-53. [DOI: 10.1016/j.cancergen.2011.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Revised: 10/14/2011] [Accepted: 10/16/2011] [Indexed: 11/16/2022]
|
16
|
Bosch LJW, Oort FA, Neerincx M, Khalid-de Bakker CAJ, Terhaar sive Droste JS, Melotte V, Jonkers DMAE, Masclee AAM, Mongera S, Grooteclaes M, Louwagie J, van Criekinge W, Coupé VMH, Mulder CJ, van Engeland M, Carvalho B, Meijer GA. DNA methylation of phosphatase and actin regulator 3 detects colorectal cancer in stool and complements FIT. Cancer Prev Res (Phila) 2011; 5:464-72. [PMID: 22135045 DOI: 10.1158/1940-6207.capr-11-0315] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Using a bioinformatics-based strategy, we set out to identify hypermethylated genes that could serve as biomarkers for early detection of colorectal cancer (CRC) in stool. In addition, the complementary value to a Fecal Immunochemical Test (FIT) was evaluated. Candidate genes were selected by applying cluster alignment and computational analysis of promoter regions to microarray-expression data of colorectal adenomas and carcinomas. DNA methylation was measured by quantitative methylation-specific PCR on 34 normal colon mucosa, 71 advanced adenoma, and 64 CRC tissues. The performance as biomarker was tested in whole stool samples from in total 193 subjects, including 19 with advanced adenoma and 66 with CRC. For a large proportion of these series, methylation data for GATA4 and OSMR were available for comparison. The complementary value to FIT was measured in stool subsamples from 92 subjects including 44 with advanced adenoma or CRC. Phosphatase and Actin Regulator 3 (PHACTR3) was identified as a novel hypermethylated gene showing more than 70-fold increased DNA methylation levels in advanced neoplasia compared with normal colon mucosa. In a stool training set, PHACTR3 methylation showed a sensitivity of 55% (95% CI: 33-75) for CRC and a specificity of 95% (95% CI: 87-98). In a stool validation set, sensitivity reached 66% (95% CI: 50-79) for CRC and 32% (95% CI: 14-57) for advanced adenomas at a specificity of 100% (95% CI: 86-100). Adding PHACTR3 methylation to FIT increased sensitivity for CRC up to 15%. PHACTR3 is a new hypermethylated gene in CRC with a good performance in stool DNA testing and has complementary value to FIT.
Collapse
Affiliation(s)
- Linda J W Bosch
- Department of Pathology, VU University Medical Center, 1007 MB, Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Bhattacharya A, Roy R, Snijders AM, Hamilton G, Paquette J, Tokuyasu T, Bengtsson H, Jordan RCK, Olshen AB, Pinkel D, Schmidt BL, Albertson DG. Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis. Clin Cancer Res 2011; 17:7024-34. [PMID: 22068658 DOI: 10.1158/1078-0432.ccr-11-1944] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Problems in management of oral cancers or precancers include identification of patients at risk for metastasis, tumor recurrence, and second primary tumors or risk for progression of precancers (dysplasia) to cancer. Thus, the objective of this study was to clarify the role of genomic aberrations in oral cancer progression and metastasis. EXPERIMENTAL DESIGN The spectrum of copy number alterations in oral dysplasia and squamous cell carcinomas (SCC) was determined by array comparative genomic hybridization. Associations with clinical characteristics were studied and results confirmed in an independent cohort. RESULTS The presence of one or more of the chromosomal aberrations +3q24-qter, -8pter-p23.1, +8q12-q24.2, and +20 distinguishes a major subgroup (70%-80% of lesions, termed 3q8pq20 subtype) from the remainder (20%-30% of lesions, non-3q8pq20). The 3q8pq20 subtype is associated with chromosomal instability and differential methylation in the most chromosomally unstable tumors. The two subtypes differ significantly in clinical outcome with risk for cervical (neck) lymph node metastasis almost exclusively associated with the 3q8pq20 subtype in two independent oral SCC cohorts. CONCLUSIONS Two subtypes of oral lesions indicative of at least two pathways for oral cancer development were distinguished that differ in chromosomal instability and risk for metastasis, suggesting that +3q,-8p, +8q, and +20 constitute a biomarker with clinical utility for identifying patients at risk for metastasis. Moreover, although increased numbers of genomic alterations can be harbingers of progression to cancer, dysplastic lesions lacking copy number changes cannot be considered benign as they are potential precursors to non-3q8pq20 locally invasive, yet not metastatic oral SCC.
Collapse
Affiliation(s)
- Aditi Bhattacharya
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Martínez-A C, van Wely KHM. Centromere fission, not telomere erosion, triggers chromosomal instability in human carcinomas. Carcinogenesis 2011; 32:796-803. [PMID: 21478459 PMCID: PMC3106440 DOI: 10.1093/carcin/bgr069] [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: 01/16/2023] Open
Abstract
The majority of sporadic carcinomas suffer from a kind of genetic instability in which chromosome number changes occur together with segmental defects. This means that changes involving intact chromosomes accompany breakage-induced alterations. Whereas the causes of aneuploidy are described in detail, the origins of chromosome breakage in sporadic carcinomas remain disputed. The three main pathways of chromosomal instability (CIN) proposed until now (random breakage, telomere fusion and centromere fission) are largely based on animal models and in vitro experiments, and recent studies revealed several discrepancies between animal models and human cancer. Here, we discuss how the experimental systems translate to human carcinomas and compare the theoretical breakage products to data from patient material and cancer cell lines. The majority of chromosomal defects in human carcinomas comprises pericentromeric breaks that are captured by healthy telomeres, and only a minor proportion of chromosome fusions can be attributed to telomere erosion or random breakage. Centromere fission, not telomere erosion, is therefore the most probably trigger of CIN and early carcinogenesis. Similar centromere–telomere fusions might drive a subset of congenital defects and evolutionary chromosome changes.
Collapse
Affiliation(s)
- Carlos Martínez-A
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, UAM Campus Cantoblanco, 28049 Madrid, Spain
| | | |
Collapse
|
19
|
Pérez-Escuredo J, García Martínez J, García-Inclán C, Vivanco B, Costales M, Álvarez Marcos C, Llorente JL, Hermsen MA. Establishment and genetic characterization of an immortal tumor cell line derived from intestinal-type sinonasal adenocarcinoma. Cell Oncol (Dordr) 2011; 34:23-31. [PMID: 21360264 DOI: 10.1007/s13402-010-0002-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2010] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Intestinal-type sinonasal adenocarcinoma (ITAC) is a rare tumor etiologically related to professional exposure to wood dust. The overall prognosis is poor, mainly due to the difficulty to resect the tumor completely in this anatomically complex region. Therefore, there is great need for alternative treatments. However, the lack of a good tumor model system for ITAC has hampered the development and testing of new therapeutic agents. Here, we report the establishment and characterization of the first human ITAC cell line named ITAC-3. METHODS The cell line was initiated from small explants of a T4bN0M0 colonic type ITAC from the ethmoid sinus. Growth and invasion parameters as well as genetic characteristics were analyzed. RESULTS The population doubling time was 18 h and the cell line was capable of invasion in matrigel. Chromosomal analysis showed a tetraploid karyotype with both numerical and structural aberrations. High resolution microarray CGH analysis identified many copy number alterations, including homozygous deletions. TP53 carried a mutation c.818G>T in exon eight concurring with a strong nuclear protein overexpression. Immunohistochemical analysis showed protein overexpression of EGFR and normal expression of β-catenin and p16. CONCLUSION This is the first report of the establishment of a cell line derived from a primary ITAC. The genomic profile of the cell line was the same as the primary tumor from which it was derived. This new cell line will be a useful tool for the development and testing of new therapeutic agents for this tumor type.
Collapse
Affiliation(s)
- Jhudit Pérez-Escuredo
- Department of Otolaryngology, IUOPA, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain.
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Secades P, Rodrigo JP, Hermsen M, Alvarez C, Suarez C, Chiara MD. Increase in gene dosage is a mechanism of HIF-1alpha constitutive expression in head and neck squamous cell carcinomas. Genes Chromosomes Cancer 2009; 48:441-54. [PMID: 19235921 DOI: 10.1002/gcc.20652] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The HIF-1alpha protein plays a key role in the cellular response to hypoxia via transcriptional regulation of genes involved in erythropoiesis, angiogenesis, and metabolism. Overexpression of HIF-1alpha is commonly found in solid tumors in significant association with increased patient mortality and resistance to therapy. The predominant mode of HIF-1alpha regulation by hypoxia occurs at the level of protein stability. In addition to hypoxia, HIF-1alpha protein stability and synthesis is regulated by nonhypoxic signals such as inactivation of tumor suppressors and activation of oncogenes. Here, we show that an increase in gene dosage may contribute to HIF-1alpha mRNA and protein overexpression in a nonhypoxic environment in head and neck squamous cell carcinomas (HNSCC). Increased HIF-1alpha gene dosage was found in one out of five HNSCC-derived cell lines and three out of 27 HNSCC primary tumors. Significantly, increased gene dosage in those samples was associated with high HIF-1alpha mRNA and protein levels. Normoxic overexpression of HIF-1alpha protein in HNSCC-derived cell lines was also paralleled by higher expression levels of HIF-1alpha target genes. Array CGH analysis confirmed the copy number increase of HIF-1alpha gene and revealed that the gene is contained within a region of amplification at 14q23-q24.2 both in the cell line and primary tumors. In addition, FISH analysis revealed the presence of 11-13 copies on a tetraploid background in SCC2 cells. These data suggest that increased HIF-1alpha gene dosage is a mechanism of HIF-1alpha protein overexpression in HNSCC that possibly prepares the cells for a higher activity in an intratumoral hypoxic environment.
Collapse
Affiliation(s)
- Pablo Secades
- Servicio de Otorrinolaringología, Hospital Universitario Central de Asturias
| | | | | | | | | | | |
Collapse
|
21
|
Snijders AM, Hermsen MA, Baughman J, Buffart TE, Huey B, Gajduskova P, Roydasgupta R, Tokuyasu T, Meijer GA, Fridlyand J, Albertson DG. Acquired genomic aberrations associated with methotrexate resistance vary with background genomic instability. Genes Chromosomes Cancer 2008; 47:71-83. [PMID: 17943968 DOI: 10.1002/gcc.20509] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Tumors vary widely in chromosomal level genome instability. To gain a better understanding of the underlying defects which foster specific types of aberrations, we investigated the response of cells of related genetic backgrounds to challenge with methotrexate. We studied mismatch repair deficient HCT116 cells, two derivatives also deficient in XRCC5 (HCT116 Ku86+/-) or BLM (HCT116 BLM-/-), and mismatch repair competent HCT116+chr3 cells. We show that colony formation occurred at a significantly higher frequency in HCT116 cells and HCT116 Ku86+/- cells compared to HCT116 BLM-/- and HCT116+chr3 cells. Visible colonies arose most rapidly in HCT116 Ku86+/- cells, whereas they formed most slowly in HCT116+chr3 cells. Copy number changes acquired by the methotrexate resistant HCT116 and HCT116 BLM-/- cells most often included whole chromosome gains or losses or no acquired copy number changes, whereas resistance in HCT116+chr3 and HCT116 Ku86+/- cells was associated with amplification of DHFR and copy number transitions leading to increased copy number of DHFR, respectively. The additional copies of DHFR were present on unstable chromosomes and organized as inverted repeats in HCT116+chr3 cells, while they were most often present as direct repeats in HCT116 Ku86+/- cells. These observations suggest that different mutational mechanisms promote drug resistance in these genetic backgrounds; mismatch repair deficiency in HCT116, high rates of chromosomal instability in HCT116 Ku86+/-, and low rates of chromosomal instability in HCT116+chr3. On the other hand, it appears that loss of BLM function suppresses the mismatch repair mutator mechanism in mismatch repair and BLM deficient HCT116 BLM-/- cells.
Collapse
Affiliation(s)
- Antoine M Snijders
- Cancer Research Institute, University of California San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Jenkins RB, Blair H, Ballman KV, Giannini C, Arusell RM, Law M, Flynn H, Passe S, Felten S, Brown PD, Shaw EG, Buckner JC. A t(1;19)(q10;p10) mediates the combined deletions of 1p and 19q and predicts a better prognosis of patients with oligodendroglioma. Cancer Res 2006; 66:9852-61. [PMID: 17047046 DOI: 10.1158/0008-5472.can-06-1796] [Citation(s) in RCA: 504] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Combined deletion of chromosomes 1p and 19q is associated with improved prognosis and responsiveness to therapy in patients with anaplastic oligodendroglioma. The deletions usually involve whole chromosome arms, suggesting a t(1;19)(q10;p10). Using stem cell medium, we cultured a few tumors. Paraffin-embedded tissue was obtained from 21 Mayo Clinic patients and 98 patients enrolled in 2 North Central Cancer Treatment Group (NCCTG) low-grade glioma trials. Interphase fusion of CEP1 and 19p12 probes detected the t(1;19). 1p/19q deletions were evaluated by fluorescence in situ hybridization. Upon culture, one oligodendroglioma contained an unbalanced 45,XX,t(1;19)(q10;p10). CEP1/19p12 fusion was observed in all metaphases and 74% of interphase nuclei. Among Mayo Clinic oligodendrogliomas, the prevalence of fusion was 81%. Among NCCTG patients, CEP1/19p12 fusion prevalence was 55%, 47%, and 0% among the oligodendrogliomas, mixed oligoastrocytomas, and astrocytomas, respectively. Ninety-one percent of NCCTG gliomas with 1p/19q deletion and 12% without 1p/19q deletion had CEP1/19p12 fusion (P < 0.001, chi(2) test). The median overall survival (OS) for all patients was 8.1 years without fusion and 11.9 years with fusion (P = 0.003). The median OS for patients with low-grade oligodendroglioma was 9.1 years without fusion and 13.0 years with fusion (P = 0.01). Similar significant median OS differences were observed for patients with combined 1p/19q deletions. The absence of alterations was associated with a significantly shorter OS for patients who received higher doses of radiotherapy. Our results strongly suggest that a t(1;19)(q10;p10) mediates the combined 1p/19q deletion in human gliomas. Like combined 1p/19q deletion, the 1;19 translocation is associated with superior OS and progression-free survival in low-grade glioma patients.
Collapse
|
23
|
Schrock E, Zschieschang P, O'Brien P, Helmrich A, Hardt T, Matthaei A, Stout-Weider K. Spectral karyotyping of human, mouse, rat and ape chromosomes--applications for genetic diagnostics and research. Cytogenet Genome Res 2006; 114:199-221. [PMID: 16954656 DOI: 10.1159/000094203] [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: 05/08/2006] [Accepted: 05/19/2006] [Indexed: 01/30/2023] Open
Abstract
Spectral karyotyping (SKY) is a widely used methodology to identify genetic aberrations. Multicolor fluorescence in situ hybridization using chromosome painting probes in individual colors for all metaphase chromosomes at once is combined with a unique spectral measurement and analysis system to automatically classify normal and aberrant chromosomes. Based on countless studies and investigations in many laboratories worldwide, numerous new chromosome translocations and other aberrations have been identified in clinical and tumor cytogenetics. Thus, gene identification studies have been facilitated resulting in the dissection of tumor development and progression. For example, different translocation partners of the TEL/ETV6 transcription factor that is specially required for hematopoiesis within the bone marrow were identified. Also, the correct classification of complex karyotypes of solid tumors supports the prognostication of cancer patients. Important accomplishments for patients with genetic diseases, leukemias and lymphomas, mesenchymal tumors and solid cancers are summarized and exemplified. Furthermore, studies of disease mechanisms such as centromeric DNA breakage, DNA double strand break repair, telomere shortening and radiation-induced neoplastic transformation have been accompanied by SKY analyses. Besides the hybridization of human chromosomes, mouse karyotyping has also contributed to the comprehensive characterization of mouse models of human disease and for gene therapy studies.
Collapse
Affiliation(s)
- E Schrock
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
| | | | | | | | | | | | | |
Collapse
|
24
|
Uchida K, Oga A, Okafuji M, Mihara M, Kawauchi S, Furuya T, Chochi Y, Ueyama Y, Sasaki K. Molecular cytogenetic analysis of oral squamous cell carcinomas by comparative genomic hybridization, spectral karyotyping, and fluorescence in situ hybridization. ACTA ACUST UNITED AC 2006; 167:109-16. [PMID: 16737909 DOI: 10.1016/j.cancergencyto.2006.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Revised: 01/18/2006] [Accepted: 01/25/2006] [Indexed: 11/28/2022]
Abstract
We investigated relationships between DNA copy number aberrations and chromosomal structural rearrangements in 11 different cell lines derived from oral squamous cell carcinoma (OSCC) by comparative genomic hybridization (CGH), spectral karyotyping (SKY), and fluorescence in situ hybridization (FISH). CGH frequently showed recurrent chromosomal gains of 5p, 20q12, 8q23 approximately qter, 20p11 approximately p12, 7p15, 11p13 approximately p14, and 14q21, as well as losses of 4q, 18q, 4p11 approximately p15, 19p13, 8p21 approximately pter, and 16p11 approximately p12. SKY identified the following recurrent chromosomal abnormalities: i(5)(p10), i(5)(q10), i(8)(q10), der(X;1)(q10;p10), der(3;5)(p10;p10), and der(3;18)(q10;p10). In addition, breakpoints detected by SKY were clustered in 11q13 and around centromeric regions, including 5p10/q10, 3p10/q10, 8p10/q10 14q10, 1p10/1q10, and 16p10/16q10. Cell lines with i(5)(p10) and i(8)(q10) showed gains of the entire chromosome arms of 5p and 8q by CGH. Moreover, breakages near the centromeres of chromosomes 5 and 8 may be associated with 5p gain, 8q gain, and 8p loss in OSCC. FISH with a DNA probe from a BAC clone mapping to 5p15 showed a significant correlation between the average numbers of i(5)(p10) and 5p15 (R(2) = 0.8693, P< 0.01) in these cell lines, indicating that DNA copy number of 5p depends upon isochromosome formation in OSCC.
Collapse
Affiliation(s)
- Kenichiro Uchida
- Department of Oral and Maxillofacial Surgery, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Alsop AE, Teschendorff AE, Edwards PAW. Distribution of breakpoints on chromosome 18 in breast, colorectal, and pancreatic carcinoma cell lines. ACTA ACUST UNITED AC 2006; 164:97-109. [PMID: 16434311 DOI: 10.1016/j.cancergencyto.2005.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2005] [Revised: 09/20/2005] [Accepted: 09/22/2005] [Indexed: 10/25/2022]
Abstract
Chromosome 18 is frequently rearranged in carcinomas. We explored the distribution of breakpoints affecting chromosome 18 by mapping 56 breakpoints in 26 carcinoma cell lines by fluorescence in situ hybridization (FISH) using bacterial artificial chromosomes (BACs) and band paints. The distribution of breaks among 18 intervals of chromosome 18 was significantly nonrandom. The interval spanning the centromere contained the greatest number of breaks and had the highest average copy number of any interval. There was a high density of breaks close to the centromere as well as actually within the centromere. A cluster of breaks encompassing SMAD4 was associated with the minimum average copy number, consistent with SMAD4 being a tumor suppressor gene. There may be another cluster of breaks around 18q12. We offer two interpretations of the concentration of breaks near the centromere. It may reflect selection for an oncogene near the centromere, or there may be an underlying bias of breakage toward the centromere. We show that the latter is predicted by a simple model that invokes random breakage following anchorage of some random point on the chromosome, or selection of breaks proximal to one of several tumor suppressor genes.
Collapse
Affiliation(s)
- Amber E Alsop
- Cancer Genomics Program, Hutchison-MRC Research Centre, Department of Pathology and Oncology, University of Cambridge, Hills Road, Cambridge CB2 2XZ, United Kingdom
| | | | | |
Collapse
|
26
|
Davison EJ, Tarpey PS, Fiegler H, Tomlinson IPM, Carter NP. Deletion at chromosome band 20p12.1 in colorectal cancer revealed by high resolution array comparative genomic hybridization. Genes Chromosomes Cancer 2005; 44:384-91. [PMID: 16110499 DOI: 10.1002/gcc.20252] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Array comparative genomic hybridization (Array CGH) with tiling path resolution for a approximately 4.61 Mb region of chromosome band 20p12.1 has been used to investigate copy number loss in 48 colorectal cancer cell lines and 37 primary colorectal cancers. A recurrent deletion was detected in 55% of cell lines and 23% of primary cancers and the consensus minimum region of loss was identified as a approximately 190 kb section from 14.85 Mb to 15.04 Mb of chromosome 20. Two noncoding RNA genes located in the region, BA318C17.1 and DJ974N19.1, were investigated by mutation analysis and real-time PCR in colorectal cancer cell lines. Sequence changes in BA318C17.1 and reduced expression of both genes was detected, suggesting that the abrogation of these genes may play a role in colorectal tumorigenesis.
Collapse
Affiliation(s)
- Eleanor J Davison
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
| | | | | | | | | |
Collapse
|