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Gender-associated genomic differences in colorectal cancer: clinical insight from feminization of male cancer cells. Int J Mol Sci 2014; 15:17344-65. [PMID: 25268611 PMCID: PMC4227166 DOI: 10.3390/ijms151017344] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 12/19/2022] Open
Abstract
Gender-related differences in colorectal cancer (CRC) are not fully understood. Recent studies have shown that CRC arising in females are significantly associated with CpG island methylator phenotype (CIMP-high). Using array comparative genomic hybridization, we analyzed a cohort of 116 CRCs (57 males, 59 females) for chromosomal copy number aberrations (CNA) and found that CRC in females had significantly higher numbers of gains involving chromosome arms 1q21.2–q21.3, 4q13.2, 6p21.1 and 16p11.2 and copy number losses of chromosome arm 11q25 compared to males. Interestingly, a subset of male CRCs (46%) exhibited a “feminization” phenomenon in the form of gains of X chromosomes (or an arm of X) and/or losses of the Y chromosome. Feminization of cancer cells was significantly associated with microsatellite-stable CRCs (p-value 0.003) and wild-type BRAF gene status (p-value 0.009). No significant association with other clinicopathological parameters was identified including disease-free survival. In summary, our data show that some CNAs in CRC may be gender specific and that male cancers characterized by feminization may constitute a specific subset of CRCs that warrants further investigation.
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An integrative CGH, MSI and candidate genes methylation analysis of colorectal tumors. PLoS One 2014; 9:e82185. [PMID: 24475022 PMCID: PMC3903472 DOI: 10.1371/journal.pone.0082185] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/21/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Different DNA aberrations processes can cause colorectal cancer (CRC). Herein, we conducted a comprehensive molecular characterization of 27 CRCs from Iranian patients. MATERIALS AND METHODS Array CGH was performed. The MSI phenotype and the methylation status of 15 genes was established using MSP. The CGH data was compared to two established lists of 41 and 68 cancer genes, respectively, and to CGH data from African Americans. A maximum parsimony cladogram based on global aberrations was established. RESULTS The number of aberrations seem to depend on the MSI status. MSI-H tumors displayed the lowest number of aberrations. MSP revealed that most markers were methylated, except RNF182 gene. P16 and MLH1 genes were primarily methylated in MSI-H tumors. Seven markers with moderate to high frequency of methylation (SYNE1, MMP2, CD109, EVL, RET, LGR and PTPRD) had very low levels of chromosomal aberrations. All chromosomes were targeted by aberrations with deletions more frequent than amplifications. The most amplified markers were CD248, ERCC6, ERGIC3, GNAS, MMP2, NF1, P2RX7, SFRS6, SLC29A1 and TBX22. Most deletions were noted for ADAM29, CHL1, CSMD3, FBXW7, GALNS, MMP2, NF1, PRKD1, SMAD4 and TP53. Aberrations targeting chromosome X were primarily amplifications in male patients and deletions in female patients. A finding similar to what we reported for African American CRC patients. CONCLUSION This first comprehensive analysis of CRC Iranian tumors reveals a high MSI rate. The MSI tumors displayed the lowest level of chromosomal aberrations but high frequency of methylation. The MSI-L were predominantly targeted with chromosomal instability in a way similar to the MSS tumors. The global chromosomal aberration profiles showed many similarities with other populations but also differences that might allow a better understanding of CRC's clinico-pathological specifics in this population.
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Dulak AM, Schumacher S, van Lieshout J, Imamura Y, Fox C, Shim B, Ramos A, Saksena G, Baca S, Baselga J, Tabernero J, Barretina J, Enzinger P, Corso G, Roviello F, Lin L, Bandla S, Luketich J, Pennathur A, Meyerson M, Ogino S, Shivdasani RA, Beer DG, Godfrey TE, Beroukhim R, Bass AJ. Gastrointestinal adenocarcinomas of the esophagus, stomach, and colon exhibit distinct patterns of genome instability and oncogenesis. Cancer Res 2012; 72:4383-93. [PMID: 22751462 PMCID: PMC3432726 DOI: 10.1158/0008-5472.can-11-3893] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A more detailed understanding of the somatic genetic events that drive gastrointestinal adenocarcinomas is necessary to improve diagnosis and therapy. Using data from high-density genomic profiling arrays, we conducted an analysis of somatic copy-number aberrations in 486 gastrointestinal adenocarcinomas including 296 esophageal and gastric cancers. Focal amplifications were substantially more prevalent in gastric/esophageal adenocarcinomas than colorectal tumors. We identified 64 regions of significant recurrent amplification and deletion, some shared and others unique to the adenocarcinoma types examined. Amplified genes were noted in 37% of gastric/esophageal tumors, including in therapeutically targetable kinases such as ERBB2, FGFR1, FGFR2, EGFR, and MET, suggesting the potential use of genomic amplifications as biomarkers to guide therapy of gastric and esophageal cancers where targeted therapeutics have been less developed compared with colorectal cancers. Amplified loci implicated genes with known involvement in carcinogenesis but also pointed to regions harboring potentially novel cancer genes, including a recurrent deletion found in 15% of esophageal tumors where the Runt transcription factor subunit RUNX1 was implicated, including by functional experiments in tissue culture. Together, our results defined genomic features that were common and distinct to various gut-derived adenocarcinomas, potentially informing novel opportunities for targeted therapeutic interventions.
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Affiliation(s)
- Austin M Dulak
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142 U.S.A
| | - Steve Schumacher
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142 U.S.A
| | - Jasper van Lieshout
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
| | - Yu Imamura
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
| | - Cameron Fox
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
| | - Byoungyong Shim
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
| | - Alex Ramos
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142 U.S.A
| | - Gordon Saksena
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142 U.S.A
| | - Sylvan Baca
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142 U.S.A
| | - Jose Baselga
- Division of Hematology and Oncology, Massachusetts General Hospital, Boston MA 02114 U.S.A
- Department of Medicine, Harvard Medical School, Boston, MA 02115 U.S.A
| | - Josep Tabernero
- Department of Medical Oncology, Hospital Vall d’Hebron, Passeig Vall d’Hebron, 119-129, 08035 Barcelona Spain
| | - Jordi Barretina
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142 U.S.A
| | - Peter Enzinger
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
- Department of Medicine, Harvard Medical School, Boston, MA 02115 U.S.A
| | - Giovanni Corso
- Department of Human Pathology and Oncology Section of Surgical Oncology, ITT Istituto Toscano Tumori, Siena Italy
| | - Franco Roviello
- Department of Human Pathology and Oncology Section of Surgical Oncology, ITT Istituto Toscano Tumori, Siena Italy
| | - Lin Lin
- Section of Thoracic Surgery, Department of Surgery and Department of Pathology, University of Michigan, Ann Arbor, Ann Arbor, MI, 48109 U.S.A
| | - Santhoshi Bandla
- Department of Surgery, University of Rochester, Rochester, NY, 14642 U.S.A
| | - James Luketich
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213
| | - Arjun Pennathur
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213
| | - Matthew Meyerson
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142 U.S.A
- Department of Pathology, Harvard Medical School, Boston, MA 02115 U.S.A
| | - Shuji Ogino
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
- Department of Pathology, Harvard Medical School, Boston, MA 02115 U.S.A
| | - Ramesh A Shivdasani
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
- Department of Medicine, Harvard Medical School, Boston, MA 02115 U.S.A
| | - David G Beer
- Section of Thoracic Surgery, Department of Surgery and Department of Pathology, University of Michigan, Ann Arbor, Ann Arbor, MI, 48109 U.S.A
| | - Tony E Godfrey
- Department of Surgery, University of Rochester, Rochester, NY, 14642 U.S.A
| | - Rameen Beroukhim
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142 U.S.A
- Department of Medicine, Harvard Medical School, Boston, MA 02115 U.S.A
| | - Adam J Bass
- Departments of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 U.S.A
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142 U.S.A
- Department of Medicine, Harvard Medical School, Boston, MA 02115 U.S.A
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Genomic aberrations in an African American colorectal cancer cohort reveals a MSI-specific profile and chromosome X amplification in male patients. PLoS One 2012; 7:e40392. [PMID: 22879877 PMCID: PMC3412863 DOI: 10.1371/journal.pone.0040392] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/06/2012] [Indexed: 02/06/2023] Open
Abstract
Objective DNA aberrations that cause colorectal cancer (CRC) occur in multiple steps that involve microsatellite instability (MSI) and chromosomal instability (CIN). Herein, we studied CRCs from AA patients for their CIN and MSI status. Experimental Design Array CGH was performed on 30 AA colon tumors. The MSI status was established. The CGH data from AA were compared to published lists of 41 TSG and oncogenes in Caucasians and 68 cancer genes, proposed via systematic sequencing for somatic mutations in colon and breast tumors. The patient-by-patient CGH profiles were organized into a maximum parsimony cladogram to give insights into the tumors' aberrations lineage. Results The CGH analysis revealed that CIN was independent of age, gender, stage or location. However, both the number and nature of aberrations seem to depend on the MSI status. MSI-H tumors clustered together in the cladogram. The chromosomes with the highest rates of CGH aberrations were 3, 5, 7, 8, 20 and X. Chromosome X was primarily amplified in male patients. A comparison with Caucasians revealed an overall similar aberration profile with few exceptions for the following genes; THRB, RAF1, LPL, DCC, XIST, PCNT, STS and genes on the 20q12-q13 cytoband. Among the 68 CAN genes, all showed some level of alteration in our cohort. Conclusion Chromosome X amplification in male patients with CRC merits follow-up. The observed CIN may play a distinctive role in CRC in AAs. The clustering of MSI-H tumors in global CGH data analysis suggests that chromosomal aberrations are not random.
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Ashktorab H, Schäffer AA, Daremipouran M, Smoot DT, Lee E, Brim H. Distinct genetic alterations in colorectal cancer. PLoS One 2010; 5:e8879. [PMID: 20126641 PMCID: PMC2811180 DOI: 10.1371/journal.pone.0008879] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 01/02/2010] [Indexed: 12/22/2022] Open
Abstract
Background Colon cancer (CRC) development often includes chromosomal instability (CIN) leading to amplifications and deletions of large DNA segments. Epidemiological, clinical, and cytogenetic studies showed that there are considerable differences between CRC tumors from African Americans (AAs) and Caucasian patients. In this study, we determined genomic copy number aberrations in sporadic CRC tumors from AAs, in order to investigate possible explanations for the observed disparities. Methodology/Principal Findings We applied genome-wide array comparative genome hybridization (aCGH) using a 105k chip to identify copy number aberrations in samples from 15 AAs. In addition, we did a population comparative analysis with aCGH data in Caucasians as well as with a widely publicized list of colon cancer genes (CAN genes). There was an average of 20 aberrations per patient with more amplifications than deletions. Analysis of DNA copy number of frequently altered chromosomes revealed that deletions occurred primarily in chromosomes 4, 8 and 18. Chromosomal duplications occurred in more than 50% of cases on chromosomes 7, 8, 13, 20 and X. The CIN profile showed some differences when compared to Caucasian alterations. Conclusions/Significance Chromosome X amplification in male patients and chromosomes 4, 8 and 18 deletions were prominent aberrations in AAs. Some CAN genes were altered at high frequencies in AAs with EXOC4, EPHB6, GNAS, MLL3 and TBX22 as the most frequently deleted genes and HAPLN1, ADAM29, SMAD2 and SMAD4 as the most frequently amplified genes. The observed CIN may play a distinctive role in CRC in AAs.
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Affiliation(s)
- Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, DC, United States of America.
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6
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Bodmer W, Bielas JH, Beckman RA. Genetic instability is not a requirement for tumor development. Cancer Res 2008; 68:3558-60; discussion 3560-1. [PMID: 18483234 DOI: 10.1158/0008-5472.can-07-6544] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Walter Bodmer
- Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, United Kingdom
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7
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Camps J, Armengol G, del Rey J, Lozano JJ, Vauhkonen H, Prat E, Egozcue J, Sumoy L, Knuutila S, Miró R. Genome-wide differences between microsatellite stable and unstable colorectal tumors. Carcinogenesis 2005; 27:419-28. [PMID: 16272173 DOI: 10.1093/carcin/bgi244] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genomic copy number changes are frequently found in cancers and they have been demonstrated to contribute to carcinogenesis; and it is widely accepted that tumors with microsatellite instability (MSI) are genetically stable and mostly diploid. In the present study we compared the copy number alterations and the gene-expression profiles of microsatellite stable (MSS) and MSI colorectal tumors. A total number of 31 fresh-frozen primary tumors (16 MSS and 15 MSI) were used. Twenty-eight samples (15 MSS and 13 MSI) were analyzed with metaphase comparative genomic hybridization (CGH), nine of which plus one additional sample (4 MSS and 6 MSI) were further analyzed by cDNA-based array-CGH. Gene expression analysis was performed with six samples [3 MSS and 3 MSI, four of these used in metaphase CGH (mCGH) analysis] to identify differentially expressed genes possibly located in the lost or amplified regions found by CGH, stressing the biological significance of copy number changes. Metaphase and array-CGH analysis of two colon cancer cell lines (HTC116 and SW480, reported as MSI and MSS archetypes) gave comparable results. Alterations found by mCGH in MSS tumors were +20, +8q, -8p and -18q. Interestingly, 1p22, 4q26 and 15q21 were found deleted preferentially in MSS tumors, while 22q13 was found gained in MSI tumors. The regions of alterations identified by array-CGH were gains at 8q24, 16q24.3 and 20q13, and the loss of 5q21, appearing in the both types of tumors. Gene expression analysis revealed genes with specific associations with the copy number changes of the corresponding genomic regions. As a conclusion, colorectal cancer is a heterogeneous disease, demonstrated by the genomic profiles of individual samples. However, our data shows that copy number changes do not occur exclusively in the MSS phenotypes.
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Affiliation(s)
- Jordi Camps
- Laboratory of Cytogenetics, Departament de Biologia Cellular, Fisiologia i Immunologia and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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8
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Sieber OM, Tomlinson SR, Tomlinson IPM. Tissue, cell and stage specificity of (epi)mutations in cancers. Nat Rev Cancer 2005; 5:649-55. [PMID: 16056260 DOI: 10.1038/nrc1674] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Most (epi)mutations in cancers are specific to particular tumours or occur at specific stages of development, cell differentiation or tumorigenesis. Simple molecular mechanisms, such as tissue-restricted gene expression, seem to explain these associations only in rare cases. Instead, the specificity of (epi)mutations is probably due to the selection of a restricted spectrum of genetic changes by the cellular environment. In some cases, the resulting functional defects might be constrained to be neither too strong nor too weak for tumour growth to occur; that is, they lie within a 'window' that is permissive for tumorigenesis.
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Affiliation(s)
- Oliver M Sieber
- Molecular and Population Genetics Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3PX, UK.
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9
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Abdel-Rahman WM, Ollikainen M, Kariola R, Järvinen HJ, Mecklin JP, Nyström-Lahti M, Knuutila S, Peltomäki P. Comprehensive characterization of HNPCC-related colorectal cancers reveals striking molecular features in families with no germline mismatch repair gene mutations. Oncogene 2005; 24:1542-51. [PMID: 15674332 DOI: 10.1038/sj.onc.1208387] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A considerable fraction of families with HNPCC shows no germline mismatch repair (MMR) gene mutations. We previously detected 'hidden' MMR gene defects in 42% of such families, leaving the remaining 58% 'truly' mutation negative. Here, we characterized 50 colorectal carcinomas and five adenomas arising in HNPCC families; 24 truly MMR gene mutation negative and 31 MMR gene mutation positive. Among 31 tumors from MMR gene mutation positive families, 25 (81%) had active Wnt signaling as indicated by aberrant beta-catenin localization with or without CTNNB1 mutations, compared to only 7/18 tumors from MMR gene mutation negative families (39%; P=0.005). CGH studies revealed stable profiles in 9/16 (56%) of MMR gene mutation negative tumors, which was significantly associated with membranous beta-catenin (P=0.005). Tumors with membranous beta-catenin from the MMR gene mutation negative group also showed low frequency of TP53 mutations compared to those with nuclear beta-catenin. Thus, a majority of the MMR gene mutation negative cases exhibited a novel molecular pattern characterized by the paucity of changes in common pathways to colorectal carcinogenesis. This feature distinguishes the MMR gene mutation negative families from both HNPCC families linked to MMR defects and sporadic cases, suggesting the involvement of novel predisposition genes and pathways in such families.
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10
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Gorringe KL, Chin SF, Pharoah P, Staines JM, Oliveira C, Edwards PAW, Caldas C. Evidence that both genetic instability and selection contribute to the accumulation of chromosome alterations in cancer. Carcinogenesis 2005; 26:923-30. [PMID: 15677628 DOI: 10.1093/carcin/bgi032] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Cancer cells contain many genetic alterations, and genetic instability may be important in tumourigenesis. We evaluated 58 breast and ovarian cancer cell lines for microsatellite instability (MSI) and chromosomal instability (CIN). MSI was identified in 3/33 breast and 5/25 ovarian cell lines, and 7/8 MSI lines showed an inactivation of mismatch repair. Average ploidy by centromeric fluorescence in situ hybridization (FISH) of MSI (n = 8, average ploidy = 2.65) and microsatellite stable (MSS; n = 7, average ploidy = 3.01) cell lines was not different, due to the presence of three aneuploid MSI lines, and two near-diploid MSS lines. However, the variability of the centromeric FISH data was different between MSI and MSS (P = 0.049). The complexity of structural chromosomal rearrangements was not different between MSI and MSS. Thus, MSI and numerical CIN are not mutually exclusive, and structural CIN occurs independently of MSI or numerical CIN. Dynamic genetic instability was evaluated in three cell lines-MSI diploid (MT-3), MSS diploid (SUM159) and MSS aneuploid (MT-1). Ten clones of each of these cell lines were analysed by centromeric FISH and six-colour chromosome painting. The variation in chromosome number was different among all three cell lines (P < 0.001). MT-3 appeared numerically constant (94% of centromeric FISH signals matched the mode). SUM159 was 88% constant; however, 7% of cells had duplicated chromosomes. MT-1 was 82% constant; most changes were chromosomal losses. The six-colour FISH data showed that SUM159 had more stable structural chromosomal alterations (e.g. chromosomal translocations) compared with MT-3 and MT-1, but had no increase in unstable changes (e.g. chromatid breaks) when compared with MT-3. MT-1 had fewer unstable changes than both MT-3 and SUM159. These data suggest that numerical CIN may contribute to aneuploidy, but that selection plays an important role, particularly for the accumulation of structural chromosomal changes.
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Affiliation(s)
- Kylie L Gorringe
- Cancer Genomics Program, Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 2XZ, UK.
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11
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Abstract
Human cancers harbour numerous mutations and it has been proposed that these result from some form of inherent genomic instability. Some cancers have proven genomic instability or features that are indicative of this. Inherited cancer syndromes exist that are caused by deficient DNA repair or chromosomal integrity. By contrast, theoretical analysis and experimental data from sporadic colorectal tumours provide little general evidence of genomic instability in early lesions. These apparently conflicting data raise the question of whether or not genomic instability is necessary for driving tumour growth, and whether or not it is the usual initiating event in tumorigenesis.
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Affiliation(s)
- Oliver M Sieber
- Molecular and Population Genetics Laboratory, London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London WC2A 3PX, UK
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12
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Abstract
Chromosome aberrations in human solid tumors are hallmarks of gene deregulation and genome instability. This review summarizes current knowledge regarding aberrations, discusses their functional importance, suggests mechanisms by which aberrations may form during cancer progression and provides examples of clinical advances that have come from studies of chromosome aberrations.
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Affiliation(s)
- Donna G Albertson
- Cancer Research Institute, University of California San Francisco, San Francisco, California 94143-0808, USA.
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13
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Snijders AM, Fridlyand J, Mans DA, Segraves R, Jain AN, Pinkel D, Albertson DG. Shaping of tumor and drug-resistant genomes by instability and selection. Oncogene 2003; 22:4370-9. [PMID: 12853973 DOI: 10.1038/sj.onc.1206482] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tumors with defects in mismatch repair (MMR) show fewer chromosomal changes by cytogenetic analyses than most solid tumors, suggesting that a greater proportion of the alterations required for malignancy occur in genes with nucleotide sequences susceptible to errors normally corrected by MMR. Here, we used genome-wide microarray comparative genomic hybridization to carry out a higher resolution evaluation of the effect of MMR competence on genomic alterations occurring in 20 cell lines and to determine if characteristic aberrations arise in MMR-proficient and -deficient HCT116 cells undergoing selection for methotrexate resistance. We observed different spectra of aberrations in MMR-proficient compared to -deficient cell lines, as well as among cell lines with different types of MMR-deficiency. We also observed different genetic routes to drug resistance. Resistant MMR-deficient cells most frequently displayed no copy number alterations (16/29 cell pools), whereas all MMR-proficient cells had unique abnormalities involving chromosome 5, including amplicons centered on the target gene, DHFR and/or a neighboring novel locus (7/13 pools). These observations support the concept that tumor genomes are shaped by selection for alterations that promote survival and growth advantage, as well as by the particular dysfunctions in genes responsible for maintenance of genetic integrity.
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Affiliation(s)
- Antoine M Snijders
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
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Abstract
Breast tumors display a wide variety of genomic alterations. This review focuses on DNA copy number variations in these tumors as measured by the recently developed microarray-based form of comparative genomic hybridization. The capabilities of this new technology are reviewed. Initial applications of array CGH to the analysis of breast cancer, and the mechanisms by which the particular types of copy number changes might arise are discussed.
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Affiliation(s)
- Donna G Albertson
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA.
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15
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Planck M, Halvarsson B, Pålsson E, Hallén M, Ekelund M, Pålsson B, Baldetorp B, Nilbert M. Cytogenetic aberrations and heterogeneity of mutations in repeat-containing genes in a colon carcinoma from a patient with hereditary nonpolyposis colorectal cancer. CANCER GENETICS AND CYTOGENETICS 2002; 134:46-54. [PMID: 11996796 DOI: 10.1016/s0165-4608(01)00587-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The majority of tumors from patients affected by hereditary nonpolyposis colorectal cancer (HNPCC) exhibit a mutator phenotype characterized by widespread microsatellite instability (MSI) and somatic mutations in repeated sequences in several cancer-associated genes. An inverse relationship between MSI and chromosomal instability (CIN) has been demonstrated and HNPCC-associated tumors are generally characterized by diploid or near-diploid cells with few or no chromosomal rearrangements. We have studied MSI, somatic mutations in repeat-containing genes, DNA-ploidy, and cytogenetic aberrations in a colon carcinoma from a patient with a germline MLH1 mutation. Mutations in coding repeats were assessed in 10 macroscopically separate areas of the primary tumor and in two lymph nodes. Some of the genes studied (E2F4, MSH3, MSH6, TCF4, and TGFBRII) showed a consistent lack of mutations, whereas others (BAX, Caspase-5 and IGFIIR) displayed alterations in some tumor regions but not in others. The tumor had DNA-index 1.1-1.2 and a stable, aberrant karyotype with extra copies of chromosomes 7 and 12 and the structural aberrations i(1q), der(20)t(8;20), and der(22)t(1;22). The finding of CIN, MSI, and somatic mutations in coding repeats in this tumor suggests that these phenomena may act together in HNPCC tumorigenesis. Furthermore, the observed intratumoral heterogeneity of mutations in coding repeats implies these changes occur late in tumorigenesis and, thus, probably play a role in tumor progression rather than initiation.
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Affiliation(s)
- Maria Planck
- Department of Oncology, University Hospital, 221 85 Lund, Sweden.
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Pibouin L, Villaudy J, Ferbus D, Muleris M, Prospéri MT, Remvikos Y, Goubin G. Cloning of the mRNA of overexpression in colon carcinoma-1: a sequence overexpressed in a subset of colon carcinomas. CANCER GENETICS AND CYTOGENETICS 2002; 133:55-60. [PMID: 11890990 DOI: 10.1016/s0165-4608(01)00634-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have identified a novel human cDNA overexpressed in a colon carcinoma cell line, TC7, established from a tumor with a normal karyotype arising in a patient with a hereditary nonpolyposis colorectal carcinoma. The OCC-1 (overexpressed in colon carcinoma-1) gene is composed of six exons and located in the q24.1 region of chromosome 12. It is transcribed as two mRNA species that differ in their 5'- and 3'-terminal ends. Abundant accumulation of both transcripts was found in placenta, skeletal muscle, kidney, and pancreas tissues. Absent or very faint expression was observed in heart, brain, lung and liver tissues. Overexpressed in colon carcinoma-1 cDNA direct in vitro translation of several polypeptides whose size is shorter than 9 kDa. Attempts to produce antibodies against these synthesized polypeptides in Escherichia coli failed. The absence of sequences at the mRNA and DNA levels hybridizing with mouse sequences together with the absence of a large open reading frame raise the possibility that OCC-1 sequences appeared recently in evolution and are transcribed as two noncoding regulatory RNA. Elevated levels of OCC-1 mRNA were observed in three of eight colon carcinomas as compared to normal mucosa of the same patient. Since these tumors shared the same characteristics of having a near diploid karyotype, OCC-1 overexpression may be a hallmark of this subset of colon carcinomas.
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Affiliation(s)
- Laurence Pibouin
- Laboratoire d'Oncogenèse, UMR147 CNRS, Institut Curie, 26, rue d'Ulm, 75248, Cedex 05, Paris, France
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17
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Nishizaki T, Harada K, Kubota H, Harada K, Furuya T, Suzuki M, Sasaki K. Chromosome instability in malignant astrocytic tumors detected by fluorescence in situ hybridization. J Neurooncol 2002; 56:159-65. [PMID: 11995817 DOI: 10.1023/a:1014570720843] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Malignant tumors intrinsically manifest genetic instability, and consequently genetic aberrations successively accumulate in tumor cells as the tumor progresses. However, the relationship of genetic instability and biological behavior still remains to be investigated in malignant tumors. In the present investigation, the relationship between chromosomal instability and patient prognosis was studied in 19 malignant gliomas. Chromosomal instability was estimated by numerical variation in chromosomes 7, 10 and 17 which was measured by fluorescence in situ hybridization (FISH), and DNA ploidy was determined by laser scanning cytometry. The mean number of fractions was significantly higher in cases with DNA aneuploidy than in those with DNA diploidy. The tendency toward higher fractions in glioblastomas existed, although it did not reach statistical significance. Kaplan-Meier survival rate analysis demonstrated significantly lower survival rates in patients with higher fractions of chromosome 7 (>5) than others. Our results suggest that DNA aneuploidy in malignant gliomas reflects an underlying chromosomal instability, and that this instability is associated with clinical behavior.
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Affiliation(s)
- Takafumi Nishizaki
- Department of Neurosugery, Yamaguchi University School of Medicine, Japan.
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18
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Masramon L, Ribas M, Cifuentes P, Arribas R, García F, Egozcue J, Peinado MA, Miró R. Cytogenetic characterization of two colon cell lines by using conventional G-banding, comparative genomic hybridization, and whole chromosome painting. CANCER GENETICS AND CYTOGENETICS 2000; 121:17-21. [PMID: 10958935 DOI: 10.1016/s0165-4608(00)00219-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The heterogeneous nature of genetic alterations in cancer cells handicaps the full characterization of its occurrence and the analysis of their molecular bases and relation to biological processes. Although many cancer cells are highly aneuploid, in other cases, as in a subset of colorectal carcinomas displaying microsatellite instability, chromosomal aberrations are scarce. The aim of this study was to fully characterize both qualitatively and quantitatively, the karyotypes of two established colon carcinoma cell lines (LoVo and HCT 116) previously reported as being near diploid. An array of complementary cytogenetic techniques were used: G-banding, comparative genome hybridization (CGH), and whole-chromosome painting (WCP). Combinations of these techniques provided an accurate karyotype for the two cell lines: LoVo cells showed 49,XY,t(2;12)(q13;p11.2),+5,+7,+12,i(15)(q10) and HCT 116 cells showed 45,X,-Y,dup(10)(q24q26),der(16)t(8;16)(q13;p13), der(18)t(17;18)(q21;p11.3). Heterogeneity was also observed in both cell lines as shown by G-banding. Chromosomal unbalances determined by CGH (many of them related to structural reorganizations) were characterized by WCP, allowing the reliable identification of those chromosome markers that could not be completely identified by G-banding. We show that combined analysis with classical and molecular cytogenetic techniques provides an accurate map of chromosomal aberrations in these two cell lines not identified in previous investigations.
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Affiliation(s)
- L Masramon
- Department of Cancer and Metastasis, Institut de Recerca Oncològica, Hospital Duran i Reynals, L'Hospitalet, Barcelona, Spain
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19
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Willenbucher RF, Aust DE, Chang CG, Zelman SJ, Ferrell LD, Moore DH, Waldman FM. Genomic instability is an early event during the progression pathway of ulcerative-colitis-related neoplasia. THE AMERICAN JOURNAL OF PATHOLOGY 1999; 154:1825-30. [PMID: 10362807 PMCID: PMC1866629 DOI: 10.1016/s0002-9440(10)65438-7] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ulcerative colitis (UC) is a chronic inflammatory disease of the colon associated with a high risk of colorectal cancer. This increased cancer risk is thought to result from the cellular damage induced by the inflammatory field. The aim of this study was to determine the pattern and time course of genomic instability occurring in UC-related neoplasia. Sites of cancer, dysplasia, and nondysplasia from 14 UC colectomy cases containing cancer were analyzed for chromosomal alterations by comparative genomic hybridization (CGH) and for microsatellite instability using a series of 10 microsatellite markers. Clonal chromosomal alterations were present in 85% of cancer sites, 86% of dysplasia sites, and 36% of nondysplasia sites. Losses of chromosome 18 or 18q and chromosome 5 or 5q were common in cancer and dysplasia and were occasionally detected in nondysplasia. High-level microsatellite instability was detected in the cancer and dysplasia of two cases. Samples that demonstrated high-level microsatellite instability were unlikely to have chromosomal alterations demonstrable by CGH. These studies suggest that the predominant type of genomic instability in UC-related neoplasia is associated with chromosomal alterations and that this type of genomic instability frequently occurs before the development of histologically defined dysplasia.
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MESH Headings
- Adult
- Aged
- Cell Transformation, Neoplastic/genetics
- Chromosome Aberrations/genetics
- Chromosomes, Human, Pair 18/genetics
- Chromosomes, Human, Pair 20/genetics
- Chromosomes, Human, Pair 5/genetics
- Chromosomes, Human, Pair 8/genetics
- Colitis, Ulcerative/complications
- Colorectal Neoplasms/complications
- Colorectal Neoplasms/genetics
- Female
- Humans
- Male
- Microsatellite Repeats/genetics
- Middle Aged
- Nucleic Acid Hybridization
- Polymerase Chain Reaction
- Precancerous Conditions/genetics
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Affiliation(s)
- R F Willenbucher
- Cancer Center* and Departments of Medicine, Laboratory Medicine, University of California, San Francisco, California, USA
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Loeb KR, Loeb LA. Genetic instability and the mutator phenotype. Studies in ulcerative colitis. THE AMERICAN JOURNAL OF PATHOLOGY 1999; 154:1621-6. [PMID: 10362784 PMCID: PMC1866616 DOI: 10.1016/s0002-9440(10)65415-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Keith R. Loeb
- University of Washington School of Medicine and the Fred Hutchinson Cancer Research Center,†
| | - Lawrence A. Loeb
- University of Washington School of Medicine and the Fred Hutchinson Cancer Research Center,†
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Watson P, Lin KM, Rodriguez-Bigas MA, Smyrk T, Lemon S, Shashidharan M, Franklin B, Karr B, Thorson A, Lynch HT. Colorectal carcinoma survival among hereditary nonpolyposis colorectal carcinoma family members. Cancer 1998. [DOI: 10.1002/(sici)1097-0142(19980715)83:2<259::aid-cncr9>3.0.co;2-l] [Citation(s) in RCA: 171] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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