Chromosomal gains and losses detected by comparative genomic hybridization and proliferation activity in renal cell carcinoma

OBJECTIVE: The number of DNA losses found using comparative genomic hybridization (CGH) and the proliferation index MIB-1 have been shown to be prognostic factors in renal cell carcinoma (RCC). We evaluated the associations of these two factors with each other and with histopathology and clinical outcome. MATERIAL AND METHODS: In this prospective study, specimens from 20 primary RCCs were investigated using CGH and MIB-1 assay. The associations of the commonest chromosomal aberrations with histopathology, stage and the clinical outcome of the disease were evaluated. RESULTS: CGH detected genetic aberrations in all tumours. Losses of genetic material (85%) were more common than gains (65%). Most common was loss in the short arm of chromosome 3, which was found in 70% of the tumours. Other frequent changes (20%) were losses of 4q, 13q, 18 and Xp, as well as gains of 5q, 7p, 7q (25%) and chromosome 12. The number of deleted chromosomal areas varied from none to six. The MIB-1 index varied from 0 to 39 (median 4.0). The total number of chromosomal aberrations or deletions showed no association with MIB-1 index or nuclear grade. Most grade 1 and 2 tumours showed a low MIB-1 index. All nuclear grade 4 tumours progressed and were associated with short survival. CONCLUSION: CGH gives an overview of DNA changes in RCC and helps to locate targets for more precise genetic evaluation. CGH findings are also helpful for classifying tumours. In this study, genetic aberrations in primary RCCs were not associated with histopathology, proliferation or clinical outcome, which suggests that CGH does not necessarily give any additional information on the prognosis of the disease. MIB-1 index and TNM stage were associated with survival.     

比较基因组杂交研究瘢痕疙瘩遗传变异

目的 了解瘢痕疙瘩遗传学改变的特征。方法 应用比较基因组杂交技术研究6例瘢痕疙瘩基因组的不平衡即遗传物质的丢失或扩增情况。结果 瘢痕疙瘩出现高频率的DNA拷贝数缺失的染色体是1p(66．7％)、16号染色体(83．3％)、20号染色体(83．3％)、22号染色体(83．3％)，其最小重叠区分别为1pter-32．2、16p13．2-p11．1、20q11．1-q13．2、16p13．2-p11．1，未发现特异区域的DNA拷贝数的高频率扩增。结论 1p、16号染色体、20号染色体、22号染色体极可能存在相关的瘢痕疙瘩抑制基因，这些基因的丢失可能参与了瘢痕疙瘩的发生、发展。     

比较基因组杂交研究原发性胃癌的遗传学变异

目的研究原发性胃癌发生、发展过程中遗传学变异情况。方法采用比较基因组杂交分析23例原发性胃癌基因组DNA拷贝数变化情况。结果原发性胃癌患者平均每例肿瘤染色体臂变化数为7.52,扩增数要明显多于丢失数(5.38∶2.14)。DNA拷贝数扩增常见于8q(9/21,42.9%)、20q(9/21,42.9%)、17q(8/21,38.1%)、3q(7/21,33.3%)、7q(7/21,33.3%)、11q(6/21,28.6%)、13q(6/21,28.6%)、1q(5/21,23.8%)、20p(5/21,23.8%);DNA拷贝数缺失常见于17p(7/21,33.3%)、18q(6/21,28.6%)、5q(5/21,23.8%)、8p(5/21,23.8%)、9p(5/21,23.8%)。结论原发性胃癌中存在多条染色体拷贝数的变化,由此引起相应癌基因的扩增和抑癌基因的丢失可能参与了胃癌的发生和发展。     

Genetic changes in pT2 and pT3 prostate cancer detected by comparative genomic hybridization

Prostate-specific antigen (PSA) screening has led to a remarkable increase in prostate cancer cases undergoing operative therapy. Over half of patients with locally advanced cancer (>or=pT3) develop rising PSA levels (biochemical failure) within 10 years. It is very difficult to predict which patients will progress rapidly to advanced disease following biochemical failure (BF). Therefore, a more useful prognostic factor is needed to suggest the most appropriate therapies for each patient. To determine chromosomal aberrations, we examined 30 patients with stage pT2 or pT3 primary prostate adenocarcinomas and no metastases (pN0M0) by comparative genomic hybridization (CGH). Laser capture microdissection (LCM) was used to gather cancer cells from frozen prostate specimens. Common chromosomal alterations included losses on 2q23-24, 4q26-28, 6q14-22, 8p12-22 and 13q21-31, as well as gains on 1p32-36, 6p21 and 17q21-22. Losses at 8p12-22 and 13q21-31 were observed more frequently in pT3 than pT2 tumors (P<0.05 and P<0.01, respectively). Losses at 8p12-22 were more frequent in tumors with BF (P<0.05), and those at 13q12-21 were more frequent in tumors with Gleason score (GS) 7 or more than lower GS (P<0.05). These findings suggest that losses of 8p12-22 and 13q21-31 are important determinants of prostate cancer progression.     

Genetic changes in familial prostate cancer by comparative genomic hybridization

BACKGROUND: Germline mutations in recessive cancer predisposition genes are uncovered by somatic genetic deletions during tumor development. Analysis of genetic changes in tumor tissues from patients with an inherited predisposition may therefore highlight regions of the genome containing susceptibility or modifier genes. Our aim was to characterize genetic changes in familial prostate cancer METHODS: Twenty-one primary prostate cancers from 19 Finnish prostate cancer families were analyzed for somatic genetic changes by comparative genomic hybridization (CGH). RESULTS: The average number of genetic alterations per tumor was 4.0 +/- 1.9, distributed equally among losses and gains. The most common losses were found at chromosomal regions 13q14-q22 (29%), 8p12-pter (24%), and 6q13-q16 (14%), and the most common gains at 19p (25%), 19q (14%) and 7q (14%). CONCLUSIONS: These results suggest that prostate cancers in genetically predisposed individuals arise for the most part through similar somatic genetic progression pathways as sporadic prostate cancers. This also implies that the biological properties of tumors from the two groups may not be different from one another.     

Chromosomal imbalances in primary oligodendroglial tumors and their recurrences: clues about malignant progression detected using comparative genomic hybridization

OBJECT: Despite the rapid increase in knowledge concerning the genetic basis of malignant progression in astrocytic tumors, progression of oligodendroglial tumors (including both pure oligodendrogliomas and mixed oligoastrocytomas) is still poorly understood. The aim of the present study is the elucidation of chromosomal imbalances involved in the progression of oligodendroglial tumors toward malignancy. METHODS: Using comparative genomic hybridization (CGH) on snap-frozen tumor tissue, the tumor genomes of five primary oligodendroglial tumors and associated recurrent tumors were screened for chromosomal imbalances. This information was correlated with clinical data (including follow-up data) and histopathological malignancy grade. In all cases an increase in chromosomal imbalances was detected in the recurrent tumor, indicating genetic progression. In three of the five cases this correlated with malignant progression detected at the histopathological level. The results indicate that, similar to what occurs in astrocytic tumors, chromosomal imbalances harboring genes involved in the cell proliferation control mechanism at the G1-S border are involved in the progression of oligodendroglial tumors. Additionally, although gains of genetic material on chromosome 7 and losses on chromosome 10 are most frequently detected in the course of malignant progression of astrocytic tumors, either or both of these can also occur during malignant progression of typical oligodendroglial tumors that contain losses involving chromosome 1p and/or chromosome 19q. CONCLUSIONS: When performed on optimally preserved material from a small set of primary oligodendroglial tumors and associated recurrent tumors, CGH detects chromosomal aberrations that potentially play a mechanistic role in the malignant progression of these tumors.     

比较基因组杂交揭示骨肉瘤相关基因变异

比较基因组杂交是诊断肿瘤发生发展的方法,能够发现与骨肉瘤相关的基因变异,从而为基因治疗提供依据.通过比较基因组杂交发现骨肉瘤患者基因扩增多于缺失,经常发生变异的基因与骨肉瘤密切相关.4q变异是儿童骨肉瘤共同的畸变;8q扩增与骨肉瘤复发和侵袭性相关;17p扩增(除17p13.1外)与骨肉瘤恶性程度相关;凋亡相关因子与骨肉瘤发生发展、预后密切相关;环氧化酶-2在骨肉瘤的高表达为骨肉瘤新辅助化疗提供依据;高频的基因变异位点主要与癌基因、抑癌基因、细胞生长和细胞周期调控、细胞凋亡、端粒、细胞因子、肿瘤免疫、肿瘤血管生成、肿瘤转移相关因子等密切相关.     

Olfactory neuroblastoma: Detection of genomic imbalances by comparative genomic hybridization

Summary Olfactory neuroblastoma (esthesioneuroblastoma) is a very rare tumour of the olfactory mucosa. Morphological features and cytogenetic studies strongly suggest a neuro-ectodermal origin. Up to now, cytogenetic studies are inconsistent. Some of them have proposed that the tumour belongs to the pPNET family. In the present study we describe genomic imbalances in olfactory neuroblastoma in a 46-year-old woman by using the molecular cytogenetic technique — comparative genomic hybridization (CGH) — in order to define the spectrum of genetic abnormalities in the tumour. The anatomical location and morphological findings were the basis for the diagnosis of esthesioneuroblastoma. Immunohistochemical reactions for NSE, synaptophysin, chromogranin A, HNK-l/Leu-7 and S-100 revealed a characteristic immunophenotype. The CGH analysis showed multiple changes including DNA overrepresentations of chromosomes 4. 8, 11 and 14, partial DNA gains of the long arms of chromosomes 1 and 17, deletions of the entire chromosomes 16, 18. 19 and X, and partial losses of chromosomes 5q and 17p. This study represents an early utilisation of the CGH technique in olfactory neuroblastoma and demonstrates that the tumour carries complex chromosomal aberrations.     

Genetic changes in stage pT2N0 prostate cancer studied by comparative genomic hybridization

OBJECTIVE: To identify chromosomal regions important for progression in clinically organ-confined prostate cancer, as the genetic changes underlying the development and progression of prostate cancer are poorly understood. MATERIALS AND METHODS: Comparative genomic hybridization (CGH) was used to search for DNA sequence copy-number changes in a series of 50 primary organ-confined prostate adenocarcinomas (pT2N0) removed by radical prostatectomy. RESULTS: CGH analysis indicated that 23 (46%) of the primary prostate adenocarcinomas showed chromosome alterations. The percentage of tumours with losses (38%) was higher than with gains (28%). Losses of 13q (24%), 8p (18%), 6q (10%), 16q (8%), 18q (6%) and 5q (6%) and gains of 17q (12%), 20q (12%), 9q (10%), 17p (8%) and 8q (6%) were the most frequent alterations. Amplifications were found at 8q24-qter. Minimal overlapping regions of loss, indicative of the presence of tumour-suppressor genes, were mapped to 13q21.1-q21.3 and 8p21.2, and minimal overlapping regions of gain, indicative of the presence of oncogenes, were found at 9q34.4-qter, 17q25-qter and 20q13.3-qter. There was a significant association between Gleason score and losses and gains (P = 0.003), and an association between chromosomal imbalance and high histological grade (P = 0.008). CONCLUSION: These results suggest that losses or gains of DNA in these regions are important for prostate cancer progression, and document the spectrum of chromosomal alterations in stage pT2N0 of clinically organ-confined prostate cancer.     

Genetic aberrations in prostate carcinoma detected by comparative genomic hybridization and microsatellite analysis: association with progression and angiogenesis

BACKGROUND: In spite of increasing knowledge about the tumor biology of prostate cancer (PC), molecular events involved in tumor progression are not well characterized. There is evidence that a number of genetic alterations play a role in tumor progression and in addition, angiogenesis also contributes. In this study, comparative genomic hybridization (CGH), a sensitive method for detecting regional DNA copy number abnormalities, and microsatellite analysis was used to identify frequent genome changes in PC. Correlation of these data with microvessel density (MVD) and clinical follow-up data was performed to determine genetic alterations that are associated with angiogenesis and subsequent tumor progression. METHODS: Fifty-seven paraffin embedded radical prostatectomy (RP) specimens were microdissected. DNA from the microdissected PC tissue was amplified by degenerate oligonucleoitide primed (DOP)-polymerase chain reaction (PCR), and CGH was performed on the PCR product. Quantitative analyses of the CGH profiles were performed using a t-statistic. Additionally, a microsatellite analysis of chromosome 13q was performed on a subgroup of 31 of the tumors. Using a polyclonal antibody against factor VIII, MVD was determined for all RP specimens. The results of CGH and microsatellite analysis were correlated with the clinical data of the patients and with MVD. RESULTS: Forty-two of the tumors (75%) showed one or more gains while 39 (70%) showed one or more losses per tumor. The most frequent DNA copy number gains were on chromosome 3, 4, 7, 8, 10, 11, 12, 13, and X. The most frequent losses were on chromosomes 2, 5, 6, 8, 10, 13, 15, and 16. Cancer recurrence occurred in 15 patients. The total number of DNA copy number losses was significantly higher in patients with this progression (86%) than without (52%) (P < 0.001). There was no significant difference in the number of gains in patients with or without progression. Contingency table analysis showed a significant correlation between progression and losses in regions of chromosomes 6q and 13q and a gain of chromosome 7q. In multivariate analysis, only loss of chromosome 6 was independently prognostic. The gains that correlated most closely with MVD > 35 were on chromosomes 2q, 7q, and Xq, while the losses most closely associated with MVD > 35 were on chromosomes 8q, 10q, and 13q. However, only the association between loss of chromosome 13q and MVD > 35 was statistically significant. Microsatellite analysis revealed a statistically significant correlation between MVD and instability of locus 171. CONCLUSIONS: This study indicates that the frequency of genetic alterations in PC as detected by CGH correlates with clinical outcome, and that losses of DNA from chromosomes 6q and 13q are important events that correlate with tumor progression, with loss of 13q, especially instability of locus 171, also associated with angiogenesis.     

Detection of chromosomal imbalances in spinal meningiomas by comparative genomic hybridization

Little is known about genetic mutations during the malignant progression of spinal meningiomas. This study investigated genomic changes across the entire genome in spinal meningioma samples to determine possible mechanism(s) of tumorigenesis. Paraffin-embedded tissue sections of 16 spinal meningiomas were analyzed by the comparative genomic hybridization (CGH) technique. Lymphocytes of the patients were evaluated as controls. Genomic change was detected in 11 samples. Complete or partial loss of chromosome 22 was the most commonly seen abnormality in eight cases. Chromosome losses on 1p, 9p, and 10q and gains on 5p and 17q were the other abnormalities. These changes are all frequently seen in meningiomas, but are mostly specific to atypical and anaplastic meningiomas. However, in the present study, copy number changes on chromosomes 9p (3 samples), 17q (2 samples), and 1p (2 samples) were seen even in the benign tumors. Our results suggest that in addition to the neurofibromatosis type 2 tumor suppressor gene, other cancer-related genes located on 1p, 9p, 10q, and 17q might be involved in the etiology of spinal meningiomas.     

Genetic alterations in microdissected prostate cancer cells by comparative genomic hybridization

Molecular genetic abnormalities were assessed on 23 cases of prostate adenocarcinoma by performing microdissection on archived tumor tissue sections followed by degenerate oligonucleotide primed PCR (DOP-PCR) on extracted DNA, providing sufficient product to carry out comparative genomic hybridization (CGH). The results of CGH show a significant regional DNA copy number alteration in 100% of the cases. Copy number gains were detected most frequently in chromosome 8q (91.3%), followed by chromosome X (43.5%), and chromosomes 20, 7, 4, and 3 (8.7%). DNA copy number losses occurred most frequently in chromosome 18 (34.8%), followed by chromosome 20 (21.7%), chromosomes 16 and 22 (17.4%) and chromosomes 12, 17, and 19 (8.7%). Since tissue microdissection and DOP-PCR yields product for analysis that represents DNA from pure tumor cells. CGH shows high sensitivity in detecting copy number alterations. This method indicates regions of the genome that are likely to be driven to amplification or deletion by the presence of oncogenes or tumor suppressor genes, respectively. The most common alteration detected was a regional gain in copy number in chromosome 8 near 8q21, indicating an oncogene in this region may be key to development of prostate adenocarcinoma. Prostate Cancer and Prostatic Diseases (2000) 3, 110-114     

Detection of chromosomal imbalances in central neurocytomas by using comparative genomic hybridization

OBJECT: Central neurocytomas are rare neuronal tumors commonly found in the intraventricular regions. Little is known about the tumorigenesis of these neoplasms. The aim of this study was to provide an overview of genetic imbalances in central neurocytomas. METHODS: In this study, comparative genomic hybridization was used to identify DNA sequence copy number changes (losses and gains) in a series of 10 central neurocytomas. Tumor DNA and normal reference DNA were differentially labeled and allowed to cohybridize to normal metaphase chromosomes. After hybridization and fluorescent staining of the bound DNA, regions of gain or of loss of DNA sequences were detected as changes in the tumor/normal fluorescence intensity ratio along the target metaphase chromosomes. A gain of DNA sequence was detected in chromosomes 2p, 10q, and 18q. A protooncogene, Bcl2, which maps to 18q21, was evaluated by immunohistochemical analysis to determine its role in the formation of central neurocytomas. CONCLUSIONS: In this study the authors identified recurrent genetic changes on chromosomes 2p, 10q, and 18q in central neurocytomas and highlighted chromosomal regions for additional mapping and cloning of candidate genes that are important in the development of central neurocytomas.     

Detection of chromosomal alterations in bladder cancer by comparative genomic hybridization.

OBJECTIVES: To characterize which genomic alterations occur in bladder cancers of different grades and stages, and to evaluate the prognostic implication of chromosomal imbalances. Materials and methods Twelve transitional cell carcinoma cell lines were used to study chromosomal aberrations, using comparative genomic hybridization to examine metaphase cells. RESULTS: There was a mean of 6.0 aberrations per tumour with 4.9 gains and 1.08 deletions per tumour cell line. The mean number of aberrations was the same in grade 2 and 3 tumours. High-stage (>/= T2) carcinomas had markedly more genomic gains than had low-stage (T1) tumours, with 7.2 gains and 1.3 deletions per >/= T2 tumour, and 2.7 gains and 0.8 deletions per T1 tumour, although the difference was not statistically significant. The most frequent changes were gains of chromosome 1 (seven), 9 and 16 (six), and losses of chromosomes 14 (three), 21 and Y (two). The changes 1p+, 3p+, 9q+, 14p-, 16q+ and Yp- were significantly more frequent in low-grade tumours, with 1p+, 3p+ and Yq- the most frequent in stage T1 tumours, and 16p+, 9q+ and 13q- the most frequent in stage >/= T2 tumours. Conclusion These findings indicate several genomic regions in chromosomes 1, 9, 14 and 16 that may carry genes for the development and progression of bladder cancers.     

Discovery of new DNA amplification loci in prostate cancer by comparative genomic hybridization

BACKGROUND: DNA sequence amplifications are involved in the progression of many tumor types, and have also been found in advanced prostate cancer. The aim of this study was to detect new loci of DNA amplifications in prostate cancer. METHODS: Comparative genomic hybridization (CGH) was used for whole genome screening of DNA sequence copy number alterations in 27 advanced prostate cancers. RESULTS: The most prevalent changes were losses of 8p, 13q (52%, each), 6q (48%), 18q (37%), 5q (30%), 2q, 4q and 16q (26%, each), and gains of 8q (48%), Xq (40%), and Xp (26%). In addition, 16 high-level amplifications were found. These included Xq12 (five), 8q24 (two), and 11q13 (one) with known putative target genes (androgen receptor, MYC and Cyclin D1), and 1q21-25 (three), 10q22 (two), 17q23-24 (two), and 8q21 (one) where the target genes remain unknown. CONCLUSIONS: High-level amplifications at different chromosomal sites occur in advanced prostate cancer. The detection of amplified chromosomal regions may serve as a starting point to discover novel oncogenes involved in prostate cancer progression.     

Screening for genetic aberrations in papillary thyroid cancer by using comparative genomic hybridization

BACKGROUND: Determination of the genetic composition of papillary thyroid cancers may help explain differences in observed clinical behavior. Comparative genomic hybridization (CGH) is a novel molecular cytogenetic assay that allows simultaneous detection of gains, losses, and amplification of genetic information, making it an ideal screening tool. The aim of this study was to identify genetic aberrations occurring in papillary thyroid cancers by using CGH analysis. METHODS: CGH analysis was performed on 21 individual cases of papillary thyroid cancers. Nonparametric statistical comparisons were performed with the Fisher exact test. RESULTS: Genetic abnormalities were identified by CGH in 10 of 21 cases (48%). A recurrent pattern of aberrations was seen in cases where genetic changes were detected, involving losses at chromosome arms 1p and 9q and chromosomes 17, 19, and 22, and gains at chromosome 4 and chromosome arms 5q, 6q, 9q, and 13q. The loss of chromosome 22 was unique to younger patients (P =.05) and was associated with a higher rate of regional lymphatic metastasis (19% vs 80%, P =.02). CONCLUSIONS: Two genetically unique groups of patients were identified by using CGH analysis. One group had no detectable aberrations; the other had a recurrent pattern of aberrations, localizing to the identical chromosomal loci. This pattern of aberrations suggests that the involved loci may contain genes important in thyroid carcinogenesis. The clinical significance of the presence of copy number changes detected by CGH needs to be determined. In addition, molecular cloning of involved genes in each of the aberrations is warranted.