Cytogenetic study of solid ovarian tumors

Rapid analysis of Saccharomyces cerevisiae genome rearrangements by multiplex ligation-dependent probe amplification

Aneuploidy and gross chromosomal rearrangements (GCRs) can lead to genetic diseases and the development of cancer. We previously demonstrated that introduction of the repetitive retrotransposon Ty912 onto a nonessential chromosome arm of Saccharomyces cerevisiae led to increased genome instability predominantly due to increased rates of formation of monocentric nonreciprocal translocations. In this study, we adapted Multiplex Ligation–dependent Probe Amplification (MLPA) to analyze a large numbers of these GCRs. Using MLPA, we found that the distribution of translocations induced by the presence of Ty912 in a wild-type strain was nonrandom and that the majority of these translocations were mediated by only six translocation targets on four different chromosomes, even though there were 254 potential Ty-related translocation targets in the S. cerevisiae genome. While the majority of Ty912-mediated translocations resulted from RAD52-dependent recombination, we observed a number of nonreciprocal translocations mediated by RAD52-independent recombination between Ty1 elements. The formation of these RAD52-independent translocations did not require the Rad51 or Rad59 homologous pairing proteins or the Rad1–Rad10 endonuclease complex that processes branched DNAs during recombination. Finally, we found that defects in ASF1-RTT109–dependent acetylation of histone H3 lysine residue 56 (H3K56) resulted in increased accumulation of both GCRs and whole-chromosome duplications, and resulted in aneuploidy that tended to occur simultaneously with GCRs. Overall, we found that MLPA is a versatile technique for the rapid analysis of GCRs and can facilitate the genetic analysis of the pathways that prevent and promote GCRs and aneuploidy.

In this study we describe an adaptation of Multiplex Ligation–dependent Probe Amplification (MLPA) for use in the study of gross chromosomal rearrangements (GCRs) that occur in S. cerevisiae mutants with increased genome instability. Our previous study found that the presence of a Ty912 element on a nonessential arm of chromosome V resulted in increased rates of non-reciprocal monocentric translocations arising from recombination between the Ty912 on chromosome V and ectopic Ty elements on other chromosomes. Using MLPA, we observed that the majority of the translocations targeted six different translocation hotspots even though there were at least 254 potential targets for Ty-mediated translocations in the S. cerevisiae genome. Most of the observed translocations were formed by RAD52-dependent recombination, although we also identified a RAD52-independent recombination pathway that promoted the formation of the same types of translocations at lower rates. Finally, we found that defects in the ASF1-RTT109–dependent histone H3 lysine 56 (H3K56) acetylation pathway caused increased rates of both Ty-mediated translocations and whole-chromosome duplications (aneuploidy). This aneuploidy often occurred simultaneously with Ty-mediated translocations. Overall, our results demonstrate that MLPA is a rapid, inexpensive method that allows the analysis of the large number of GCRs needed to understand the pathways that suppress or promote genome instability.

Cytogenetic alterations in ovarian clear cell carcinoma detected by comparative genomic hybridisation

Ovarian clear cell carcinoma (OCCC) accounts for a small but significant proportion of all ovarian cancers and is a distinct clinical and pathological entity. It tends to be associated with poorer response rates to chemotherapy and with a worse prognosis. Little is known about possible underlying genetic changes. DNA extracted from paraffin-embedded samples of 18 pure OCCC cases was analysed for genetic imbalances using comparative genomic hybridisation (CGH). All of the 18 cases showed genomic alterations. The mean number of alterations detected by CGH was 6 (range 1-15) indicating a moderate level of genetic instability. Chromosome deletions were more common than amplifications. The most prominent change involved chromosome 9 deletions in 10 cases (55%). This correlates with changes seen in other epithelial ovarian cancers. This deletion was confirmed using microsatellite markers to assess loss of heterozygosity (LOH) at four separate loci on chromosome 9. The most distinct region of loss detected was around the IFNA marker at 9p21 with 41% (11 out of 27 cases) LOH. Other frequent deletions involved 1p (five out of 18; 28%); 11q (four out of 18; 22%) and 16 (five out of 18; 28%). Amplification was most common at chromosome 3 (six out of 18; 33%); 13q (four out of 18; 22%) and 15 (three out of 18; 17%). No high-level amplifications were identified. These features may serve as useful prognostic indicators in the management of OCCC.

Cytogenetics and molecular genetics of ovarian cancer

Genetic alterations identified in human ovarian tumors by conventional banding, fluorescence in situ hybridization, comparative genomic hybridization, chromosome microdissection, loss of heterozygosity, chromosome microcell-mediated chromosome transfer, and microarray gene expression analysis are summarized and correlated. The significance of these findings with respect to pathologic classification and clinical application are discussed.

Detection of numerical chromosomal abnormalities in epithelial ovarian neoplasms by fluorescence in situ hybridization (FISH) and a review of the current literature

Preliminary retrospective chromosomal analysis was performed using fluorescence in situ hybridization (FISH) with alphoid DNA probes for chromosomes 1, 3, 6, 8, 12, 17, and X. Twenty-four epithelial ovarian tumors were examined in this pilot study, including 8 borderline (LMP) serous tumors, 9 serous carcinoma, and 7 mucinous carcinoma. Hybridization signals were counted to demonstrate the frequency of aneusomy, trace chromosomal progression, and identify the predominance of chromosome copy number abnormalities that are specific to a particular histotype. The preliminary results revealed almost an equal number of mean aneusomies in serous (58.13 +/- 13%) and mucinous (64.33 +/- 10%) carcinoma, both of which were slightly higher than borderline serous tumors (50.57 +/- 17%). Hyposomies 3 and X were significantly higher in mucinous than in serous ovarian carcinomas, and lowest in borderline serous tumors (P<0.05 and P<0.01). Signal losses were a more frequent abnormality in all three histologic subtypes. Mucinous carcinomas showed a loss of chromosomes 8 (45.00 +/- 28%) and 3 (43.14 +/- 16%), in addition to a loss of chromosome X (56.29 +/- 12%). Serous carcinomas showed a gain of chromosome 1 (39.44 +/- 32%), followed by losses of chromosomes 6 (37.00 +/- 20%), 17 (36.44 +/- 19%), and 8 (36.89 +/- 19%). In borderline serous tumors, the most frequent findings were losses of chromosomes 6 (38.00 +/- 17%), 12 (36.88 +/- 17%), and 3 (36.13 +/- 21%). However, further research is necessary to substantiate these preliminary results and elucidate their clinical significance. A brief review of the literature pertaining to interphase cytogenetics in ovarian epithelial tumors is discussed also.

ARHI is the center of allelic deletion on chromosome 1p31 in ovarian and breast cancers

In our previous work, we had characterized ARHI as an imprinted putative tumor-suppressor gene in ovarian and breast cancers. ARHI is expressed in primary breast and ovarian cell lines but largely absent from the corresponding malignant tumors. Moreover, the non-imprinted functional allele is typically deleted in malignant cells. Since ARHI had been mapped to 1p31, a common deletion site in breast and ovarian cancer and male germ-cell tumors, in this study, we set out to define precisely the physical location of ARHI at 1p31 and to determine if this location lies within the smallest common region of deletion in breast and ovarian cancers. To this end, we first carried out radiation hybrid mapping of ARHI and surrounding markers, followed by a high-resolution study of loss of heterozygosity at 1p31 in 49 ovarian and breast cancers. Combining a radiation hybrid map and a physical map of the region encompassing ARHI, 3 discrete regions of minimal deletion were found at 1p31 in breast and ovarian cancers. ARHI is the most common deletion region at 1p31. Two other less common regions of deletion were found centromeric to this gene. One of them centered on D1S207 and the other one included and was proximal to D1S488. We also confirmed the preferential loss of non-imprinted functional allele in 7 of 9 tumor specimens. These data support the possibility that ARHI is a tumor-suppressor gene and suggest that additional tumor-suppressor genes may lie proximal to ARHI at 1p31. The data obtained from our study should aid in the identification and characterization of genes in this novel imprinted region.

Chromosomal breakage-fusion-bridge events cause genetic intratumor heterogeneity

It has long been known that rearrangements of chromosomes through breakage-fusion-bridge (BFB) cycles may cause variability of phenotypic and genetic traits within a cell population. Because intercellular heterogeneity is often found in neoplastic tissues, we investigated the occurrence of BFB events in human solid tumors. Evidence of frequent BFB events was found in malignancies that showed unspecific chromosome aberrations, including ring chromosomes, dicentric chromosomes, and telomeric associations, as well as extensive intratumor heterogeneity in the pattern of structural changes but not in tumors with tumor-specific aberrations and low variability. Fluorescence in situ hybridization analysis demonstrated that chromosomes participating in anaphase bridge formation were involved in a significantly higher number of structural aberrations than other chromosomes. Tumors with BFB events showed a decreased elimination rate of unstable chromosome aberrations after irradiation compared with normal cells and other tumor cells. This result suggests that a combination of mitotically unstable chromosomes and an elevated tolerance to chromosomal damage leads to constant genomic reorganization in many malignancies, thereby providing a flexible genetic system for clonal evolution and progression.

Numerical abnormalities of chromosomes 1, 11, 17, and X are associated with stromal invasion in serous and mucinous epithelial ovarian tumours

The clinical behaviour of ovarian tumours of low malignant potential (LMP) is unpredictable and it has been suggested that the majority of these lesions have no invasive potential. This study has analysed 92 epithelial ovarian tumours [11 mucinous cystadenomas, 18 mucinous LMP tumours, 15 mucinous carcinomas (9 FIGO stage I), 16 serous cystadenomas, 15 serous LMP tumours, and 17 serous carcinomas (11 FIGO stage I)] for numerical abnormalities of chromosomes 1, 11, 17, and X by interphase cytogenetics. Overall, numerical aberrations were identified in none of the cystadenomas, 15 per cent of serous LMP tumours, 17 per cent of mucinous LMP tumours, 67 per cent of mucinous carcinomas, and 82 per cent of invasive serous carcinomas. In mucinous LMP tumours, chromosome gains were associated with spindled nuclear morphology. Chromosome abnormalities were significantly more frequent in invasive mucinous (overall p< 0.01; stage I p< 0.05) and serous (overall p< 0.001; stage I p< 0.01) carcinomas than in the corresponding LMP tumours. No significant relationship between either stromal invasion or tumour type and the pattern of chromosome loss or gain was identified, although monosomy X was identified almost exclusively in invasive serous carcinomas. These observations are consistent with the concept that LMP tumours are unlikely to be precursors of ovarian carcinoma, but suggest that chromosome instability is important in the development of the invasive phenotype.

Molecular aspects of ovarian cancer. Is gene therapy the solution?

Genetic abnormalities of cancer cells are complex and usually nonspecific. Genetic anomalies specific to ovarian cancer have not been reported. This article focuses on what molecular anomalies are known in ovarian cancer and describes the first trials that have used transfer of genes to reestablish a normal cellular function in this disease. Suicide gene therapy has been the prototype of this new therapeutic approach.

Karyotypic analysis of 32 malignant epithelial ovarian tumors

The identification of recurrent specific cytogenetic findings in various malignancies has provided an improved means to diagnose and treat patients. To date, no characteristic markers have been found for epithelial ovarian cancer. This is due, in part, to several contributory factors, including the inability to identify optimal growth conditions for culture and the fact that most analyses of advanced-stage tumors are obtained from malignant effusions rather than from solid tissue. In addition, many reports include previously treated patients. In this study, 32 untreated solid epithelial ovarian tumors, including 8 tumors of low malignant potential (LMP), were obtained from primary and metastatic sites at initial surgical staging. Using a 2-culture plastic technique for tissue growth, we achieved a 96% short-term culture success rate. Only 4 normal 46,XX karyotypes were identified. Diploid or near-diploid genomes were associated with few cytogenetic alterations. Complex karyotypic morphologies were consistently associated with advanced or poorly differentiated tumors. Nonrandom cytogenetic aberrations most commonly involved chromosomes 1 and 6. A novel translocation, t(1;6)(p10;p10), was identified in both a metastatic LMP tumor and a poorly differentiated invasive tumor. This cytogenetic rearrangement can potentially be regarded as a clinically relevant early marker for tumorogenesis. Finally, karyotypes from both primary and metastatic sites were subject to a comparative analysis in 11 patients. In 4 cases, greater chromosomal complexity was associated with the primary site.

Detection of numerical chromosome anomalies in interphase cells of ovarian carcinomas using fluorescence in situ hybridization

Fluorescence in situ hybridization was used in interphase cells of 30 ovarian carcinomas to detect numerical changes in copy number of 13 different centromeres (1, 2, 3, 4, 6, 7, 8, 10, 11, 12, 17, 18, and X). Thirty-seven percent of samples (11/30) were near diploid and demonstrated only minor changes in centromere copy number, involving gain and/or loss of one or a few centromeres. The most common changes included loss of centromeres 4,6, 17, and 18 and gain of centromere 1. The remaining 63% of samples were hyperdiploid and demonstrated a general increase in copy number of most or all centromeres examined. Among these samples, the centromere of chromosome I was most often found to be at higher copy number. Centromeres that were less often at increased copy or deleted within the hyperdiploid samples include centromeres 4, 17, 18, and X. These results suggest that tumor-suppressor genes that are located on chromosomes 4, 6, 17, and 18 may be involved in the development and progression of ovarian cancer.

Chromosome abnormalities in primary endometrioid ovarian carcinoma

Specific and recurrent chromosome abnormalities may occur in regions of the genome that are involved in the conversion of normal cells to those with tumorigenic potential. Ovarian cancer is the primary cause of death among patients with gynecologic malignancies. We performed cytogenetic analysis in a subgroup of epithelial ovarian tumors, the endometrioid tumors, which are histologically indistinguishable from endometrial carcinoma of the uterus. We studied 10 endometrioid tumors to determine the degree of cytogenetic similarity between these two carcinomas. Six of 10 endometrioid tumors showed a near-triploid modal number, and one had a tetraploid modal number. Eight of the 10 contained structural chromosome abnormalities, of which the most frequent were 1p-- (5 tumors), 6q-- (4 tumors), 19q+ (4 tumors), and chromosome 3 rearrangements (4 tumors). These cytogenetic results resemble those reported for papillary ovarian tumors and differ from those of endometrial carcinoma of the uterus. We conclude that despite the histologic similarities between the endometrioid and endometrial carcinomas, the genetic abnormalities in the genesis of these tumors differ significantly.

Genetic changes in ovarian cancer

The development of cancer is a multistep process involving accumulation of genetic changes which progressively transform normal cells to neoplastic cells. During the last few years, our understanding and knowledge of the genetic changes involved in ovarian carcinogenesis have increased dramatically. In this review I will focus on karyotypic abnormalities in ovarian cancer and will also refer to molecular studies involving alterations in oncogenes and tumour suppressor genes in ovarian tumorigenesis. Cytogenetic analyses have identified two distinct subgroups. Simple karyotypic changes, trisomy 12 being the most common aberration in this group, are recurrently found in well differentiated ovarian carcinomas. Complex karyotypic abnormalities, including predominantly chromosome losses, deletions and unbalanced translocations, are found in moderately and poorly differentiated carcinomas. The bands and regions most commonly involved in structural rearrangements have been, in decreasing order of frequency, 19p13, 1p36, 1q21, 1q23-25, 3p11-13, 6q21, 19q13, 11p13-15, 11q13, 11q23, 12q24, 12p11-13, and 7p13-22. The finding of identical karyotypic and other genetic changes in tumour samples taken from different sites, such as tumours from both ovaries and omental metastases, indicate that ovarian cancer is of unicentric origin with subsequent metastatic spread giving rise to multiple implants. Molecular genetic changes important in ovarian cancer involve both classes of tumor-associated genes: RAS activation is generally not observed in ovarian cancer. Alterations of MYC1, ERBB2, AKT2, TP53 has been described in some ovarian carcinomas. The temporal relationship of these mutations, i.e. early or late events in ovarian carcinogenesis, remains to be determined.

Fluorescence in situ hybridization analysis using cosmid probes to define chromosome 6q abnormalities in ovarian carcinoma cell lines

Deletion of 6q is a frequent finding in ovarian carcinoma, which would suggest that this region contains one or more putative tumor suppressor genes. Chromosome 6q abnormalities in six ovarian carcinoma cell lines were analyzed by G-banding and fluorescence in situ hybridization (FISH). Using a variety of probes, including a chromosome 6 paint, a probe specific for the chromosome 6 centromere, and cosmids that map to q24 (cCI6-115), q25 (cCI6-4), q26 (cCI6-91, cCI6-119), and q27 (cCI6-13, cCI6-24, and cCI6-111), abnormalities of 6q were found in three cell lines. In cell line OAW42 (hypotetraploid), the sequences complementary to cCI6-119, cCI6-91, and cCI6-13 probes were lost in two homologues of chromosome 6, which indicates the deletion of genetic material from bands q26-27. The same bands were translocated in cell line PEO1 (hypertriploid). The probes from this region were absent on two copies of chromosome 6, but hybridized to two or three markers. In cell line 59M (hyperdiploid) an interstitial deletion proximal to q24 was detected in one chromosome 6. We conclude that it is very likely that a gene or genes localized in bands 6q26-27, and perhaps in the region proximal to 6q24, play a critical role in the development or progression of ovarian carcinoma.

Identification of chromosomal structural alterations in human ovarian carcinoma cells using combined GTG-banding and repetitive fluorescence in situ hybridization (FISH)

In order to identify chromosomal structural alterations in the ovarian carcinoma cell line MLS/P, fluorescence in situ hybridization with centromeric probes for chromosomes 1, 8, 9, 13/21, 14/22, 15, 17, and X and whole chromosome painting probes for chromosomes 1, 3, 4, 5, 7, 8, 9, 10, 12, 13, 14, 17, 19, 22, and X were performed subsequent to GTG-banding. This combined approach identified 14 of the 18 clonal structurally rearranged chromosomes, with the X chromosome involved in three aberrations. In contrast, only eight of the 14 rearrangements were identifiable by G-banding alone. These results indicate that the combined G-banding and FISH approach can significantly improve the cytogenetic analysis of human neoplasia.

Clonal chromosome abnormalities in 54 cases of ovarian carcinoma

As a prelude to assessing the relationship of chromosome alterations to clinical outcome in ovarian carcinoma, we report on the cytogenetic analysis on short-term cultures from 54 patients. All patients had histopathologically confirmed malignancy, with the majority of cases demonstrating serous ovarian adenocarcinomas. Structural alterations were evident in 52 cases, whereas numeric changes were identified in 13 cases. The most notable numeric abnormalities were loss of the X-chromosome (9/13 total cases) and +7 (3/9 diploid cases). Structural alterations most frequently involved chromosomes 1, 3, 6, 7, 11, and 12. Chromosomal breakpoints were shown to cluster in several chromosomal banding regions, including 1p36, 1p11-q21, 3p23-p10, 7p (especially 7p22), 11p, 11q, 12p13-q12, and 12q24. The frequency of structural alterations involving the following chromosome arms was found to be significantly increased: 1p (p < 0.01), 7p (p < 0.01), 11p (p < 0.01), 11q (p < 0.05), and 12p (p < 0.05). An analysis of the net gain or loss of chromosome segments was also performed, with the most consistent tendency observed being over-representation of 1q and chromosome 7, deletion of 1p, and loss of the X chromosome.

Genetic epidemiology of epithelial ovarian cancer

BACKGROUND

Aside from age, family history is the strongest predictor of ovarian cancer risk. Genetic components of risk for ovarian cancer have been evaluated by a number of designs, including case-control studies of family history and other risk factors, segregation and genetic linkage studies, and studies of biomarkers and tumor-specific cytogenetic abnormalities.

METHODS

Data were extracted from all available case-control studies that included family history. Cytogenetic, biomarker, segregation, analytic, and genetic linkage studies were reviewed.

RESULTS

Family history of ovarian cancer confers a 3.6-fold increased risk for this disease. Segregation studies of breast and ovarian cancer in five large families were consistent with dominant inheritance. Low levels of alpha-L-fucosidase confer mildly increased risk for ovarian cancer. Low galactose-1-phosphate uridyl transferase and type A blood group may increase risk for ovarian cancer. Cytogenetic and oncogene studies have identified regions that may be important in tumorigenesis and metastasis, but discriminating between early and late changes is difficult from these studies. Presence of a genetic susceptibility locus for breast and ovarian cancer has been confirmed on chromosome 17q21.

CONCLUSIONS

Family history is an important predictor of ovarian cancer risk. In rare families, a specific dominantly acting gene can be identified, but in the vast majority of familial ovarian cancers the underlying mechanism remains unclear. Specific studies are needed for women with a family history of ovarian cancer because evidence suggests modification of the effects of oral contraceptive use and reproductive patterns in this population of women.

Oncogenesis in ovarian cancer

Tumorigenesis is a multistep process involving mutations of dominantly acting proto-oncogenes and mutations and loss-of-function mutations of tumor suppressor genes. Some of these mutations may be inherited, but most of them are acquired. Models for the sequential steps of the genetic changes involved in tumor development have been proposed for certain cancers, such as colon cancer. In the case of ovarian cancer, relatively little is known about the genetic events associated with the initiation or subsequent progression and metastases of the tumor. Cytogenetic analysis has revealed a high incidence of both structural and numerical chromosome changes, and the extent of these changes seems to increase with tumor progression. Oncogene activations of the proto-oncogenes K-ras, c-myc and c-erbB-2 have been found more frequently in aggressive ovarian tumors and may be associated with poor survival. Tumor-specific allele loss involving putative tumor suppressor genes has been observed for loci at chromosomes 11p, 17p, and 17q,--loci commonly deleted in other cancers too. A relatively high incidence of allelic loss on chromosome 6q appears to be specific to ovarian carcinoma. Familial breast/ovarian cancer has been suggested to map to chromosome 8q. Recently we have found a germ-line mutation in the tumor suppressor gene p53 in a family with breast- and ovarian cancers, indicating that this is the predisposing gene in this family. Genetic changes important for the etiology of ovarian cancers seem to involve both somatic mutations of oncogenes and somatic or germ-line inactivation of tumor suppressor genes.

Chromosome aberrations in 35 primary ovarian carcinomas

Cytogenetic analysis was performed on short-term cultures of primary ovarian carcinomas from 62 patients. Cytogenetic analysis was successful in 59 cases. Clonal chromosome aberrations were detected in 35 tumors. Only numerical changes or a single structural change were found in five carcinomas: trisomy 12 was the sole anomaly in two tumors, one tumor had the karyotype 50,XX, + 5, + 7, + 12, + 14, a fourth tumor had a balanced t(1;5), and the fifth tumor had an unbalanced t(8;15). The fact that four of these five carcinomas were well differentiated suggests that simple karyotypic changes are generally characteristic of these less aggressive ovarian tumors. The majority of the cytogenetically abnormal tumors (n = 30) had complex karyotypes, with both numerical and structural aberrations and often hypodiploid or near-triploid stemlines. The numerical imbalances (comparison with the nearest euploid number) were mostly losses, in order of decreasing frequency -17, -22, -13, -8, -X, and -14. The structural aberrations were mostly deletions and unbalanced translocations. Recurrent loss of genetic material affected chromosome arms 1p, 3p, 6q, and 11p. The breakpoints of the clonal structural abnormalities clustered to several chromosome bands and segments: 19p13, 11p13-15, 1q21-23, 1p36, 19q13, 3p12-13, and 6q21-23. The most consistent change (16 tumors) was a 19p + marker, and in 12 of the tumors the 19p + markers looked alike.