Consistent occurrence of a 19p+ marker chromosome and loss of 11p material in ovarian seropapillary cystadenocarcinomas

Involvement of DPP9 in gene fusions in serous ovarian carcinoma

Background

A fusion gene is a hybrid gene consisting of parts from two previously independent genes. Chromosomal rearrangements leading to gene breakage are frequent in high-grade serous ovarian carcinomas and have been reported as a common mechanism for inactivating tumor suppressor genes. However, no fusion genes have been repeatedly reported to be recurrent driver events in ovarian carcinogenesis. We combined genomic and transcriptomic information to identify novel fusion gene candidates and aberrantly expressed genes in ovarian carcinomas.

Methods

Examined were 19 previously karyotyped ovarian carcinomas (18 of the serous histotype and one undifferentiated). First, karyotypic aberrations were compared to fusion gene candidates identified by RNA sequencing (RNA-seq). In addition, we used exon-level gene expression microarrays as a screening tool to identify aberrantly expressed genes possibly involved in gene fusion events, and compared the findings to the RNA-seq data.

Results

We found a DPP9-PPP6R3 fusion transcript in one tumor showing a matching genomic 11;19-translocation. Another tumor had a rearrangement of DPP9 with PLIN3. Both rearrangements were associated with diminished expression of the 3′ end of DPP9 corresponding to the breakpoints identified by RNA-seq. For the exon-level expression analysis, candidate fusion partner genes were ranked according to deviating expression compared to the median of the sample set. The results were collated with data obtained from the RNA-seq analysis. Several fusion candidates were identified, among them TMEM123-MMP27, ZBTB46-WFDC13, and PLXNB1-PRKAR2A, all of which led to stronger expression of the 3′ genes. In view of our previous findings of nonrandom rearrangements of chromosome 19 in this cancer type, particular emphasis was given to changes of this chromosome and a DDA1-FAM129C fusion event was identified.

Conclusions

We have identified novel fusion gene candidates in high-grade serous ovarian carcinoma. DPP9 was involved in two different fusion transcripts that both resulted in deregulated expression of the 3′ end of the transcript and thus possible loss of the active domains in the DPP9 protein. The identified rearrangements might play a role in tumorigenesis or tumor progression.

Electronic supplementary material

The online version of this article (10.1186/s12885-017-3625-6) contains supplementary material, which is available to authorized users.

Bilateral ovarian carcinomas differ in the expression of metastasis-related genes

The mechanisms behind bilaterality of ovarian carcinomas are not fully understood, as the two tumors could possibly represent two primary tumors, a primary tumor and a metastasis, or two metastases. The gene expression profiles from bilateral high-grade serous carcinomas (HGSCs) and clear cell carcinomas (CCCs) of the ovary were compared to study the association between the tumors of the two sides. A separate analysis of genes from chromosome 19 was also performed, since this chromosome is frequently rearranged in ovarian carcinomas. Tumors from four patients were included (three pairs of HGSC and one pair of CCC). The gene expression was analyzed at the exon level, and bilateral tumors were compared to identify within-pair differences. Gene expression data were also compared with genomic information on the same tumors. Similarities in gene expression were observed between the tumors within each pair, as expected if the two tumors were clonally related. However, certain genes exhibited differences in expression between the two sides, indicating metastasis involvement. Among the most differently expressed genes, one gene was common to all four pairs: Immunoglobulin J. In all HGSC pairs, serpin peptidase inhibitor, clade B (ovalbumin), member 2, serpin family E member 1 and phospholipase A2, group IIA (platelets, synovial fluid) were also among the differentially expressed genes. The specific analysis of chromosome 19 highlighted expression differences in the zinc finger protein 36 gene. These results indicate that bilateral ovarian tumors represent different stages during progression of a single clonal process. Several of the genes observed to be differently expressed are known to be metastasis-related, and are likely to be also involved in spreading from one side to the other in the bilateral cancer cases examined.

[On the possibility to determine genetic identity of the tissues with malignant tumours imbedded in paraffin blocks]

The results of analysis of the literature data were used to develop the forensic medical criteria for the assessment of the suitability of paraffin blocks containing the imbedded malignant tumours for the genetic identification of the tissues. The forensic medical criteria and the algorithm for the preliminary characteristic of the material of interest were proposed to avoid the potential errors. It is not recommended to use gastrointestinal carcinomas, breast tumours, and poorly differentiated ovarian tumours. Also unsuitable is the material formerly exposed to radio- and chemotherapeutic agents or paraffin blocks stored during more than 5-7 years. In the doubtful cases, immunohistochemical studies must be carried out to confirm microsatellite instability. Moreover, the tumour genotype and DNA composition from the patients' blood should be confirmed.

Chromosome 19 rearrangements in ovarian carcinomas: zinc finger genes are particularly targeted

Chromosome 19 is frequently rearranged in ovarian carcinomas, but the pathogenetic consequences of this are not clearly understood. We performed microarray gene expression analysis on 12 ovarian carcinomas that carry a rearranged chromosome 19 in their karyotype. These aberrant chromosomes have previously been microdissected and analyzed by array-based CGH. In the current study, we wanted to explore whether the genomic alterations thus detected correlated with changes in gene expression. The microarray gene expression analysis gave information on 407 genes mapping in gained genomic regions on chromosome 19, of which 92 showed association between DNA gain and upregulated expression. Of the genes showing this association, 39 (42%) showed gain in at least two samples. The majority of these 39 genes of interest (n = 24, 62%) encode zinc finger proteins, which otherwise make up only 15% of the approximately 1,400 genes on chromosome 19. The strongest association was found for ZNF223 which was upregulated in samples with genomic gain compared with samples without gain. We suggest that DNA copy number changes brought about by rearrangements of chromosome 19 contribute to ovarian carcinogenesis by leading to upregulation of ZNF223 and other zinc finger genes. © 2014 Wiley Periodicals, Inc.

Frequent translocations of 11q13.2 and 19p13.2 in ovarian cancer

Aberrations of chromosome arm 19p in ovarian cancer were first described decades ago and have been confirmed in recent publications, which have focused on chromosome 11 as a translocation partner. Recently, genetic analysis of the ovarian cancer cell line SKOV3 revealed a rearrangement described as der(19)t(11;19)(q13.2;p13.2), which lead to a fusion protein containing parts of HOOK2 and frame shifted ACTN3 that had unknown functionality. To evaluate the frequency of these breakpoints, we used fluorescence in situ hybridization (FISH) probes flanking these genes for interphase analysis of ovarian cancer cells. We analyzed 49 primary cell cultures of ovarian cancers using FISH probes next to these breakpoints on chromosomes 11 and 19 defined in SKOV3. Co-localizations of the signals in interphase nuclei were considered to be positive fusions when the frequency was over the experimentally calculated cutoff of 24.3% (mean average value for normal ovary cells plus three times the standard deviation). Fusions between 11q13.2 and 19p13.2 were confirmed in 22 (45%) primary cell cultures of ovarian cancers. However, by PCR, the fusion originally described in SKOV3 was not detected in any of the primary cell cultures. Our results confirm other reports and show that these regions are very frequently involved in chromosomal rearrangements in ovarian cancer. Furthermore, they reveal a significant correlation (P = 0.023) of co-localized signals of 11q13.2 and 19p13.2 with low and intermediate grades in ovarian cancer.

Tumor spreading to the contralateral ovary in bilateral ovarian carcinoma is a late event in clonal evolution

Cancer of the ovary is bilateral in 25%. Cytogenetic analysis could determine whether the disease in bilateral cases is metastatic or two separately occurring primary tumors, but karyotypic information comparing the two cancerous ovaries is limited to a single report with 11 informative cases. We present a series of 32 bilateral ovarian carcinoma cases, analyzed by karyotyping and high-resolution CGH. Our karyotypic findings showed that spreading to the contralateral ovary had occurred in bilateral ovarian cancer cases and that it was a late event in the clonal evolution of the tumors. This was confirmed by the large number of similar changes detected by HR-CGH in the different lesions from the same patient. The chromosomal bands most frequently involved in structural rearrangements were 19p13 (n = 12) and 19q13 (n = 11). The chromosomal bands most frequently gained by both tumorous ovaries were 5p14 (70%), 8q23-24 (65%), 1q23-24 (57%), and 12p12 (48%), whereas the most frequently lost bands were 17p11 (78%), 17p13 (74%), 17p12 (70%), 22q13 (61%), 8p21 and 19q13 (52%), and 8p22-23 (48%). This is the first time that 5p14 is seen gained at such a high frequency in cancer of the ovary; possibly oncogene(s) involved in bilateral ovarian carcinogenesis or tumor progression may reside in this band.

Detection of differentially expressed HES-6 gene in metastatic colon carcinoma by combination of suppression subtractive hybridization and cDNA library array

The molecular mechanisms involved in the progression of colon carcinomas from a primary to a metastatic tumor have been only partially elucidated and poorly understood. This study combines suppression subtractive hybridization and cDNA array hybridization to identify genes with expression differences between a primary human colon tumor cell line (HT29) and three isogenic lung tumor metastases. The positive clones isolated in this screen were further validated and quantitated with real-time reverse transcription polymerase chain reactions. HES-6 was identified as up-regulated in each of the individual tumor metastases, as well as in a panel of primary human tumors derived from the lung, breast and kidney. These findings demonstrate that it is possible to utilize longitudinal samples from an in vivo model of colon carcinoma to identify genes up-regulated in metastases and that HES-6 may be an important marker of a range of primary cancers as well as metastatic colon carcinoma.

A new method for improving metaphase chromosome spreading

BACKGROUND

The success of complex molecular cytogenetic studies depends on having properly spread chromosomes. However, inconsistency of optimum chromosome spreading remains a major problem in cytogenetic studies.

METHODS

The metaphase spreading process was carefully timed to identify the most critical phase of chromosome spreading. The effects of dropping height of cell suspension, slide condition, drying time, fixative ratio, and relative humidity on the quality of metaphase spreads were studied by quantitative examination of metaphase chromosome spreads. Normal and immortalized human epithelial ovarian cells, neuroblastoma cells, and normal lymphocytes were tested.

RESULTS

Humidity over the slide was the most important variable affecting the quality of chromosome spreads. Consistent improvement in chromosome spreading (larger metaphase area, less chromosome overlaps, or lower frequencies of broken metaphases) was obtained for all cell types if dynamic cell rehydration, occurring as fixative absorbs moisture from air, was made to coincide with the prompt fixation of spread chromosomes to the slide. This was achieved by dropping cells on dry glass slides placed in a shallow metal tray and then quickly lowering the tray into a covered 50 degrees C water bath for slide drying.

CONCLUSIONS

A new and simple method for improving metaphase chromosome spreading was developed based on our study on the characteristics of chromosome spreading.

The 90- and 110-kDa human NFAR proteins are translated from two differentially spliced mRNAs encoded on chromosome 19p13

The NFAR gene (nuclear factor associated with dsRNA) encodes a putative transcription-associated factor that we have shown is a substrate for the interferon-inducible, dsRNA-dependent protein kinase, PKR. However, our protein expression analysis has revealed that NFAR exists as two major protein species of 90 kDa (NFAR-1) and 110 kDa (NFAR-2) in the cell. To resolve the genetic identity of NFAR-1 and -2, we carried out sequence analysis of genomic and cDNA NFAR clones and determined that the coding region of this gene spans 16.2 kb and comprises 21 exons. Our data indicate that NFAR-1 and -2 arise from a single gene on chromosome 19p13 and are generated through alternative splicing events. NFAR-1 (HGMW-approved symbol ILF3) was found to comprise 1 extra exon, 18, that contains several stop codons to ensure termination of the protein at amino acid 702. In contrast, NFAR-2 lacks this exon, though it comprises an additional 3 coding exons (exons 19, 20, and 21) located at the carboxyl region to generate an extended product of 894 amino acids. Our studies, the first to elucidate the gene structure and chromosomal assignment of NFAR, establish the genetic basis for future NFAR research in humans.

BRCA1 and BRCA2 mutations in ovarian cancer: Covariation with specific cytogenetic features

We analyzed 37 primary invasive carcinomas for BRCA1 and BRCA2 mutations by screening the entire coding regions of both genes. Seven predicted truncating mutations (four in BRCA1 and three in BRCA2) and one novel BRCA1 missense variant (S1542C) were identified (8/37, 22%). Two of the BRCA1 mutations were somatic changes, whereas the remaining three BRCA1 changes and all mutations of BRCA2 were found to be of germline origin. All eight BRCA-positive tumors were serous or seropapillary carcinomas (8/27 serous tumors, 30%), and all but one were poorly differentiated. The correlation between tumor karyotype and BRCA status showed that clonal chromosomal aberrations were present in all BRCA-positive tumors (8/8) compared with 20 of 29 BRCA-negative ones. The most consistently affected region in BRCA-positive tumors was the long arm of chromosome 6; alterations within this arm with a breakpoint in band 6q21 were seen in four of five BRCA1-positive and in two of three BRCA2-positive tumors, but only in four of 20 karyotypically abnormal tumors without BRCA mutations, suggesting that the genetic pathways of tumor progression differ in the two groups. The high frequency of germline BRCA mutations detected in this pilot study (16% of 37 invasive carcinomas) points to the need for more extended analyses of population-based series of patients to determine the true contribution of these predisposing genes to the overall incidence of ovarian cancer in this population.

Molecular cloning, chromosomal localization, and cell cycle-dependent subcellular distribution of the A-kinase anchoring protein, AKAP95

The cyclic AMP-dependent protein kinase (PKA) type II is directed to different subcellular loci through interaction of the RII subunits with A-kinase anchoring proteins (AKAPs). A full-length human clone encoding AKAP95 was identified and sequenced, and revealed a 692-amino acid open reading frame that was 89% homologous to the rat AKAP95 (V. M. Coghlan, L. K. Langeberg, A. Fernandez, N. J. Lamb, and J. D. Scott (1994) J. Biol. Chem. 269, 7658-7665). The gene encoding AKAP95 was mapped to human chromosome 19p13.1-q12 using somatic cell hybrids and PCR. A fragment covering amino acids 414-692 of human AKAP95 was expressed in Escherichia coli and shown to bind RIIalpha. Competition with a peptide covering the RII-binding domain of AKAP Ht31 abolished RIIalpha binding to AKAP95. Immunofluorescence studies in quiescent human Hs-68 fibroblasts showed a nuclear localization of AKAP95, whereas RIIalpha was excluded from the nucleus. In contrast, during mitosis AKAP95 staining was markedly changed and appeared to be excluded from the condensed chromatin and localized outside the metaphase plate. Furthermore, the subcellular localizations of AKAP95 and RIIalpha overlapped in metaphase but started to segregate in anaphase and were again separated as AKAP95 reentered the nucleus in telophase. Finally, RIIalpha was coimmunoprecipitated with AKAP95 from HeLa cells arrested in mitosis, but not from interphase HeLa cells, demonstrating a physical association between these two molecules during mitosis. The results show a distinct redistribution of AKAP95 during mitosis, suggesting that the interaction between AKAP95 and RIIalpha may be cell cycle-dependent.

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.

Involvement of chromosome 6 in endometrial cancer

Cytogenetic investigation was performed on direct preparations of 15 endometrial cancers showing different histotypes. Clonal abnormalities were found in 11 out of 13 analysable cases. The modal chromosome number was near diploid in all cases. The abnormal karyotypes contained relatively simple numerical or structural aberrations in the majority of tumours. In contrast, two neoplasms with serous papillary and mixed mullerian morphological features shared multiple complex changes as well as cytogenetic evidence of intratumoral heterogeneity. The most frequent chromosome abnormality in our series of endometrial neoplasms was 6q deletion, which was detected in serous papillary, endometrioid and mixed mullerian tumours. The loss of the 6q region, which is also frequently involved in ovarian carcinoma, suggests a relationship between endometrial and ovarian cancers based on a common histogenesis.

Karyotypic characteristics of borderline malignant tumors of the ovary: trisomy 12, trisomy 7, and r(1) as nonrandom features

Clonal karyotypic abnormalities were detected in five of 14 cytogenetically analyzed borderline malignant ovarian tumors of clinical stages I-II. One mucinous and one seropapillary tumor had trisomy 7 and r(1)(p36q42) as the sole chromosome abnormality, respectively. Trisomy 12 was found in the remaining three cases. It was the only change in one mucinous and one serous tumor, whereas the third, a seropapillary borderline tumor, had the karyotype 49,XX,+5,+8, +12. These findings, especially when collated with those of previous reports on ovarian borderline tumor cytogenetics, indicate that +12 is the most consistent chromosomal aberration in this group of neoplasms and that also +7 and r(1) are nonrandom features. From the karyotypic point of view, benign ovarian tumors and well-differentiated carcinomas are similar to borderline ovarian tumors, with the possible exception that the former have no tendency to form r(1). Highly malignant carcinomas, on the other hand, are typically much more complex. Chromosome-level changes therefore cannot account for the putative phenotypic passage through the most innocuous tumor stages as epithelial ovarian neoplasms go from benign to fully malignant.

Cytogenetic changes in ovarian mucinous cystadenocarcinoma of low malignant potential with persistent pseudomyxoma peritonei

Minimal cytogenetic data are available for low malignant potential ovarian neoplasms, and none for those complicated by pseudomyxoma peritonei. Cytogenetic analysis was performed on tissue obtained from a patient undergoing repeat evacuation of mucin and mucin-producing implants in pseudomyxoma peritonei originating from an ovarian mucinous cystadenocarcinoma of low malignant potential. Specimens obtained from intraperitoneal implants during one of the cyto/mucin-reductive procedures revealed a mixture of normal female karyotype (46,XX) and an abnormal karyotype with a deletion involving the short arm of chromosome 1, and a balanced translocation involving chromosomes 2 and 6, [46,XXdel(1)(p21p31), t(2;6)(q35;p21)]. The vast majority of the cells from three subsequent cyto/mucin-reductive procedures displayed a normal female karyotype with few cells containing random abnormalities.

Simple numeric abnormalities as primary karyotype changes in ovarian carcinoma

Simple near-diploid karyotypes in ovarian cancer may indicate either primary alterations related to tumor pathogenesis or abnormalities associated with early tumor progression. We have identified a series of 13 epithelial ovarian tumors with very simple karyotypes. Specifically, these karyotypes were near-diploid and displayed numeric abnormalities alone or combined with one or two structural alterations. The present series includes samples from 10 patients with newly diagnosed adenocarcinomas and 3 patients having borderline malignancies. Recurrent numeric abnormalities were identified and included 9/13 cases (69%) with +12, eight cases (62%) with +8, five cases (38%) with +7, three cases (23%) each with +3 or +5, and two cases (15%) with -X. Five cases in this series displayed certain numeric abnormalities (+12, +7, and -X) as the sole anomalies, thereby qualifying as primary karyotype changes. Of the 6 cases with structural abnormalities, 4 involved chromosome 19, 2 involved chromosome 1, and the remaining abnormalities or translocation partners involved other chromosomes. These findings indicate that some numeric abnormalities are primary karyotype alterations in patients with malignant epithelial ovarian tumors and that chromosome 19 may be preferrentially involved in structural rearrangements during early tumor progression.

Polymerase chain reaction allelotyping of human ovarian cancer

We have used a set of microsatellite polymorphisms (MSPs) to examine the location and frequency of allele loss throughout the genome in a panel of 25 human epithelial ovarian tumours. When more than one MSP was employed per arm, mean informativity was 85.2% (range 64-100%). The average fractional allelic loss was 0.28 (range 0-0.65). A high frequency of allele loss was seen at 5q (40%), 9q (48%), 11p (43%), 14q (46%), 15q (40%), 17p (61%), 17q (64%), 19p (45%) and Xp (40%), confirming previous findings at some sites, but also suggesting the existence of new tumour-suppressor genes in regions (9q, 14q, 15q) which have not previously been studied in ovarian cancer. For 9q and 14q, partial loss of the arm was more common than loss of heterozygosity for all loci. There was a significant relationship between allele loss affecting the short arm of chromosome 17 and allele loss affecting 17q (P < 0.001). No other relationship was detected between allele losses at different sites. Polymerase chain reaction allelotyping is suitable for the examination of very small tumour samples and tumours in which classical karyotyping is problematic.

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.

Loss of heterozygosity on chromosome 5 in sporadic ovarian carcinoma is a late event and is not associated with mutations in APC at 5q21-22

Frequent loss of heterozygosity in ovarian carcinoma (OC) has been reported on several different chromosomes. We have studied 27 OCs and corresponding normal tissue for loss of heterozygosity (LOH) using 10 markers detecting polymorphisms on chromosome 5 (two on 5p and eight on 5q). Three tumours showed extra copies, rather than loss, of one homologue. Twelve of 24 remaining tumours showed LOH on 5q (50%), and 8 of 21 on 5p (38%). Of the 12 showing LOH on 5q, 7 showed reduction to homozygosity at all informative markers over the chromosome. The remaining 5 showed LOH over all of 5q. These data are consistent with the localisation of a tumour suppressor gene on 5q involved in OC. A good candidate is the APC gene, which is mutated in a number of adenocarcinoma derived from several tissues and is located at 5q21-22. The APC gene was studied in 40 ovarian tumours, including all the OCs showing LOH, by single-strand conformation polymorphism (SSCP). Analysis of all the exons containing published mutations (approximately 4.7 kb of the cDNA) did not reveal any band shifts that could be attributed to mutations. However, a new polymorphism was detected, as well as 7 known polymorphisms. Together, these data indicate that (1) LOH is common on chromosome 5 in OC, (2) APC is not mutated in OC, and (3) another gene (or genes) on chromosome 5q is responsible for the LOH seen.

Cytogenetic studies of epithelial ovarian carcinoma

We performed cytogenetic studies of 36 human epithelial ovarian carcinomas using in situ culture and robotic harvest. We obtained analyzable metaphases of all 36 tumors (100%). One or more chromosomally abnormal clones were observed in 80% of tumors. Common clonal chromosome gains (each occurring in six or more cases) included +1, +2, +3, +6, +7, +9, and +12. Common clonal chromosome losses (occurring in 12 or more cases) included -X, -4, -8, -11, -13, -15, -17, and -22. Common clonal structural abnormalities (occurring in four or more cases) involved regions 1p36, 1q32, 1q42, 3p13-->p26, 3q26-->q29, 7p22, 9q34, 11p13-p15, 17q21-->q23, 19p13.3, and 19q13.3. Trisomy 12 was noted as the sole anomaly in three of five borderline and grade 1 tumors. Two grade 2 tumors contained i(1q), -14, -15 and -22. The results suggest that the pathogenesis of borderline and low-grade tumors may differ from that of higher grade tumors. Two high-grade tumors had an apparent translocation between 17q21 and 19p13.3, two chromosome regions believed to be critical to ovarian carcinogenesis.

Mapping of the 19p13 breakpoint in an ovarian carcinoma between the INSR and TCF3 loci

Chromosome rearrangements involving band 19p13 have been described in about half of all ovarian carcinomas. Four ovarian carcinomas with translocations of 19p13 were investigated with 11 DNA probes for markers localized to this band. All markers exhibited normal restriction patterns, suggesting that they were not rearranged. The 19p13 breakpoint of one tumor was mapped to a location between the INSR and the TCF3 loci.

Integration of Epstein Barr virus near the breakpoint of a translocation 11;19 in a Burkitt's lymphoma cell line

The physical state of Epstein Barr virus (EBV) DNA was analyzed in the Burkitt's lymphoma (BL) cell line BL60 and in the autologous EBV-immortalized lymphoblastoid cell line (LCL) IARC 277 by Gardella gel analysis, Southern blotting, and nonradioactive in situ hybridization to metaphase chromosomes. Although only episomal viral DNA was detected in the LCL, the 6-12 copies of EBV DNA in the BL cell line are integrated in one site of the host cell genome. The integration site is located near the breakpoint of a translocation 11;19 which is present in this cell line in addition to the BL-specific t(8;22).

Loss of heterozygosity and amplification on chromosome 11q in human ovarian cancer

The 11q13 chromosomal region encodes oncogenes relevant to a variety of human cancers as well as a tumour suppressor gene implicated in multiple endocrine neoplasia type 1. In addition, high affinity folate receptor (FOLR1), which maps to 11q13.3-13.5, is expressed at an elevated level on the surface of over 80% of nonmucinous epithelial ovarian cancers. Further telomeric, 11q breakpoints are found in many cancers. We studied the involvement of 11q markers in ovarian cancer by looking for tumour-specific loss of heterozygosity (LOH), as well as amplification or rearrangements that might explain the overexpression of FOLR1. Twenty eight epithelial ovarian cancers, along with lymphocyte DNA from the same individual were used for Southern blotting with polymorphic probes from 11q. PCR primers from 11q23.3 were also used. The 11q13 band was amplified in four out of 28 cancers. The amplicon included the probe D11S146 as well as FGF3 (formerly INT2) and FOLR1 in one out of these four cases, thus crossing the bcl1 translocation breakpoint. LOH was seen in three out of 16 cases with FGF3 (11q13). A much higher frequency of LOH (8/12) was found at 11q23.3-qter, implying the presence of a tumour suppressor gene in this region.

Isochromosome 1q as the sole karyotypic abnormality in a Sertoli cell tumor of the ovary

Sertoli cell tumors are rare low-grade malignancies occurring in the testis and the ovary. No chromosome studies of this tumor type have yet been reported. We observed an extra i(1q) as the sole chromosome anomaly in an ovarian Sertoli cell tumor.

Cytogenetic analysis of an adenoid cystic carcinoma of the Bartholin's gland. A rare, semimalignant tumor of the female genitourinary tract

Cytogenetic analysis has been performed on short-term cultures from a 56-year-old woman suffering from an adenoid cystic carcinoma of Bartholin's gland. Beside a normal female karyotype, the tumor revealed an abnormal cell line with complex chromosome changes involving the chromosomes 1, 4, 6, 11, 22, and 14. The mainly structural and nonbalanced rearrangements led to the loss of the chromosome segments 1p31----qter, 4q22----q28, 6p12----qter, 11p11.2----pter, 14q24----qter, and 22q13----qter. Clonal numerical aberrations were not observed. To our knowledge, such a tumor has to-date not been cytogenetically investigated.

Cytogenetic findings in a malignant fibrous histiocytoma of the gallbladder

We report the cytogenetic findings in a rare tumor, a malignant fibrous histiocytoma of the gallbladder. Four related clones, two near-diploid and two near-tetraploid, which appeared to have been formed by a doubling of the near-diploid clones, were present. Numerous structural and numerical abnormalities characterized the tumor. Structural rearrangements included reciprocal translocations, translocations of unidentified material onto chromosomes, and deletions. Chromosomes involved in the rearrangements included 1, 3, 10, 12, 14, 16, and 19. Numerical changes included trisomy of chromosomes 2, 8, 10, and 20. Double minute chromatin bodies ranging in number from 5 to several were present in over a third of the cells.

Absence of structural rearrangements of chromosome 11 in human primary malignant melanoma

Cytogenetic analysis of 10 primary and 18 metastatic malignant melanomas revealed that structural abnormalities of chromosome 11 were present in 50% of metastatic lesions and were not found in primary tumors. Our findings suggest that chromosome 11 aberrations represent secondary changes in malignant melanoma tumorigenesis.

Prognostic impact of chromosome aberrations in ovarian cancer

Clinico-cytogenetic correlations were assessed in 88 patients with malignant ovarian tumours. Cytogenetic analysis of the primary tumours yielded normal karyotype (N) in 33 patients and abnormal karyotypes (A) in 55 patients. Within the A group, seven tumours had simple abnormalities (AS), i.e., numerical changes only or a single structural aberration, and 48 had karyotypes with complex aberrations (AC). A correlation analysis between groups N and A revealed that cytogenetic abnormalities were more often found among seropapillary tumours, and that cases with abnormal karyotypes on average were of higher stage and more often had residual tumour mass after initial surgery (P less than 0.05 for all variables). When the three groups N, AS, and AC were compared, they were found to be significantly different with regard not only to the three parameters mentioned above, but now tumour grade also appeared to correlate with karyotypic pattern (P = 0.001), with poorly differentiated tumours having the most complex karyotypes. In a correlation analysis between karyotypic pattern and survival, group A patients had shorter survival than group N (P = 0.049). In the corresponding analysis between groups N, AS, and AC, the differences were also significant (P = 0.039), with shorter survival in group AC than in groups N and AS. Stage, grade, residual tumour after primary surgery, and performance status also correlated with survival time. A multivariate analysis identified abnormal karyotype as being independently associated with short survival in advanced clinical stages (P = 0.030) of ovarian carcinoma. We conclude that cytogenetic analysis of tumour cells may be of clinical value in the assessment of prognosis in patients with malignant ovarian tumours.

Cytogenetic analysis of 57 primary prostatic adenocarcinomas

Cytogenetic analysis after short-term culture in vitro of primary tumor samples was attempted in 82 patients with prostatic cancer. Tumor material was obtained by radical prostatectomy or transurethral resection. Successful cytogenetic studies were performed on 57 tumors of which five were well, 30 moderately, and 22 poorly differentiated adenocarcinomas. Only normal karyotypes were found in 24 tumors. Structural nonclonal aberrations were detected in 18 and clonal karyotypic abnormalities in 15 tumors. The most common clonal numerical aberration was loss of the Y chromosome; a missing Y was found in six tumors, in three of these as the sole anomaly. Clonal structural chromosomal rearrangements, usually accompanied by numerical changes, were detected in 12 tumors. The rearrangements involved 18 of the 22 autosomes and the X chromosome. Chromosomes 1, 7, and 10 were most frequently affected. Deletions, duplications, inversions, insertions, and balanced as well as unbalanced translocations were represented. The breakpoints in chromosome 1 were scattered along both the short and long arms with no obvious clustering, whereas those in chromosomes 7 and 10 were clustered at bands 7q22 (two deletions and two duplications in four different tumors) and 10q24 (two translocations, one deletion, and one inversion in four tumors). One additional tumor displayed a derivative chromosome 10 with a breakpoint in 10q23, and one had monosomy 10. Altogether, these abnormalities resulted in loss of 10q24----qter in five tumors. Monosomy 8 and rearrangements of the short arm of chromosome 8 leading to loss of 8p21----pter were seen in four tumors. Double minute chromosomes were found in two tumors.

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.

Clonal chromosomal abnormalities in hemangiopericytoma

We report the cytogenetic findings in nine hemangiopericytomas studied after short-term culture. Clonal chromosome abnormalities were present in four cases. One case had a simple translocation (12;19)(q13;q13.3) as the sole abnormality whereas complex and multiple chromosomal abnormalities involving almost all chromosomes in the complement characterized tumors from the three other cases.

Improved interpretation of complex chromosomal rearrangements by combined GTG banding and in situ suppression hybridization using chromosome-specific libraries and cosmid probes

Chromosome aberrations of a hypodiploid ovarian carcinoma cell line (modal chromosome number 38) having a complex karyotype were analyzed using biotinylated DNA library probes that specifically hybridize to chromosomes 3, 6, 7, 8, 11, 13, and 16 from telomere (pter) to telomere (qter). A series of cosmid probes localized to the short arm of chromosome 16 were used to further investigate one of the two aberrant chromosomes 16 present in this cell line. The competitive in situ suppression (CISS) hybridization of DNA-libraries was mostly performed subsequent to GTG-banding of the same metaphase cell in order to interpret the hybridization signals optimally. This combined approach made it possible to detect the origin of chromosomal material that could not be identified using GTG-banding. Furthermore, the in situ hybridization techniques appeared to be helpful in the characterization of complex translocations and for accurate breakpoint determination.

Bilateral ovarian carcinoma: cytogenetic evidence of unicentric origin

Cytogenetic analyses were performed on the tumors from both ovaries in 15 patients with bilateral ovarian carcinoma. In 4 of them, omental implants were also examined. Abnormal karyotypes were detected in 11 cases. The baseline karyotypes in the 2 tumorous ovaries were identical in each patient, indicating that bilateral ovarian cancer develops by metastatic spreading. There was no clear-cut evidence of differences in the clonal evolution between the tumors of the 2 ovaries, and hence the side harboring the primary tumor could never be determined. The metastatic nature of the omental implants was proved by the fact that their karyotypes were indistinguishable from those of the ovarian tumor tissue.

Simple numerical chromosome aberrations in well-differentiated malignant epithelial tumors

Cytogenetic analysis of four well-differentiated malignant epithelial tumors revealed primary clones with only numerical abnormalities. The karyotypes were 49,XX, +5, +5, +7, +7, -17/50,XX, +5, +5, +7, +7, -17, +r in an adenocarcinoma of the lung; 47,XX, +3/47,XX, +5/47,XX, +7 in a squamous cell carcinoma of the epiglottis; 47,XX, +5/48,XX, +5, +10 in a squamous cell carcinoma developing in an ovarian dermoid cyst; and 52,XX, +5, +7, +8, +14, +15, +21 in a seropapillary ovarian adenocarcinoma. Also, in previously published cases exclusively numerical aberrations were much more common in highly differentiated epithelial tumors (22/74) than in moderately to low-differentiated carcinomas (13/281). Our findings and the literature data thus agree with a developmental scheme in which numerical changes, possibly reflecting an early-onset genomic instability in the tumor cells, may precede massive structural anomalies in the gradual malignization of epithelial tumors.

Trisomy 12 is a consistent chromosomal aberration in benign ovarian tumors

Clonal karyotypic abnormalities were detected in 7 of 42 cytogenetically analyzed benign ovarian tumors. An adenofibroma had -X and a mucinous cystadenoma had t(1;11)(q25;q23) as the sole abnormality. Trisomy 12 was found in the remaining five tumors. It was the only change in two fibromas and a serous cystadenoma; the fourth tumor, a mucinous cystadenoma, had one clone with +12 and one with +12 and +10, and the fifth tumor, a fibrothecoma, had +4,+9,+12. The finding of trisomy 12 in five of seven karyotypically aberrant tumors suggests that this aberration characterizes a hitherto unrecognized cytogenetic subgroup of benign ovarian neoplasms.