Trisomy 7 and sex chromosome loss need not be representative of tumor parenchyma cells in malignant glioma

Deletions on Chromosome Y and Downregulation of the SRY Gene in Tumor Tissue Are Associated with Worse Survival of Glioblastoma Patients

BACKGROUND

Biological causes of sex disparity seen in the prevalence of cancer, including glioblastoma (GBM), remain poorly understood. One of the considered aspects is the involvement of the sex chromosomes, especially loss of chromosome Y (LOY).

METHODS

Tumors from 105 isocitrate dehydrogenase (IDH) wild type male GBM patients were tested with droplet digital PCR for copy number changes of ten genes on chromosome Y. Decreased gene expression, a proxy of gene loss, was then analyzed in 225 IDH wild type GBM derived from TCGA and overall survival in both cohorts was tested with Kaplan-Meier log-rank analysis and maximally selected rank statistics for cut-off determination.

RESULTS

LOY was associated with significantly shorter overall survival (7 vs. 14.6 months, p = 0.0016), and among investigated individual genes survival correlated most prominently with loss of the sex-determining region Y gene (SRY) (10.8 vs. 14.8 months, p = 0.0031). Gene set enrichment analysis revealed that epidermal growth factor receptor, platelet-derived growth factor receptor, and MYC proto-oncogene signaling pathways are associated with low SRY expression.

CONCLUSION

Our data show that deletions and reduced gene expression of chromosome Y genes, especially SRY, are associated with reduced survival of male GBM patients and connected to major susceptibility pathways of gliomagenesis.

Genomic aberrations in 80 cases of primary glioblastoma multiforme: Pathogenetic heterogeneity and putative cytogenetic pathways

Screening the whole glioblastoma multiforme (GBM) genome for aberrations is a good starting point when looking for molecular markers that could potentially stratify patients according to prognosis and optimal treatment. We investigated 80 primary untreated GBM using both G-banding analysis and high-resolution comparative genomic hybridization (HR-CGH). Abnormal karyotypes were found in 83% of the tumors. The most common numerical chromosome aberrations were +7, -10, -13, -14, -15, +20, and -22. Structural abnormalities most commonly involved chromosomes 1 and 3, and the short arm of chromosome 9. HR-CGH verified these findings and revealed additional frequent losses at 1p34-36, 6q22-27, and 19q12-13 and gains of 3q26 and 12q13-15. Although most karyotypes and gain/loss patterns were complex, there was also a distinct subset of tumors displaying simple karyotypic changes only. There was a statistically significant association between trisomy 7 and monosomy 10, and also between +7/-10 as putative primary aberrations and secondary losses of 1p, 9p, 13q, and 22q. The low number of tumors in the rarer histological tumor subgroups precludes definite conclusions, but there did not seem to be any clear-cut cytogenetic-pathological correlations, perhaps with the exception of ring chromosomes in giant cell glioblastomas. Our findings demonstrate that although GBM is a pathogenetically very heterogeneous group of diseases, distinct genomic aberration patterns exist.

Gain of 1q and loss of 22 are the most common changes detected by comparative genomic hybridisation in paediatric ependymoma

Ependymomas are the third most common brain tumour in the paediatric population. Although cytogenetic and molecular analyses have pinpointed deletions of chromosomes 6q, 17, and 22 in a subset of tumours, definitive patterns of genetic aberrations have not been determined. In the present study, we analysed 40 ependymomas from paediatric patients for genomic loss or gain using comparative genomic hybridisation (CGH). Eighteen of the tumours (45%) had no detectable regions of imbalance. In the remaining cases, the most common copy number aberrations were loss of 22 (25% of tumours) and gain of 1q (20%). Three regions of high copy number amplification were noted at 1q24-31 (three cases), 8q21-23 (two cases), and 9p (one case). Although there was no association with the loss or gain of any chromosome arm or with benign versus anaplastic histologic characteristics, the incidence of gain of 7q and 9p and loss of 17 and 22 was significantly higher in recurrent versus primary tumours. This study has identified a number of chromosomal regions that may contain candidate genes involved in the development of different subgroups of ependymoma.

Karyotype studies in 18 ependymomas with literature review of 107 cases

Cytogenetic studies from 17 pediatric ependymomas and 1 ependymoblastoma are presented. Eight tumors had abnormal karyotypes. Another 107 published cases of cytogenetic analyses from pediatric and adult ependymomas or ependymoblastomas were reviewed. Of the total 125 tumors, 83 (66%) had abnormal karyotypes, of which 24 had a sole autosomal abnormality. Approximately one third had monosomy 22 (-22) or breakpoint 22q11-13, with a higher incidence in adult (56%) versus pediatric (28%) tumors. Structural abnormalities of chromosomes 1, 6, and 17, and numerical abnormalities of 7, 9, 12, and 20, in particular, are also discussed. Although no primary cytogenetic abnormality is evident, these findings may provide direction for additional investigations regarding the classification of these tumors.

A recurrent 19q11-12 breakpoint suggested by cytogenetic and fluorescence in situ hybridization analysis of three glioblastoma cell lines

Loss of genetic material at chromosome 19 is a rather frequent finding in malignant gliomas. Loss of heterozygosity at region 19q13.3 is common in oligodendrogliomas and is also present, together with other genetic alterations on the same chromosome, in glioblastoma multiforme (GBM). Here we describe the results of cytogenetic and fluorescence in situ hybridization analysis on three GBM cell lines in which a series of complex chromosomal rearrangements affecting chromosome 19 were present. These genetic alterations suggest the presence of a common breakpoint at 19q11-12 which may point to the localization of a fragile site and/or to the presence of tumor suppressor gene(s) in the pericentromeric region of chromosome 19.

Chromosome arm 6q loss is the most common recurrent autosomal alteration detected in primary pediatric ependymoma

We analyzed 23 samples of primary pediatric ependymoma for significant gains or losses of genomic DNA, using comparative genomic hybridization (CGH) and a rigorous statistical approach. Nine of the tumors in this series (39%) appeared normal by CGH. The remainder had a limited number of regions of genomic imbalance, most often involving losses of chromosome arms 6q and 22q and the X chromosome, or gains of either 1q or 9. Recurrent and exclusive losses of 6q or 22q suggest that these regions harbor tumor suppressor genes that may contribute independently to the pathogenesis of childhood ependymoma.

Clonal chromosome abnormalites found in three non-neoplastic proliferative brain lesions

Chromosome analysis was made of brain lesions from three patients which, according to classical histopathological criteria, did not contain tumor cells. In addition to normal cells, we identified abnormal karyotypes with clonal numerical and structural chromosome alterations in at least two independently originated primary cultures from each lesion. Our data suggest that chromosomal aberrations can exist in vivo in non-neoplastic lesions. Other abnormalities may be due to genetic instability manifested only in vitro (culture artifacts) or may already have been present in brain tissue, reflecting previous chromosome damage (as a result of exposure to chemical treatment or enviromental clastogens).

Genomic changes in glioblastoma cell lines detected by comparative genomic hybridization

Comparative genomic hybridization serves as a screening test for regions of copy number changes in tumor genomes. We have applied the technique to map DNA gains and losses in 5 cell lines derived from glioblastoma multiforme, the most common primary neoplasm of the central nervous system. The most frequent losses occurred on chromosomes 10 and 13. The most common gains were observed on chromosomes 5, 6, 7 and 20. Some novel sites of genomic alterations were also observed. Analysis of common areas of loss and gain in these cell lines provides a basis for future attempts to more finely map these genetic changes and for elucidation of genes involved in tumor progression.

Non-isotopic molecular cytogenetics in neuro-oncology

The molecular genetic analysis of brain tumours has been the focus of considerable interest for a number of years. However, these studies have been largely directed towards understanding the fundamental biological processes involved in tumorigenesis and the techniques which have been used require considerable molecular biological skills. Unfortunately, there has not been the impetus to correlate basic biological studies with clinical or neuropathological features. The development of non-isotopic molecular cytogenetic in situ hybridization (ISH) techniques which can be applied to archival tumour material provides an opportunity to address a wide range of neuropathological questions at a genetic level. Identification of specific chromosomes has been made possible by the isolation of probes which recognize the highly repeated sequences present in the centromeric regions of individual chromosomes. Libraries of human chromosome-specific painting probes are also available. A range of probes which bind to the whole or part of specific single copy genes are becoming available. These can be detected with either fluorochromes with different emission colours or with enzymatic detection systems in either interphase nuclei derived from fresh, fixed and embedded tumour samples, touch preparations or smears (so-called 'interphase cytogenetics') as well as conventional metaphase spreads. Comparative genomic hybridization can be used to scan the entire genome for deletions or amplifications without any pre-existing information about the likely locations of these abnormalities or the availability of any specific DNA probes. These techniques can be used to identify aneuploidy or structural alterations in individual chromosomes and are likely to yield important information about the location of genes important in the pathogenesis of brain tumours and may also provide the basis for the refinement of diagnostic or prognostic criteria of these neoplasms.

Cytogenetic evaluation of 20 primary breast carcinomas

Chromosome analysis was performed on samples from 20 Brazilian patients with breast cancer. All the samples were from untreated patients who presented the clinical symptoms for months or years before surgical intervention. Six cases showed axillary lymph node metastases. Clonal chromosome abnormalities were detected in all cases. The numerical alterations most frequently observed involved the loss of chromosomes X, 19, 20, and 22 followed by gain of chromosomes 9 and 8. Among the structural anomalies observed, there was preferential involvement of chromosomes 11, 6, 1, 7, 3, and 12, supporting previous reports that these chromosomes may harbour genes of importance in the development of breast tumors. Two cases with a family history of breast cancer had in common total or partial trisomy 1.

Chromosomal characteristics of childhood brain tumors

In the present cytogenetic analysis of 116 pediatric brain tumors, chromosomal abnormalities were demonstrated in 44 cases, 48 cases revealed only 46,XX or 46,XY cells, and 24 cases were nonproductive. In contrast to studies of adult brain tumors in which isolated loss of one X or the Y chromosome is often encountered, 45,X,-X and 45,X-Y stemlines or sidelines were not observed in this series of childhood tumors. Among the 17 medulloblastomas with cytogenetic abnormalities, chromosome 1 was most frequently affected by structural deviations; the most prevalent specific alteration (7 of 17 tumors) was loss of 17p, through i(17)(q10) or unbalanced translocation. The majority of low grade astrocytomas had normal stemlines, although one pilocytic astrocytoma and one cerebellar astrocytoma had frequent telomeric associations and a second pilocytic astrocytoma had a clone with trisomy 11. Thirteen of 19 high-grade and recurrent astrocytic tumors had abnormal stemlines that were approximately equally divided among cases with chromosomal counts in the near-diploid, hyperdiploid, and near-triploid-tetraploid ranges. Although no consistent abnormalities were observed, subsets of cases had structural abnormalities of chromosome 3, 7q, 9q, or 17p. The cases of childhood brain tumors described here demonstrate that 45,X,-X, and 45,X,-Y stemlines or sidelines are rare in these tumors and confirm frequent loss of 17p in medulloblastomas. High-grade astrocytic tumors in children frequently have abnormal stemlines, often in the hyperdiploid and polyploid ranges, and they differ from high-grade gliomas in the adult by lacking consistent numerical and structural deviations.

Therapy-related chromosomal changes and cytogenetic heterogeneity in human gliomas

The karyotypes of 18 primary 'untreated' gliomas, 6 recurrent gliomas treated with radiotherapy and/or chemotherapy and 2 gliomas before and after treatment are described, based on observations using standard cytogenetic techniques. In comparison to the untreated gliomas there were relatively consistent chromosome differences in the treated gliomas, including (1) deletions of the long arm of chromosome 7 with breakpoint at q22, possibly induced by alkylating agents, and (2) numerous single cell abnormalities or unrelated clones of structural abnormalities, presumably induced by radiotherapy.

Nonrandom gain of chromosome 7 in central neurocytoma: a chromosomal analysis and fluorescence in situ hybridization study

Central neurocytoma is a benign, slow-growing neoplasm with favourable prognosis. Biomolecular analysis has failed to demonstrate significant alterations, and no cytogenetic alterations have been reported. In this study we demonstrate chromosome 7 gain in three of nine neurocytomas (33%). Traditional cytogenetic analysis performed in four of the nine cases identified trisomy 7 as the sole chromosomal abnormality in one case. Interphase cytogenetics utilizing fluorescent in situ hybridization (FISH) on cell suspensions from formalin-fixed paraffin-embedded tumour tissue performed in all nine cases detected trisomy 7 in two more cases and tetrasomy in another. Our results suggest that chromosome 7 gain is a feature of neuroectodermal tumorigenesis, possibly conferring growth advantage on the neoplastic cells. FISH on interphase nuclei is a valuable adjunct in the genetic evaluation of rare central nervous system neoplasms with low baseline proliferative activity.

Cytogenetic analysis of a case of myxoid liposarcoma with cartilaginous differentiation

The cytogenetic analysis of a patient with a myxoid liposarcoma exhibiting cartilaginous differentiation is presented. A complex translocation involving chromosome 12, 16, and 19 was found, instead of the t(12;16), specific for myxoid liposarcoma. The involvement of 19q13 in a tumor with cartilaginous differentiation, and the assignment of TGF beta 1 to 19q13.1-13.2, which appears to play a role in the formation of bone and cartilage, suggest a possible relation between both.

Short arm of chromosome 1 aberration recurrently found in pigmented villonodular synovitis

Pigmented villonodular synovitis (PVNS) is a relatively uncommon benign lesion that is characterized by diffuse synovial proliferation, mainly occurring in knee joints. Cytogenetic reports about this lesion are few and they describe the presence of numerical and structural chromosome aberrations. We obtained PVNS tissue from the left knee joint of a 53-year-old female, and performed cytogenetic analysis. Fluorescence in situ hybridization (FISH) was also performed by using the formalin fixed, paraffin embedded PVNS tissue. Two seemingly unrelated clones were found: the first clone had structural abnormalities of chromosome 1, 3, and 18, and the second one had trisomy 7 as a sole numerical abnormality. FISH using a chromosome 7 specific alpha-satellite DNA probe revealed that interphase nuclei possessed two or three signals. We describe the clonal aberrations found in a case of PVNS. The deleted lesion of the chromosome 1 (1p10-1p31.3) includes the locus of coagulation factor III gene (1p22-p21), and the coagulation factor V (1q21-q25) locus includes another breakpoint that is 1q25. In addition, recurrent structural abnormalities at the short arm of chromosome 1 have been reported. These facts might play some role in the hemorrhagic tendency and histogenesis of these lesions.

Combined cytogenetic and molecular genetic analyses of fifty-nine untreated human prostate carcinomas

G-banding analyses and molecular genetic investigations (fluorescence in situ hybridization (FISH) and loss of heterozygosity (LOH) studies) were performed in 59 tumor and nontumorous samples of human prostate carcinoma. Clonal chromosome aberrations were detected in 16 tumors of which nine were poorly differentiated (G3) and 11 in an advanced stage (pT3). Six cases showed numerical chromosome aberrations. The most common numerical aberrations were trisomy 7 and loss of the Y chromosome each present in three tumors. Clonal structural aberrations were detected in 12 tumors. Deletions could be observed in two cases affecting chromosome 6q23 and in two cases affecting chromosomal region 16q. A structural variant of the pericentromeric heterochromatin of chromosome 9 became apparent in six cases. The Y chromosome was involved in clonal translocations in two cases, additionally an inversion occurred on chromosome 19 in one case. All clonal chromosomal changes were found exclusively in the tumor sample. For an analysis of the pericentromeric heterochromatin of chromosome 9, FISH using a chromosome 9-specific sat III DNA probe was carried out on metaphase preparations of tumor and nontumorous tissues of two cases showing var(9)(qh). The FISH data suggest a deletion in the pericentromeric heterochromatin. Loss of heterozygosity studies on chromosomal regions 10q and 16q were carried out because both chromosomes were frequently affected by nonclonal structural aberrations. Loss of heterozygosity could be verified in 11 cases.

Massive cytogenetic heterogeneity in a pancreatic carcinoma: fifty-four karyotypically unrelated clones

Chromosome analysis after short-term culture revealed remarkable cytogenetic heterogeneity in a pancreatic carcinoma. The patient had no prior history of radio- or chemotherapy. A total of 54 aberrant, near-diploid, karyotypically unrelated clones were identified, three of which displayed clonal evolution. The abnormalities were unbalanced in 30% of the clones. From one to eight karyotypic anomalies per clone were found. Numerical changes were rare, whereas structural aberrations were numerous and diverse and included deletions, duplication, insertions, inversions, translocations, ring formation, and telomeric associations. All chromosomes except No. 15 were involved in structural rearrangements, chromosomes 1, 6, 7, 8, 11, and 12 being the most frequently affected. A similarly massive cytogenetic polyclonality has never been reported previously. Although the spectrum of epithelial neoplasms characterized by karyotypically unrelated clones is increasing, the pathogenetic role of this type of cytogenetic intratumor heterogeneity remains unknown.

Accumulation of chromosomal changes in human glioma progression. A cytogenetic study of 50 cases

Cytogenetic studies of 50 human gliomas, including three oligodendrogliomas, 16 grade I-III astrocytomas, and 31 glioblastomas multiforme, were performed using the short-term tissue culture method. The most common numerical chromosome aberrations were +7, -9, -10, -14, and loss of a sex chromosome. Structural changes involved predominantly the following chromosome arms: 1q, 2q, 6q, 7q, 9p, 14q, 17p, and 18p. Losses of chromosomes 9, 10, and 14, often occurring simultaneously and in polyploid clones, were observed almost exclusively in high-grade gliomas, and appear to constitute important events during glioma progression.

Cytogenetics of malignant gliomas. II. The sex chromosomes with reference to X isodisomy and the role of numerical X/Y changes

Sex chromosomal monosomy with total loss of an X or Y is frequently observed in malignant gliomas. Beyond that, not much is known about the behavior of the sex chromosomes in these tumors. We noted loss of the X from 3 of 13 gliomas from women (23%) compared to loss of the Y from 16 of 28 gliomas from men (57%). There were two structural rearrangements of the Y (an inversion and a translocation with chromosome 4). Most unexpectedly, clones with sex chromosome reversal were encountered in 3 cases. These XX clones in gliomas from men are perforce the consequence of Y loss coupled with X isodisomy, a nonrandom sequence of sex chromosome changes. We examined the company kept by numerical X and Y changes in clones and found that clones with numerical sex chromosome changes had fewer autosomal abnormalities, reflecting a distinct tendency to clonal separation of sex chromosome from autosomal abnormalities. We conclude that the sex chromosome changes are not a necessary part of the neoplastic process in malignant gliomas but that they must be of biologic significance to the brain since they are highly nonrandom in frequency, type, and sequence in brain cells.

Cytogenetics of malignant gliomas: I. The autosomes with reference to rearrangements

Autosomal chromosome abnormalities are far from always detectable and, when detected, far from fully consistent in malignant gliomas. In 15 of 41 malignant gliomas, we found autosomal chromosome aberrations ranging from solitary trisomy to a wildly abnormal polyploid complement. The sequence of chromosome events appears to proceed from the normal to the near-diploid state (via structural and numerical changes) to near-tetraploidy (via polyploidization), and finally toward near-triploidy (via chromosome loss and additional rearrangements). Characteristic chromosome changes of trisomy 7 and monosomy 10 were repeatedly found, usually together in the same cell clones. In only one case was trisomy 7 an isolated change. We observed structural rearrangements of chromosomes 7 and 10 which may be of some use in mapping specific genes duplicated or deleted by the whole-chromosome changes of chromosomes 7 and 10. Nonrandom structural changes of other autosomes, including chromosomes 1, 5, and 11, fit with the model of malignant glioma as a process involving multiple genes. An unusual concentration of breakpoints in 12q13, juxtaposing it to at least five other regions, reflects the presence of genetic information in 12q13 important to the development of malignant gliomas.

Chromosomes in gliomatosis cerebri

Gliomatosis cerebri is a rare brain tumor which histologically resembles a diffuse cerebral astrocytoma. It can simultaneously infiltrate multiple sites in the cerebrum, cerebellum, brainstem, and spinal cord. This remarkable diffuseness has led to the idea that gliomatosis cerebri does not derive from a solitary focus but must arise from a broad field of glial cells. We studied the chromosomes from gliomatosis cerebri in a 12-year-old boy by conventional cytogenetics and fluorescence in situ hybridization (FISH). Aside from normal cells, we found a majority of cells with the karyotype 44,XY,del(6)(q25),del(14)(q21), der(15;21)(q10;q10),add(18)(q22),del(19)(p12),add(20)(p13),-21. A smaller proportion of cells had 88 chromosomes with a doubling of this abnormal karyotype. These findings are consistent with a clonal neoplasm stemming from a single cell. The chromosome changes we observed, with the possible exception of the chromosome 6 deletion, did not resemble those frequently found in astrocytomas. Gliomatosis cerebri may therefore belong to a separate category of brain tumors.

Cytogenetic studies of breast carcinomas: different karyotypic profiles detected by direct harvesting and short-term culture

Chromosome analysis was performed on samples from 85 consecutive patients with breast cancer by one or more of three different methods: direct harvest, culture after mechanical disaggregation, and culture after collagenase digestion. Metaphases suitable for karyotyping were obtained in 70% of the cases; direct harvest yielded metaphases in 29% and cultures without and with digestion in 40% and 59%, respectively. Chromosomal abnormalities were detected in 37 cases. Cells judged to be phenotypically abnormal in culture were twice as likely to reveal chromosomal aberrations as normal-looking cells. Eight cases showed multiclonal abnormalities. Significant differences were detected in the karyotypic profile depending on the method used. With direct harvest, the yield of complex chromosomal changes was 87%, compared to 44% after culture of digested tissue (P < 0.01), and also polyploidy was more common in direct-harvested samples. Detailed karyotypic analysis was possible in 29 primary tumors. The chromosomes most frequently involved were 1, 3, 7, 11, 16, and 17. Recurrent structural abnormalities were der(1;16)(q10;p10), i(1)(q10), del(6)(q21), and del(1)(p22). Breakpoints clustered to the centromere regions of chromosomes 1, 3, 11, 15, and 16 and to the short arms of chromosomes 7, 17, and 19. Seven of twenty-nine fully analyzed cases had a family history of breast cancer, and changes of chromosomes 1, 3, and 15 seemed to be more common in these cases. There was an association between karyotype and survival: The 3 year survival was 63% in patients with complex karyotypic changes and 92% in those without complex changes.

Cytogenetically detected clonal heterogeneity in a duodenal adenocarcinoma

A primary duodenal adenocarcinoma, a tumor type for which no previous chromosome data existed, was cytogenetically analyzed after short-term culture. The main tumor mass was localized in the pancreatic head, but the histopathologic examination revealed its duodenal origin. A total of six abnormal, karyotypically unrelated, clones were identified. The largest exhibited clonal evolution and consisted of two subclones with massively rearranged karyotypes in the hypodiploid and hypotetraploid range. Chromosome imbalances brought about by these complex changes were gain of 1q, losses of chromosomes 6 and 9, and total or partial losses of 1p, 3p, 3q, 9p, 10p, 17p, 17q, 18q, 20p, and 20q. The remaining five smaller clones had 1-2 numerical or balanced structural chromosome aberrations. The present study thus revealed yet another epithelial tumor type characterized by karyotypically unrelated clones. For this as for other tumors, the pathogenetic significance of such cytogenetic polyclonality remains uncertain.

Clonal chromosome aberrations in a case of nodular fasciitis

We report a case of nodular fasciitis with clonal chromosome aberrations including a reciprocal t(3;15)(q21;q22) and interstitial deletion (13)(q14q21).

Increasing complexity of the karyotype in 50 human gliomas. Progressive evolution and de novo occurrence of cytogenetic alterations

We studied the karyotypes of eight differentiated gliomas, 19 anaplastic gliomas, and 23 glioblastomas (GBM). Normal stemlines were present in 70% of the differentiated and anaplastic gliomas; abnormalities were mostly characterized by loss of sex chromosomes. In GBM, on the contrary, only 13% of the stemlines were normal and three groups, 45,XO, near-diploid, and near tetraploid, could be identified. The most frequent alterations among GBM were: total or partial loss of chromosome 10 in nine cases, structural abnormalities of chromosome 9 in seven cases, and loss of the Y chromosome in stemline clones of seven cases. Less frequent abnormalities included chromosomes 7, 1, 3, and 19. Our data support the cytogenetic model of gliomas as multi-stage tumors. GBM, in particular, can originate from the evolution of astrocytomas but can also develop de novo. In both cases loss of genetic material on chromosome 10 seems to play a crucial role.

Molecular analysis of chromosome 1 abnormalities in human gliomas reveals frequent loss of 1p in oligodendroglial tumors

Alterations of the short arm of chromosome 1 are recurrently found in cytogenetic analysis of malignant gliomas, and deletions of 1p36-p32 region characterize at least the higher-grade tumors, glioblastoma multiforme. Molecular analysis of tumor-derived and normal genomic DNA from 57 cases of gliomas, using a panel of chromosome 1-specific DNA probes showed LOH in 16 tumors. Allelic losses on 1p were primarily restricted to glioblastoma multiforme (2/11) and to tumors with a major oligodendroglial component: grade II oligodendrogliomas (6/6), grade III anaplastic oligodendrogliomas (5/6) and grade II-III mixed oligo-astrocytomas (2/3). Losses for 1q markers were detected in only 1 tumor (glioblastoma multiforme). Our data suggest that anomalies of 1p primarily characterize oligodendrogliomas, whereas they are rare events in astrocytic tumors and indicate that a tumor-suppressor gene on 1p36-p32 is involved in the development of brain tumors with oligodendroglial differentiation.

Numerical abnormalities of chromosome 7 in human prostate cancer detected by fluorescence in situ hybridization (FISH) on paraffin-embedded tissue sections with centromere-specific DNA probes

Fluorescence in situ hybridization (FISH) using chromosome-specific alpha-satellite DNA probes for chromosomes 7, 8, and 12 was performed on paraffin-embedded tissue sections and touch imprint preparations of 53 cases of human prostate cancer. Subsequent haematoxylin and eosin (H & E) staining of the hybridized tissue sections allowed unambiguous assignment of hybridization signals either to tumour or to non-tumorous parenchyma. Fifty-three cases of human prostate cancer were evaluated for numerical aberrations of chromosome 7. Scoring 200 cells of tumour and non-tumorous parenchyma in each case revealed abnormalities exclusively in tumour parenchyma in 41 cases (77 per cent). Ten of 41 cases (24 per cent) showed trisomy 7, and 15 cases (37 per cent) monosomy 7 or trisomy 7 in combination with monosomy 7, respectively. Sixteen cases (39 per cent) exhibited polysomy 7 in cells of the tumour parenchyma. In the tumour tissue in one case, different polyploid clones (triploid, tetraploid) and polysomy 7 could be identified by double hybridization with chromosome-specific DNA probes for chromosome 7, plus 8 or 12. The indicated numerical aberrations of chromosome 7 were correlated with 78 per cent of advanced pathological stages or poorly differentiated tumours (pT3/4 or G3) of prostate carcinomas. A statistical analysis of the data revealed significant relationships of particular numerical abnormalities of chromosome 7 to different pathological categories (pT, G, pN) of tumour classification. For the T-classification, the frequency of cells carrying polysomy 7 and polysomy 7/+7 increases significantly from pT1 to pT3/4 (P = 0.022).(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular analysis of genomic abnormalities in human gliomas

A series of 57 malignant gliomas, including 27 astrocytomas grade III-IV (glioblastoma multiforme), 15 astrocytomas grade I-II, and 15 tumors with major oligodendroglial component, was examined to detect molecular abnormalities of loci at specific chromosome regions. At the cytogenetic level, these regions have been shown to be nonrandomly involved in neoplastic development of these histologic subtypes of tumor. We used a panel of 24 polymorphic DNA probes to analyze loss of heterozygosity (LOH) at loci on chromosomes 7, 9, 10, 13, 17p, and 22q. In addition, the retinoblastoma (RB1) oncosuppressor gene, the platelet-derived growth factor A (PDGFA) gene, and the epidermal growth factor receptor (EGFR) gene were analyzed directly. Loss of genetic information on the short arm of chromosome 17 was observed in both low- and high-grade astrocytomas, whereas no oligodendroglial tumor was characterized by this type of aberration. LOH for chromosome 10, mainly compatible with loss of the entire chromosome, was primarily evidenced in the more malignant forms and in isolated cases diagnosed as low-grade astrocytomas. Again, no oligodendroglial tumor displayed losses of chromosome 10. In contrast, four tumors with major oligodendroglial component showed losses involving 9p markers, primarily interferon A and B (IFNA, IFNB); this feature was also observed in two low-grade astrocytomas and in 11 high-grade tumors. Isolated cases displayed LOH for markers on chromosomes 13 and 22, whereas EGFR amplification was almost exclusively evidenced in the more malignant forms which, in most instances, also presented LOH for chromosome 10. In general, the samples with lower malignancy stage displayed a lesser grade of abnormalities, mainly restricted to losses at 17p and chromosome 10 in astrocytomas grade I-II and at 9p in oligodendrogliomas. In contrast, about 50% of the high-grade tumor samples analyzed included abnormalities at two or more loci, with a recurrent association of EGFR amplification and LOH for chromosome 10; this association was evident in 26% of the high-grade astrocytomas.

Chromosome studies in 70 brain tumors with special attention to sex chromosome loss and single autosomal trisomy

Chromosome analysis was performed on 70 brain tumors. Thirty-six tumors showed clonal karyotypes characterized by many autosomal abnormalities; 20 meningiomas revealed monosomy 22 as a consistent abnormality, and 12 gliomas showed various abnormalities frequently involving chromosomes 3, 7, and 22. Of the remaining 34 tumors, 24 had normal karyotypes and 10 had clonal cells with loss and/or an extra sex chromosome with single trisomy of chromosomes 3, 6, 7, or 14. Sex chromosome aneuploidy was mostly due to loss of the Y or an X chromosome and was observed in 25 tumors, usually together with autosomal abnormalities. In these tumors the average frequency of cells with sex chromosome aneuploidy was 52%, with a range from 12% to 100%. Loss of the Y was found significantly more frequently in tumors of aged patients. Chromosome analysis in materials subcultured for a long period showed a tendency for cellular selection in which clonal cells with many autosomal abnormalities disappeared rapidly and karyotypes having loss or an extra sex chromosome and/or trisomy 7 were present in an increasing proportion with advance of cell generations in vitro. We infer that the cells having loss of one sex chromosome or trisomy 7 have a proliferative advantage. And that cells bearing only these abnormalities may exist in normal brain tissue more abundantly than in any other body tissue. The possibility of tissue-specific aneuploid mosaicism in the normal tissue would allow an alternative interpretation for simple autosomal trisomy in solid tumors.

Ascertainment of chromosome 7 gains in malignant gliomas by cytogenetic and RFLP analyses

The incidence of gains involving chromosome 7 was determined independently using cytogenetic and molecular genetic analyses in a series of 57 malignant gliomas. Coincidental results were observed in the group of tumors in which trisomy 7 was identified on the same cells that also displayed other clonal abnormalities (i.e., losses of chromosome 10, and structural rearrangements of 1p, 9p, etc., and the presence of dmin). On the other hand, molecular detection of gain of material from this chromosome was obtained in only one of nine cases in which trisomy 7 had been identified as a solitary anomaly at the cytogenetic level. Thus, although trisomy 7 has been identified as a clonal abnormality in about 60% of gliomas analyzed cytogenetically so far, our findings suggest that the anomaly may be representative of tumor parenchyma in half of them, while in the remaining cases (mainly those in which trisomy 7 is observed at the cytogenetic level as the sole chromosomal deviation) our data agree with those suggesting that the anomaly is the result of an in vitro non-disjunction, or represent in vivo mosaicism of the non-tumoral cells.

Molecular and cytogenetic analysis of chromosome 9 deletions in 75 malignant gliomas

A deletion mapping analysis of chromosome 9 has been performed on a series of 75 samples derived from malignant gliomas. A total of 27 tumors displayed different deletions for the loci studied (D9S1, NRASLI, D9S18, IFNA, and IFNBI). In most instances, losses involving the markers located on the short arm of chromosome 9 were observed, and only two samples were characterized by losses of the short and long arms. Either partial or complete homozygous deletions of IFN genes were observed in 15 cases, and 12 other samples showed hemizygous deletions for these genes. The results show that the 9p abnormalities are not exclusive to high-grade astrocytic tumors, as some low-grade samples (two astrocytoma grade II and six oligodendrogliomas) displayed this anomaly which, in a few instances, was the sole abnormality detected.

Cytogenetics of cranial base tumors

Many different tumor types can arise in or invade the skull base. The more common tumors include, but are not limited to, angiofibromas, chondrosarcomas, chordomas, hemangiopericytomas, meningiomas, carcinomas, olfactory neuroblastomas, paragangliomas, pituitary adenomas, and rhabdomyosarcomas. Several of these tumors, including meningiomas, hemangiopericytomas, and rhabdomyosarcomas are characterized by nonrandom cytogenetic abnormalities. In this paper, we review the recognized chromosomal aberrations in cranial base tumors and illustrate the insights that can be gained into the genetic basis of tumor formation using karyotypes from skull base tumors that we have examined. As in tumors in other locations, chromosomal findings may be of diagnostic and prognostic value in cranial base tumors.

Y chromosome loss in esophageal carcinoma: an in situ hybridization study

Carcinoma of the esophagus shows a strong male predominance and other epidemiologic differences from cancers arising at other sites. In this study, the prevalence of Y chromosome loss in 29 carcinomas of the esophagus and 53 carcinomas arising elsewhere in the aerodigestive tract was assessed by in situ hybridization of formalin-fixed paraffin-embedded tissue sections. Absence of the Y chromosome was defined as (1) negative staining for Y in neoplastic cells with positive staining for Y in immediately adjacent nonneoplastic epithelial and stromal cells, (2) positive staining of neoplastic cells with control probes for chromosomes X and 17, and (3) similar results at different stringencies and levels of protein digestion. According to these criteria, absence of the Y chromosome was observed in 13 of 14 (93%) adenocarcinomas of the esophagus, 8 of 13 (62%) squamous cell carcinomas of the esophagus, and 5 of 53 (9%) carcinomas arising in other sites. For the neoplasms examined, Y chromosome deletion was strongly and selectively associated with carcinomas, particularly adenocarcinomas, of the esophagus (P < .0001). These findings suggest that Y chromosome loss may be pathogenetically significant in these neoplasms.

Cytogenetic analysis of 109 pediatric central nervous system tumors

Reports of cytogenetic abnormalities in pediatric central nervous system (CNS) tumors are important for collection and comparison of large numbers of karyotypes of primary CNS neoplasms to produce statistically significant correlations. We report cytogenetic results of 119 samples of pediatric CNS tumors from 109 patients. Tumors included 33 low-grade astrocytomas, 18 high-grade astrocytomas, 14 gangliogliomas, 13 ependymomas, 17 primitive neuroectodermal tumors (PNET), three choroid plexus papillomas and carcinomas, and a miscellaneous group of 20 rare primary CNS tumors and metastases. In each group, cytogenetic results were correlated with histologic subtype and survival. The study indicated specific chromosome abnormalities in different groups of tumors. Low-grade astrocytomas showed mostly numeric abnormalities with gains of chromosome 7, high-grade astrocytomas showed differences from karyotypic changes observed in adults in lacking double minutes (dmin) and monosomy 10. The ependymoma group showed the largest proportion of abnormal karyotypes with frequent involvement of chromosome 6 and 16. Chromosome 6 was the single most common abnormal chromosome in this study, closely followed by chromosomes 1 and 11. Pediatric CNS neoplasms differ from adult tumors cytogenetically as well as histologically and biologically.

Chromosomes in the genesis and progression of ependymomas

Cytogenetic analysis was performed on cultures of primary ependymal tumors with different degrees of malignancy (I-IV) obtained from four patients, none of whom had received therapy before karyotypic evaluation. The most common abnormalities were monosomy 17 and 22 in four cases and losses of sex chromosomes in three cases. Structural rearrangements of chromosome 2 were a finding for all cases and involved loss of material at 2q32-34. Other structural chromosome abnormalities detected involved chromosomes 4, 6, 10, 11, 12, and X. We also reviewed data on 22 cases previously reported.

Biologic and clinical significance of cytogenetic and molecular cytogenetic abnormalities in benign and malignant cartilaginous lesions

Cartilaginous neoplasms are often histologically and therapeutically challenging. Predicting biologic behavior can be difficult. In this study, 120 nonneoplastic, benign, and malignant cartilaginous lesions from 103 patients were cytogenetically analyzed in a 6-year period after short-term culture. For selected cases, fluorescent in situ hybridization (FISH) techniques using chromosome-specific probes were performed on metaphase/interphase preparations and on paraffin-embedded tissue sections. Clonal abnormalities of chromosomes 2, 3, 5, 7, 8, and 12 were most frequently observed. Involvement of chromosomes 5, 8, and 12 may be etiologically significant because of the gene localizations for the human cartilage link protein, Langer-Giedion syndrome (a rare syndrome characterized by multiple exostoses), and type II collagen (a major component of normal cartilage) respectively, to these three chromosomes. That chromosome 7 abnormalities were observed only in malignant tumors is of diagnostic value. The identity of three marker chromosomes and the significance of trisomy 7 (a finding of controversial meaning), were determined with FISH. That the presence of chromosome aberrations and increasing histologic grade strongly correlated (p = 0.001) is of prognostic importance. Moreover, complex aberrations were observed nearly exclusively in high-grade tumors (p = 0.001). The data show that nonrandom chromosome loci are aberrantly affected in cartilaginous lesions and that these abnormalities may be of significant histopathogenetic consequence. In addition, these chromosome abnormalities appear to be diagnostically and prognostically valuable in classifying and grading chondromatous neoplasms.

Gliosis specimens contain clonal cytogenetic abnormalities

The relevance of sex chromosome aneusomy and trisomy 7 in neoplastic brain tissue is controversial. For better understanding of the relative importance of these anomalies, we made a conventional cytogenetic study of cells from tissue obtained from patients who underwent partial cerebral resection for a seizure disorder. Each specimen exhibited "gliosis," but none contained histologically identifiable tumor cells. Sixty-six specimens were analyzed by routine cytogenetic methods. Nonclonal abnormalities were observed in 11.6% of the cells (86% of cases) analyzed. In 11 cases, however, simple clonal karyotypes were observed. Of these cases, six involved loss of a Y chromosome and three involved loss of an X chromosome. Among the cases with loss of an X chromosome, two exhibited multiple abnormal clones. One of these cases had trisomy 7 as well as trisomy 18, and another had a supernumerary psu dic(15)(q13). The supernumerary chromosome was constitutional. One patient had possible Klinefelter syndrome. An additional case had a clonal del(10)(q23) that may have resulted from a hereditary fragile site. We conclude that although some of the apparently acquired clonal and nonclonal abnormalities may be due to a consistent in vitro artifact, it is probable that they are present in the brain tissue itself. Whatever the cause, caution should be used in interpretating cytogenetic abnormalities observed in brain tumor specimens.

Fluorescent in situ hybridization assessment of chromosome 7 copy number in uncultured lung and kidney cells

Trisomy 7 is common in cells cultured from nonneoplastic lung and kidney tissues, but the frequency of trisomy 7 in uncultured lung and kidney has not been determined. In this study, we used fluorescent in situ hybridization (FISH) to assess chromosome 7 copy number in uncultured interphase nuclei from lung and kidney specimens. All specimens had low level mosaicism for trisomy 7(1.5-5.25%), but control experiments indicated a potential wide margin of error in quantifying these events.

Trisomy 7 in nonneoplastic cells

The somatic mutation theory of tumorigenesis states that mutations are necessary for tumor development. On the other hand, acquired, clonal chromosomal alterations are occasionally detected in otherwise normal, nonneoplastic cells--for example, loss of sex chromosomes occurs in bone marrow cells and lymphocytes in elderly individuals--and it is therefore evident that not all mutations are by themselves sufficient for neoplasia to occur. Thus, the finding of an acquired, clonal chromosomal abnormality does not constitute proof that a lesion is neoplastic. Trisomy 7 has, as the sole clonal chromosomal aberrations, been reported in a wide variety of epithelial tumor types but also in some mesenchymal and neurogenic neoplasms. It has been suggested to be a primary, i.e., tumor-initiating, abnormality in tumors of the bladder, brain, colon, kidney, lung, ovary, prostate, and thyroid. But data from cytogenetic studies of solid tumors, macroscopically normal tissue in the proximity of solid tumors, and nonneoplastic lesions now question the importance of a solitary +7 as a neoplasia-associated change. Most solid tumors in which trisomy 7 has been found as the sole change in one clone have also displayed other, cytogenetically unrelated, clones with complex karyotypic abnormalities. Such karyotypic differences among coexisting clones could indicate that the neoplasm is polyclonal, that the cytogenetically disparate clones have emerged during tumor progression from one original clone carrying submicroscopic genomic changes only, or that the clone with +7 does not represent the tumor parenchyma. The latter interpretation is supported by the finding of cells with trisomy 7 in macroscopically normal tissue outside tumors of the brain, kidney, and lung.(ABSTRACT TRUNCATED AT 250 WORDS)

Cytogenetic survey of 32 cancers of the prostate

Cytogenetic studies after short-term culture were performed on 32 adenocarcinomas of the prostate from patients without prior treatment. The tumor specimens, ranging from stage B1 to D1, were obtained by radical prostatectomy or diagnostic biopsies. Fourteen tumors showed a normal diploid chromosome complement in all metaphases examined. Clonal chromosomal alterations were detected in 16 tumor samples and the remaining two cases contained double minute (dmin) chromosomes in some cells. The most frequent numerical changes included loss the Y chromosome and trisomy 7, both found in four cases. The only recurrent structural aberration was del(10)(q24), seen in three cases both as a sole anomaly and within multiple rearrangements. Six patients showed cytogenetically unrelated clones. The occurrence of the chromosomal changes found in this study shows no relationship to certain histopathologic characteristics of the tumors. The recurrent finding of del(10)(q24) as sole anomaly and the evidence for clonal evolution in one patient demonstrates that this change is an early karyotypic event which may be important for the pathogenesis in at least a subset of prostatic cancers.

Cytogenetic analysis of six bronchial carcinoids

Short-term cultures from four typical and two atypical primary bronchial carcinoids were cytogenetically analyzed. A lung metastasis from one of the atypical carcinoids was also analyzed. Of the four typical carcinoids, two had normal chromosome complements, while the other two had the karyotypes 46,X, -X, +7/47,XX, +7/47,XX, +X/46,XX and 47,XX, +7/46,XX. Both atypical carcinoids had chromosome abnormalities. One had the karyotype 45-46,X, -X,del(1)(q32),add(17)(p13), +add(19)(p13), -22, +r/47,XX, +X. The second carcinoid had the karyotype 78-81,XXY, +Y, +1,t(2;8)(q21;q24), +3, +4, +del(4) (q25), +5, +6,der(6)t(6;6)(q21;p21)x2, +7, +7, -10,add(14)(p11-13), +19, -21, +1-4mar. The metastasis from this carcinoid had the same aberrations, except that the del(4)(q25) had been lost and one to two markers had been gained.

Abnormalities of chromosome 22 in human brain tumors determined by combined cytogenetic and molecular genetic approaches

Southern blot hybridization studies were performed on a panel of 130 blood/tumor samples from brain neoplasms including all major histologic subtypes: 50 meningiomas, 18 neurinomas, 56 gliomas, and six others. To detect abnormalities involving chromosome 22, polymorphic probes were used to analyze eight loci located in this chromosome: D22S9, IGLV, D22S20, D22S32, MB, PDGF-B, D22S80, and D22S171. Loss of heterozygosity (LOH) was observed in 40 cases including monosomy, terminal, and interstitial deletions, which suggest the location of recessive tumor genes in certain chromosome 22 subregions (22q11.3-q12 in neurinomas and meningiomas, and 22q13 in malignant gliomas). Cytogenetic studies were performed in parallel on the same tumors, in most instances corroborating the presence of abnormalities for chromosome 22. Nevertheless, discrepancies between the cytogenetic and molecular findings were observed in several cases, suggesting that the use of both methodologies in combination might provide key information on the incidence and extent of the abnormalities involving chromosome 22 in human brain tumors.

Cytogenetic aberrations in colorectal adenocarcinomas and their correlation with clinicopathologic features

BACKGROUND

Little is known about the karyotypes of colorectal carcinomas and, in particular, about how the cytogenetic findings correlate with clinicopathologic features.

METHODS

Short-term cultures from 49 colorectal adenocarcinomas were analyzed cytogenetically. The karyotypes were correlated with grade, stage, lymphocytic infiltration, and site (using the chi-square test), with patient age and tumor size (using the Student t test), and with survival (using the log-rank or Mantel-Haenszel test).

RESULTS

Normal karyotypes were detected in 17, simple numeric changes in 22, and multiple structural and numeric abnormalities in 10. The most common numeric aberrations were +7, -Y, -18, and -22. The most common structural rearrangements were, in decreasing order of frequency, of chromosomes 1 (eight samples, leading to loss of 1p material in five), 3, 11, 17, 6, 8, 13, and 20. Marked or moderate lymphocytic infiltration was seen significantly less often (P < 0.05) in tumors with complex chromosomal abnormalities than in those with simple anomalies or normal karyotypes. The subset of patients who had tumors with multiple chromosomal abnormalities had a significantly shorter survival time (P < 0.025) than those who had lesions with simple changes or normal karyotypes.

CONCLUSIONS

Loss of 1p material is the most consistent chromosomal change in colorectal carcinomas but probably represents a progressional rather than a primary event. Structural changes of chromosomes 3 and 11 seem to be more common in tumors located in the distal part of the large intestine. The significantly shorter survival time of patients with complex aberrations indicates that the karyotype could be used as a prognostic parameter in patients with colorectal cancer.

Chromosome analysis of 20 breast carcinomas: cytogenetic multiclonality and karyotypic-pathologic correlations

Short-term cultures from 20 breast carcinomas were analyzed cytogenetically. A normal female chromosome complement was found in 4 cases. Clonal chromosome aberrations were detected in 16 tumors. In 10 tumors, multiple cytogenetic clones were found; in 2 cancers the clones were related, reflecting clonal evolution, but in the remaining 8 tumors the clones were cytogenetically unrelated, indicating clonal heterogeneity in the origin of the tumor parenchyma. Correlation analysis between karyotypic and pathologic parameters indicated that cases with complex karyotypes and/or cytogenetically unrelated clones, when compared with cases with a single simple karyotypic abnormality, were generally of higher histologic malignancy grade, had more mitoses in the histologic sections, and also more often had carcinoma in situ lesions in the same breast.

Trisomy 7 in nonneoplastic focal steatosis of the liver

Cytogenetic analysis of short-term cultures of a nonneoplastic focal steatosis of the liver showed trisomy 7 as the sole chromosomal change. This finding, especially when viewed in light of previous reports describing +7 in nonneoplastic tissues, strongly suggests that trisomy 7 cannot be considered a tumor-specific abnormality when it occurs as the only change. The cell type in which +7 is present is not yet known.