Concordant deletions of chromosome 3p and loss of heterozygosity for chromosomes 13 and 17 in small cell lung carcinoma

Common regions of loss of heterozygosity on chromosomes 3, 13, and 17 were determined by restriction fragment length polymorphism analysis in 34 tumors and nine cell lines from 27 patients with small cell lung carcinoma. The common regions of loss of heterozygosity on chromosomes 3, 13, and 17 reside between D3S2 (3p14-p21) and ERBA beta (3p22-p24.1), between D13S1 (13q12) and D13S2 (13q22), and distal to MYH2 (17p13.1), respectively. Allele loss in each of these regions has been previously shown in several human tumors. Thus, the present findings indicate the pleiotropy of recessive genetic lesions in these genomic areas. Cytogenetic analysis was performed on three small cell lung carcinoma cell lines which had allele loss on all three chromosomes, and although chromosome 3p deletions were observed in two of three cell lines, no obvious structural abnormalities involving chromosomes 13 and 17 were detected. Mitotic recombination or mitotic nondisjunction rather than deletion may thus be the frequent chromosomal mechanism for attaining homozygosity of chromosomes 13 and 17 in small cell lung carcinoma.     

Histopathological, cytogenetic, and molecular characterization of renal cortical tumors.

We used cytogenetic and restriction fragment length polymorphism (RFLP) analysis methods to define genetic alterations and also correlate the changes with histopathology in renal cortical tumors. The study series is comprised of 50 renal tumors in 4 histological categories: (a) clear cell, nonpapillary, renal cell carcinoma (RCC) (n = 32); (b) nonclear cell, nonpapillary RCC (n = 10); (c) papillary RCC (n = 3); and (d) oncocytic tumors (n = 5). Successful karyotypes were obtained from 28 tumors (56%), of which 17 (61%) were abnormal. Abnormalities of chromosome 3p were seen in 9 tumors, which included unbalanced translocations and terminal or interstitial deletions. Abnormalities of chromosome 5 were identified in 11 tumors, 8 of which were due to unbalanced translocations between 3p and 5q, resulting in an extra copy for the region 5q22----ter. In addition, trisomy or tetrasomy of chromosome 17 was seen in 6 (5 with normal chromosome 3 and one with 3p deletion), trisomy or more copies of chromosome 7 in 8 (4 with 3p deletion, 2 with trisomy or tetrasomy 17, and 2 with trisomy alone), and trisomy 12 in 3 (all with trisomy 17) tumors. Furthermore, relative deficiency of chromosome 17p was seen in 3 (all with deletion 3p) and chromosome 18 in 4 (all with deletion 3p) tumors. RFLP analysis with four chromosome 3 specific probes detected 3p deletions in 19 tumors with the most common breakpoint located between 3p14-21. The 19 3p deletions detected by RFLP included tumors that also showed rearrangement of 3p by cytogenetics (n = 4) and those that showed normal karyotypes (n = 3) in addition to cytogenetic failures (n = 12). Deletions of 17p were seen in 5 of 31 informative cases. Thus, deletions of 3p were seen in a total of 24 tumors by cytogenetic and/or RFLP analysis, 21 of which were clear cell, nonpapillary RCC, whereas 3 had a minor clear-cell component. Oncocytic and nonclear, nonpapillary tumors, on the other hand, did not demonstrate 3p deletions by either technique, whereas trisomy 17 was seen in 3 of the 3 papillary tumors. The loss of alleles from chromosome 17p and 18 and an increased dosage of gene or genes on chromosomes 5q and 7 as seen in high-stage tumors of various histological subtypes may be associated with progression of disease.     

A role for telomeric and centromeric instability in the progression of chromosome aberrations in meningioma patients

BACKGROUND: The primary chromosome aberration in meningiomas is monosomy or deletion of chromosome 22. Common secondary aberrations include losses or deletions of chromosomes 1p, 14q, and 10q and unstable chromosome aberrations including rings, dicentrics, and telomeric associations. Despite the analysis of several hundred tumors by cytogenetic and molecular techniques, the mechanisms involved in the progression of chromosome aberrations in meningioma remain poorly understood. METHODS: Sixty-seven meningiomas were cultured successfully using a short term in situ technique and harvested incorporating a high resolution G-banding technique with ethidium bromide. RESULTS: Twenty-six tumors (39%) showed normal karyotypes, whereas 41 tumors (61%) showed clonal chromosome aberrations. The most frequently observed aberration was the loss of chromosome 22 or structural aberrations involving 22q12, which occurred in 30 tumors (45%). The second most common aberrations were whole arm translocations involving the centromeric breakpoint at 1q10, resulting in the loss of the entire 1p chromosome in 12 tumors (18%). Two tumors showed a new, recurring, unbalanced, whole arm translocation der(1;2)(q10;q10). A third aberration, telomeric associations, were observed in 16 tumors (24%), occurring transiently in 11 tumors and recurring clonally in 5 tumors. Dicentric chromosome 22 was found in 7 tumors (10%), with the progressive loss of chromosome 22q material being found in 2 tumors. CONCLUSIONS: The chromosome instability demonstrated in the current series of tumors suggests that the progression of chromosome aberrations in meningioma is mediated in some respects by both telomeric and centromeric instability. These two types of instability may be early events in the progression of chromosome aberrations in meningioma and each can account for at least some of the loss of heterozygosity of chromosomes 22q and 1p detected by molecular analysis.     

Detailed assessment of chromosome 22 aberrations in sporadic pheochromocytoma using array-CGH

Pheochromocytoma is a predominantly sporadic neuroendocrine tumor derived from the adrenal medulla. Previous low resolution LOH and metaphase-CGH studies reported the loss of chromosomes 1p, 3q, 17p and 22q at various frequencies. However, the molecular mechanism(s) behind development of sporadic pheochromocytoma remains largely unknown. We have applied high-resolution tiling-path microarray-CGH with the primary aim to characterize copy number imbalances affecting chromosome 22 in 66 sporadic pheochromocytomas. We detected copy number alterations on 22q at a frequency of 44%. The predominant finding was monosomy 22 (30%), followed by terminal deletions in 8 samples (12%) and a single interstitial deletion. We further applied a chromosome 1 tiling-path array in 7 tumors with terminal deletions of 22q and found deletions of 1p in all cases. Our overall results suggest that at least 2 distinct regions on both 22q and 1p are important in the tumorigenesis of sporadic pheochromocytoma. A large proportion of pheochromocytomas also displayed indications of cellular heterogeneity. Our study is to our knowledge the first array-CGH study of sporadic pheochromocytoma. Future analysis of this tumor type should preferably be performed in the context of the entire human genome using genome-wide array-CGH, which is a superior methodological approach. Supplemental material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7136/suppmat/index.html.     

Molecular cytogenetic study of derivative chromosome 9 deletion in chronic myeloid leukemia patients

The aims of this study are to investigate the frequency of derivative chromosome 9 (der (9)) deletion in Tunisian patients with chronic myeloid leukemia (CML) and to assess the correlation between this deletion and the cytogenetic response for patients treated with hydroxyurea (HU) or imatinib (IM). Karyotype analysis of 336 patients with CML was performed with R-banding technique. Fluorescence in situ hybridization (FISH) was carried using home-brew probes 17L7 and 248J22 for detecting, respectively, adjacent 5??ABL and 3??BCR deletions on der(9). Cytogenetic study demonstrated typical t(9;22)(q34;q11) translocation in 89.6% and variant translocation in 10.4% of patients. Interphase FISH studies showed deletion of der(9) in 59 (17.6%) of the 336 patients, 23 (39%) of them had variant rearrangements. There are 19 patients with solely 5??ABL deletion and 40 with concomitant 5??ABL and 3??BCR deletions. Cytogenetic response was evaluated during 18?months with HU or IM therapy. Our results demonstrate that (a) 3??BCR deletion is associated with 5??ABL deletion in all patients with der(9) deletions, (b) the 5??ABL and 3??BCR deletions arise simultaneously with t(9;22), (c) deletions on der(9) chromosome were frequently encountered in older patients and in patients presenting variant rearrangements, (d) both 5??ABL and 3??BCR deletions were associated with cytogenetic response failure in patients treated with HU, however, patients treated with IM and carrying der(9) deletions presented better cytogenetic response.     

Reduction to homozygosity and gene amplification in central nervous system primitive neuroectodermal tumors of childhood

The loss of genetic material from specific chromosomal locations has been identified for a number of pediatric tumors. This loss has been taken as evidence for the importance of tumor suppressor genes at these loci in the genesis of these tumors. One of these pediatric tumors, the primitive neuroectodermal tumor of the central nervous system, has not been well studied. In this report, an analysis of primitive neuroectodermal tumors for allelic deletions on chromosomes 1p, 7q, 10, 11p, 13q, and 17p has been performed. One of ten tumors was found to have increased copies of c-myc. Three different patients were found to reduce to homozygosity at one of three different locations. Significantly, however, three of nine informative patients showed a reduction to homozygosity on chromosome 17p. Thus, primitive neuroectodermal tumor is one of a growing number of tumor types in which deletions in the short arm of chromosome 17 might be important in oncogenesis.     

Deletion of chromosome 17p loci in breast cancer cells detected by fluorescence in situ hybridization.

Allelic loss of tumor suppressor genes on chromosome 17p has been implicated in the progression of breast cancer. This is in principle detectable by fluorescence in situ hybridization if the loss occurs by deletion. In order to determine if detectable deletions occur in primary breast cancer, we used dual-color hybridization with chromosome 17 pericentromeric and region-specific DNA probes to study 19 primary breast cancers. The copy numbers of 17 centromere and 17p13.1 sequences were compared with the loss of heterozygosity (LOH) for probe YNZ22 at 17p13.3 detected by restriction fragment length polymorphism. Nine of 11 cases showing LOH also showed the major population of nuclei with a deletion. The remaining two tumors with LOH were trisomic for both the centromere and 17p13.1 cosmid. In contrast, seven of eight tumors without LOH had no deletions by fluorescence in situ hybridization. These data suggest that the dominant mechanism of allelic loss at 17p in breast cancer is a physical deletion and that analysis of deletions by fluorescence in situ hybridization is a rapid and sensitive approach to studying chromosomal aberrations.     

Deletion mapping of 6q21-26 and frequency of 1p36 deletion in childhood endodermal sinus tumors by microsatellite analysis.

The most common malignant germ cell tumor of early childhood is the endodermal sinus tumor (CEST), also known as yolk sac tumor. Previous cytogenetic studies of CEST have demonstrated recurrent deletion of distal regions of chromosomes 1p and 6q. Studies utilizing comparative genomic hybridization have likewise demonstrated loss of distal 6q, however these studies show discrepant data concerning chromosome 1 abnormalities. This study analyses 18 CESTs for loss of heterozygosity (LOH) of distal chromosome 6q utilizing 17 microsatellite markers and 13 tumors were analysed for LOH of distal 1p using two microsatellite markers. LOH of 6q was found in 13/18 tumors (72 %). This data confirms that loss of genetic material on 6q is one of the most common abnormalities in CESTs and narrows the region of loss, enabling candidate tumor suppressor genes to be identified and analysed. In addition, LOH of 1p36 was identified in five of 11 informative tumors, clarifying prior conflicting data and confirming that 1p deletion is a common event in CESTs.     

Chromosomal abnormalities in glioblastoma multiforme tumors and glioma cell lines detected by comparative genomic hybridization

Comparative genomic hybridization (CGH) is a recent molecular cytogenetic method that detects and localizes gains or losses in DNA copy number across the entire tumor genome. We used CGH to examine 9 glioma cell lines and 20 primary and 10 recurrent glioblastoma tumors. More than 25% of the primary tumors had gains on chromosome 7; they also had frequent losses on 9p, 10, 13 and Y. The losses on chromosome 13 included several interstitial deletions, with a common area of loss at 13q21. The recurrent tumors not only had gains on chromosome 7 and losses on 9p, 10, 13 and Y but also frequent losses on 6 and 14. One recurrent tumor had a deletion of 10q22-26. Cell lines showed gains of 5p, 7 and Xp; frequent amplifications at 8q22-24.2, 7q2l-32 and 3q26.2-29 and frequent losses on 4, 10, 13, 14 and Y. Because primary and recurrent tumors and cell lines showed abnormalities of DNA copy number on chromosomes 7, 10, 13 and Y, these regions may play a fundamental role in tumor initiation and/or progression. The propensity for losses on chromosomes 6 and 14 to occur in recurrent tumors suggests that these aberrations play a role in tumor recurrence, the development of resistance to therapy or both. Analysis of common areas of loss and gain in these tumors and cell lines provides a basis for future attempts to more finely map these genetic changes.     

Rearrangements of the short arm of chromosome No. 6 in T-cell lymphomas

Cytogenetic studies on four patients with T-cell lymphomas are reported. In all four the short arm of chromosome No. 6 (6p) was abnormal. In three cases it was involved in a translocation, and in one there was a deletion of the terminal part: del(6)(p23-24). One of the translocations could be identified as a t(2:6)(q24;p24). Identification was not possible in the others. These 6p anomalies were associated with complex structural and numerical abnormalities of other chromosomes in three out of four cases. In three patients chemo- and/or radiotherapy administration preceded cytogenetic investigations.     

Computer-assisted cytogenetic analysis of 51 malignant peripheral-nerve-sheath tumors: sporadic vs. neurofibromatosis-type-1-associated malignant schwannomas.

Cytogenetic studies in small groups of patients with malignant peripheral-nerve-sheath tumors (MPNST) revealed complex karyotypes with no consistent changes. A computer-assisted cytogenetic analysis using a cytogenetic database was performed to determine recurrent cytogenetic alterations in 51 MPNSTs (44 from the literature and 7 new cases) and to allow direct cytogenetic comparison between NF-1-associated and sporadic MPNSTs. Significant loss (p < 0.05) was observed in the chromosomal regions 9p2, 11p1, 11q2 and 18p1. Also, loss in 1p3, 9p1, 11q1, 12q2, 17p1, 18q1-q2, 19p1, 22q1, X and Y was detected. Gain of chromosomal material was found in chromosome 7, especially 7q1 (p < 0.05). Most involved breakpoints were: 1p13, 1q21, 7p22, 9p11, 17p11, 17q11, 22q11. Cytogenetic differences between NF-1-associated and sporadic MPNSTs included a relative loss of chromosomal material in NF-1-associated MPNSTs in 1p3, 4p1 and 21p1-q2 and a relative gain in 15p1-q1. Differences in breakpoints between the NF-1 associated and the sporadic MPNST group were observed in 1p21-22 (28% of NF-1 vs. 0% of sporadic MPNSTs), 1p32-34 (17% vs. 0%), 8p11-12 (7% vs. 27%) and 17q10-12 (24% vs. 7%). This approach, in which the cytogenetic results of various reports are combined, shows that losses in 9p2 and gains in 7q1 could be of oncogenetic importance in MPNSTs. Loss of 17q1, on which the NF-1 gene has been located (17q11.2), is not a common cytogenetic finding in NF-1-associated MPNSTs. The observed differences between NF-1-associated and sporadic MPNSTs might reflect different oncogenetic pathways.     

Evidence for a 17p tumor related locus distinct from p53 in pediatric primitive neuroectodermal tumors.

Primitive neuroectodermal tumors of the central nervous system are the most common malignant brain tumors in children. Cytogenetic analysis of these tumors has demonstrated alterations of chromosome 17, in particular isochromosome 17q, as the most frequent chromosomal abnormality detected. Since the consistent loss of a specific chromosomal region in a given tumor type most likely indicates the presence of a tumor related gene in that region, we undertook a combined molecular and cytogenetic approach to examine alterations of chromosome 17 in primitive neuroectodermal tumors. Seven of 14 tumors analyzed demonstrated loss of alleles for loci on 17p. In three of the seven tumors tested, a loss in copy number was observed for only the most telomeric locus on 17p13.3, D17S34. Limited sequence analysis of the same seven tumors did not reveal mutations in four highly conserved coding regions of the p53 gene. These data suggest a new tumor associated locus on 17p distinct from and distal to TP53, which is involved in the initiation or progression of at least a subset of primitive neuroectodermal tumors.     

Role of chromosomal loss in the progression of prostate cancers

Cytogenetic, molecular cytogenetic, and molecular studies of prostate cancer have produced a large volume of data about chromosomal loci that are aberrant in prostate cancer. The cumulative data on prostate cancer reveal allelic losses on chromosome arms 2q, 3p, 5q, 6q, 7q, 8p, 9p, 10p, 10q, 11p, 11q, 12p, 13q, 16q, 17p, 17q, 18q, and 21q, but there is a great deal of variability between studies. In most cases, the frequency of allelic loss is higher in metastatic tissues or hormone-refractory tumors than in primary tumors. There also seem to be discrepancies in the genetic findings depending on methods employed. Molecular genetic studies, using polymerase chain reaction (PCR) analysis of microsatellite markers, demonstrated allelic loss at 7q31.1, whereas fluorescence in situ hybridization analysis showed a gain at the same region. Com-mon sites of allelic loss that are consistently observed by various methods seem to exist on chromosome arms 8p, 10q, 13q, and 16q. PTEN/MMAC1 has been identified on 10q23.3 and was found to be frequently mutated in advanced prostate cancer. Other regions are also considered to harbor genes associated with the development and progression of prostate cancer, and these could be included in the diagnostic methods for the substaging of prostate cancer. Received: September 22, 2000     

Cytogenetic and molecular findings in 75 clear cell renal cell carcinomas

Cytogenetic analysis of 75 clear cell renal cell carcinomas (RCC) from adult patients revealed abnormal karyotypes in 59 (79%) tumors. Among structural abnormalities, the most frequent were deletions and unbalanced translocations leading to loss of 3p (found in 68% of karyotypically abnormal tumors), followed by rearrangements of chromosomes 5 (in 37%) and 1 (in 20%). Fifteen unbalanced interchromosomal rearrangements and one reciprocal translocation have not been hitherto reported in clear cell RCC. The most common numerical aberrations were trisomy 7, seen in 44% of tumors, and loss of chromosome Y, detected in 48% of RCCs diagnosed in male patients. In 25 tumors, loss of heterozygosity (LOH) analysis was performed using five polymorphic markers spanning region 3p13-p25. LOH was identified in 10 RCCs with 3p loss detected cytogenetically and 4 karyotypically aberrant tumors without cytogenetic rearrangements of 3p; no LOH was found in 3 tumors with 3p loss seen at the cytogenetic level. Overall, 3p loss was detected by cytogenetic and/or LOH analyses in 75% of RCCs with abnormal karyotype studied. The presence or absence of 3p loss did not correlate with tumor size, nodal involvement, tumor grade or its ability to metastasize. However, karyotypes of metastasizing tumors contained more aberrations than those of non-metastasizing RCCs (5.5 versus 2.9 aberrations per tumor, respectively), and -14/14q-, -17 and -10 were significantly more frequent in metastasizing tumors, suggesting that these aberrations might contribute to the progression of RCC. One patient had t(X;1)(p11.2;p34) as a sole abnormality in the stemline. This is the sixth case with this translocation reported to date. Together with our case, all but 1 RCC with t(X;1)(p11.2;p34) had morphology with a clear cell component, which contrasts these RCCs from tumors harboring t(X;1)(p11.2;q21) that largely had papillary morphology.     

Human colorectal cancer: high frequency of deletions at chromosome 1p35

Cytogenetic analyses of human colon cancer cells have revealed a high frequency of chromosome 1p deletions among other chromosomal abnormalities. In order to find out whether these chromosomal alterations are manifestations of loss of genetic material, we surveyed DNA of 62 primary tumors, 7 metastases, and matching peripheral blood cells with a panel of polymorphic DNA probes that detect different loci on chromosome 1p. A portion of the probes was derived from a microclone bank generated by microdissection and microcloning of 1p35----pter DNA. In 42% of the colon carcinomas allelic loss was observed with at least one probe. The deletions were of different sizes but always included a region involving band 1p35, except for two tumors in which allelic loss was detected more proximally. The frequency of 1p deletion in the metastases was higher than in the primary tumors. These data indicate that genetic information related to tumorigenesis is located within or nearby region 1p35 and that deletion of this region occurs later in tumor development. Our results add to the number of genetic changes presumably involved in colon cancerogenesis.     

Cytogenetic studies on human breast carcinomas

Cytogenetic studies were performed on cell material obtained from surgical specimens of 50 human breast carcinomas and from 61 cancerous effusions of 46 patients. Classical cytogenetic analyses of numerical chromosome changes and marker chromosomes revealed the non-random involvement of chromosomes #X and #22 as monosomics, of chromosomes #3, #7, and #19 as trisomics, and chromosome #1 (particularly p 13 to q 12) in marker formation. Karyotypic evolution was followed in vitro and in vivo and showed a highly individualistic pattern of stability and variability.In addition, a systematic screening for the presence of cytogenetic equivalents of gene amplification (double minutes DM, homogeneously staining regions HSR) was carried out. A high incidence of DM-positive cases was detected in primary tumors (48%) as well as in metastatic cells from effusions (40%), with the frequency of DM-containing metaphases ranging from 1 to 100% in the positive cases. This finding supports the assumption of the fundamental biological importance of gene amplification in human solid tumors.Furthermore, chromosome breakage and micronuclei were observed in breast carcinoma cells as an apparent consequence of therapy-independent mutability.     

Cytogenetic and histopathologic studies of congenital supratentorial primitive neuroectodermal tumors: A case report

Primitive neuroectodermal tumors (PNET) represent about 25% of primary central nervous system tumors in childhood, but congenital PNETs are rare. Cytogenetic studies and studies on molecular pathology have identified several genetic alterations in medulloblastoma, but molecular investigations on supratentorial PNETs are infrequent. We present a male newborn with a large congenital PNET of the right cerebral hemisphere and the molecular analysis of the tumor. Tumor tissue was investigated by routine histology and immunohistochemistry. Fluorescence in-situ hybridization was carried out on native tumor tissue to investigate deletions on chromosome 17p and to analyze c-Myc or N-Myc amplifications. Histologic examination revealed a primitive neuroectodermal tumor with massive extension covering almost the entire right hemisphere. Genetic analysis of the native tumor tissue of our patient excluded a deletion of chromosome 17p. An amplification of the c-Myc or N-Myc oncogene was absent using fluorescence in-situ hybridization. Despite unremarkable genetic analysis in our case prognosis was poor, suggesting that there are additional, yet unknown constitutional genetic aberrations in the pathogenesis of congenital supratentorial PNET.     

Accumulation of genetic alterations and progression of primary breast cancer.

In order to detect common regions of deletion, 219 breast tumors were examined for loss of heterozygosity at several loci on chromosomes 3p, 16q, and 17 by restriction fragment length polymorphism analysis. Allelic deletions of loci on chromosomes 3p, 13q, 16q, and 17, and amplification of the erbB2 oncogene, were analyzed and compared with histopathological and clinical features. Common regions of deletion were detected within chromosomal bands 3p13-14.3, 16q22-23, 17p13 (two separated loci), and 17q21. Concordant losses of alleles on chromosomes 3p, 13q, 16q, 17p, and 17q were observed. A significant association was detected between loss of heterozygosity on chromosomes 17p and 17q and amplification of the erbB2 oncogene (17p, P = 0.000721, by Fisher's exact test; 17q, P less than 0.001, chi 2 = 12.135). Furthermore, tumors showing highly malignant phenotypes had accumulated more genetic changes at the loci studied than those having less malignant phenotypes on the basis of histopathological classification, lymph node metastasis, and tumor size. These results suggested that accumulation of genetic alterations, including loss of function of tumor suppressor genes on chromosomes 3p, 13q, 16q, and 17, and amplification of the erbB2 oncogene, may contribute to tumor development and/or progression in primary breast cancer.