Abnormalities in the p34cdc2-related PITSLRE protein kinase gene complex (CDC2L) on chromosome band 1p36 in melanoma

The two genes encoding the PITSLRE protein kinase isoforms, CDC2L1 and CDC2L2, are localized to human chromosome band 1p36. The PITSLRE protein kinases are a part of the p34cdc2 supergene family. Several protein products of the CDC2L locus may be effector(s) in apoptotic signaling. The larger PITSLRE p110 isoforms appear to regulate some aspect of RNA splicing/transcription during the cell cycle. One or more of these genes may function as tumor suppressor genes in melanoma. Using fluorescence in situ hybridization, one allele of the CDC2L gene complex on chromosome 1 was either deleted or translocated in 8 of 14 different melanoma cell lines. We also observed mutations in the 5' promoter region of the CDC2L1 gene in four different cell lines relative to normal melanocytes using PCR-SSCP analysis and direct DNA sequencing. Western blot analysis revealed decreased level of PITSLRE protein expression in several cell lines, as well as in four surgical malignant melanoma specimens relative to normal melanocytes. Thus, the decreased PITSLRE protein expression appears to result from deletion of the CDC2L alleles and possibly by mutations within the 5' promoter region. We propose that aberrations in the CDC2L genes may contribute to the pathogenesis or progression of melanoma.

Increased chromosome 20 copy number detected by fluorescence in situ hybridization (FISH) in malignant melanoma

DNA amplification is an important mechanism of tumor progression that allows cancer cells to up-regulate the expression of critical genes such as oncogenes and genes conferring drug resistance. Recent studies using comparative genomic hybridization (CGH) revealed increased DNA copies of 20q sequences in 7 melanoma cell lines and B archival metastatic melanoma lesions. To evaluate chromosome 20 abnormalities in more detail and to resolve discrepancies between karyotype and CGH findings, we performed FISH analysis of metaphase cells in 13 melanoma cell lines (including the 7 lines used for CGH) and 9 primary melanoma specimens by using a whole chromosome paint specific for chromosome 20. All 13 cell lines (100%) and 8/9 primary tumors (89%) showed extra copies of chromosome 20 relative to tumor ploidy. Additionally, 6/14 cell lines (43%) and 2/8 primary tumors (25%) showed translocated chromosome 20 material previously undetected by standard cytogenetics. Cytologic evidence for gene amplification was also found in one cell line, which contained an add(20)(p13), with additional DNA being derived from 20q sequences. These data suggest that overrepresentation of a gene or genes important for melanoma pathogenesis resides on the long arm of chromosome 20.

Band 1p36 abnormalities and t(1;17) in ovarian carcinoma

In a series of 128 karyotyped ovarian carcinomas, 42% of cases with chromosome 1 clonal structural abnormalities had breaks at band 1p36 (usually involving translocations of unknown material). Fluorescent in situ hybridization (FISH) studies using combinations of 1 centromere and 1p36.3-specific probes (16 cases) or 1 centromeric and 17 whole-chromosome paint probes (11 cases with 1p+) revealed a trend toward deletion of 1pter relative to 1 centromere (63%); intratumor heterogeneity; and the origin of 1p+ in 3/11 cases (27%) from chromosome 17 [t(1;17)(p36;?)]. The frequency of this specific breakpoint and its involvement in recurrent translocations suggest that these regions are loci for genes important in the pathogenesis of a subset of sporadic ovarian carcinomas.

Clinical implications of cytogenetic abnormalities in melanoma

Unlike leukemia, in which specific reciprocal translocations are frequently observed, melanomas involve complex recurring chromosome anomalies. Analysis of the constituted genome of melanoma patients should identify cancer susceptibility genes and at-risk individuals in families with a history of melanoma. The first of these genes to be cloned is the cell cycle regulatory protein inhibitor--the p16 gene-- and a second gene locus for melanoma predisposition has been linked to the chromosome 1p36 band region. Detection of the most common somatic genetic alterations in melanoma enhances our understanding of molecular mechanisms of melanoma development and may lead to genetic markers in melanoma. Some alterations may be used to identify interesting subpopulations. Others may be of prognostic value when they are considered in tandem with clinical data.

Size of 22q deletions in four previously reported patients with conotruncal anomaly face syndrome

Conotruncal anomaly face syndrome (CTAFS) was distinguished from velo-cardio-facial syndrome (VCFS) in a bind study, yet shared the finding of 22q11.2 deletions. This work has been extended to show that the 22q11.2 deletions in CTAFS greatly overlap those found in VCFS and many DiGeorge patients. The reason for dissimilar phenotypes with apparently similar 22q11.2 deletions is not yet known.

Expression of the zinc finger gene EVI-1 in ovarian and other cancers

The EVI-1 gene was originally detected as an ectopic viral insertion site and encodes a nuclear zinc finger DNA-binding protein. Previous studies showed restricted EVI-1 RNA or protein expression during ontogeny; in a kidney and an endometrial carcinoma cell line; and in normal murine oocytes and kidney cells. EVI-1 expression was also detected in a subset of acute myeloid leukaemias (AMLs) and myelodysplasia. Because EVI-1 is expressed in the urogenital tract during development, we examined ovarian cancers and normal ovaries for EVI-1 RNA expression using reverse transcription polymerase chain reaction (RT-PCR) and RNAase protection. Chromosome abnormalities were examined using karyotypes and whole chromosome 3 and 3q26 fluorescence in situ hybridisation (FISH). RNA from six primary ovarian tumours, five normal ovaries and 47 tumour cell lines (25 ovarian, seven melanoma, three prostate, seven breast and one each of bladder, endometrial, lung, epidermoid and histiocytic lymphoma) was studied. Five of six primary ovarian tumours, three of five normal ovaries and 22 of 25 ovarian cell lines expressed EVI-1 RNA. A variety of other non-haematological cancers also expressed EVI-1 RNA. Immunostaining of ovarian cancer cell lines revealed nuclear EVI-1 protein. In contrast, normal ovary stained primarily within oocytes and faintly in stroma. Primary ovarian tumours showed nuclear and intense, diffuse cytoplasmic staining. Quantitation of EVI-1 RNA, performed using RNAase protection, showed ovarian carcinoma cells expressed 0 to 40 times the EVI-1 RNA in normal ovary, and 0-6 times the levels in leukaemia cell lines. Southern analyses of ovarian carcinoma cell lines showed no amplification or rearrangements involving EVI-1. In some acute leukaemias, activation of EVI-1 transcription is associated with translocations involving 3q26, the site of the EVI-1 gene. Ovarian carcinoma karyotypes showed one line with quadruplication 3(q24q27), but no other clonal structural rearrangements involving 3q26. However, whole chromsome 3 and 3q26 FISH performed on lines with high EVI-1 expression showed translocations involving chromosome 3q26. EVI-1 is overexpressed in ovarian cancer compared with normal ovaries, suggesting a role for EVI-1 in solid tumour carcinogenesis or progression. Mechanisms underlying EVI-1 overexpression remain unclear, but may include rearrangements involving chromosome 3q26.

Amplification of 19q13.1-q13.2 sequences in ovarian cancer. G-band, FISH, and molecular studies

In this study of ovarian carcinoma, we extended previous findings by performing FISH using chromosome 19 paint and microFISH probes and patient samples with and without abnormalities of chromosome 19 identified by G-banding. Karyotype interpretations of der(19) were confirmed, while additional 19 translocations were also detected by FISH with 19WCP in some cases. Similar FISH studies of ovarian carcinoma cell lines found chromosome 19 abnormalities even after extensive in vitro culture. MicroFISH probes were generated by chromosome microdissection from two cases with hsr(19) and mapped to 19q13.2 and 19q13.1-.2, respectively. FISH with these microFISH probes alone or in combination with a 19WCP probe to four patient samples and seven cell lines showed that 65% of chromosome 19 structural abnormalities contained 19q13.1-q13.2 sequences, sometimes as large hsrs. Ovarian cancer cell lines showed amplification and overexpression of the AKT2 putative oncogene, but not the ERCC-2 DNA repair gene in this chromosomal region. In addition to AKT2, amplification and overexpression of other yet-unidentified genes in the 19q13.1-q13.2 region may contribute to ovarian carcinoma pathogenesis or progression.

Regional mapping of the human platelet-activating factor receptor gene (PTAFR) to 1p35-->p34.3 by fluorescence in situ hybridization

The human platelet-activating factor cell-surface receptor (PTAFR) is a G protein-coupled receptor thought to contribute to many atopic and inflammatory diseases and, perhaps, to the growth of some neoplasms. Exploring the possibility that the PTAFR might be involved in the genetic predisposition to any disease requires knowledge of its chromosomal localization. In this paper we have used a 20-kb human genomic fragment containing the coding sequence of the cloned PTAFR to determine the regional chromosomal localization of the gene. Using fluorescence in situ hybridization, the localization of the human PTAFR gene was mapped to 1p35-->p34.3.

Cytogenetics of 158 patients with regional or disseminated melanoma. Subset analysis of near-diploid and simple karyotypes

We report on the cytogenetic analyses of 158 cases of metastatic malignant melanoma, comprised of 63 cases with regional disease (RD) and 95 cases with distant (metastatic) disease (DD). Clonal structural abnormalities were identified in 126 (80%) cases and were significantly increased ( < 0.01 after adjusting for multiple comparisons) on chromosomes (in order of frequency of involvement) 1, 6, 7, 11, 9, and 3. Clustering of breakpoints occurred at 1p36, 1p22-q21, 6p11-q21, 9p, 11q23-qter, 13p (especially for cases with DD), and 19q13. The most common clonal numerical abnormalities, in a subset of 49 near-diploid cases were -10, -22, -9, +7, -19, and -Y. Analysis of chromosome segment gains and losses (CSRP) showed frequent loss of chromosomes 6 and 10, followed by equal rates of involvement of chromosomes 1, 7, and 9. Whole or segmental losses of chromosome 9 (especially 9p) correlate well with recent molecular genetic studies identifying putative suppressor genes, and are also likely important genetic abnormalities. However, based on the frequency of abnormalities in this large series of metastatic melanomas, it is likely that structural abnormalities of 1 and 6, and 10 are important in the pathogenesis of sporadic advanced melanoma.

Chromosome microdissection identifies cryptic sites of DNA sequence amplification in human ovarian carcinoma

DNA sequence amplification contributes to the multistep process of carcinogenesis, and overexpression of amplified genes has been shown to contribute to the malignant phenotype. Cytogenetic analyses of human tumor cells, including ovarian malignancies, frequently show cytological evidence of DNA amplification in the form of double minutes and homogeneously staining regions. In this report, we have combined the techniques of chromosome microdissection and fluorescence in situ hybridization (P. S. Meltzer et al., Nat. Genet., 1: 24-28, 1992) to identify the composition and chromosomal origin of seven homogeneously staining regions from seven cases of ovarian cancer. Twelve specific chromosome band regions were identified as amplified including 11q, 12p, 16p, 19p, and 19q. These results provide important insights into the organization of amplified sequences within ovarian malignancies and add further to our recognition of regions likely to harbor genes important to the development or progression of ovarian cancer.

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.

Establishment of a new lung sarcoma cell line from a human lung carcinosarcoma

A cell-line (UACC 2561), was established from a biopsy specimen of a lung carcinosarcoma. The patient had Stage III non-small cell lung cancer. Characterization of this cell line revealed highly aneuploid cells containing multiple clonal chromosome alterations with growth in nude mice within 3 weeks following subcutaneous injection. The cell line UACC 2561 stained positive for vimentin and displayed resistance to a variety of chemotherapeutic agents. Polymerase chain reaction followed by single-strand conformational polymorphism analysis revealed the presence of a K-ras 12 codon mutation. This mutation was confirmed by mutation specific PCR analysis for mutant K-ras alleles and direct DNA sequencing to be a GGT to GTT at codon 12 of the K-ras gene. Examination by PCR-SSCP for p53 mutations did not reveal any point mutations in exon 5-8 of the p53 gene. This relatively rare cell line may represent a useful model to investigate human lung sarcomas.

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 tumorigenicity in a methotrexate-resistant human leukemia cell line

We have studied the tumorigenicity of a CCRF-CEM-derived cell line (CEM/MTX-3) resistant to MTX. Eight of nine mice inoculated with drug-sensitive CEM cells developed tumors within 5 weeks, but 16 weeks after inoculation with CEM/MTX-3 cells, none of nine mice developed tumors. We were unable to detect dihydrofolate reductase gene overexpression, amplification, or rearrangement in CEM/MTX-3 cells. Instead, the resistance in CEM/MTX-3 cells appeared to be due largely to decreased methotrexate accumulation. Because tumorigenicity could have been related to intracellular folate levels, we cultured CEM and CEM/MTX-3 cells in folate-rich and folate-deprived media. When inoculated in mice, CEM cells cultured in either medium rapidly formed tumors. As before, CEM/MTX-3 cells grown in either medium did not, suggesting that factors other than low folate levels contributed to the inability of CEM/MTX-3 cells to form tumors. Cytogenetic analysis revealed that the CEM/MTX-3 karyotype contained a unique and complex translocation marker chromosome that was not observed in the CEM cell line and which involved chromosomal breakpoints at bands 11p14, 22p11, and 22p13. Although biochemical mechanisms are not yet delineated, this remodeled chromosome could be related to the loss of tumorigenicity in CEM/MTX-3 cells.

Characterization of the P-glycoprotein over-expressing drug resistance phenotype exhibited by Chinese hamster ovary cells following their in-vitro exposure to fractionated X-irradiation

Exposure of the Chinese hamster ovarian AuxB1 cell line in vitro to fractionated X-irradiation generated sublines designated DXR-10, which proved resistant to multiple drugs and overexpressed P-glycoprotein (Pgp), as judged by Western blotting using the C219 monoclonal antibody. Further characterization of these irradiated DXR-10 sublines has provided evidence for: (i) the expression of cross-resistance to gramacidin D, taxol, puromycin and Navelbine, but not to daunomycin or mitoxantrone; (ii) overexpression of the class I Pgp, as judged by Western blotting using the C494 monoclonal antibody; (iii) decreased accumulation of 3H-vincristine, which could be enhanced by verapamil addition; (iv) unaltered accumulation and subcellular distribution of adriamycin; (v) significantly increased rhodamine 123 accumulation in the presence of verapamil; (vi) plasma-membrane ultrastructural modifications resulting in a significantly increased surface area; (vii) numerous clonal karyotypic alterations, with abnormalities involving the long arm of chromosome 1 being consistently identified; (viii) a lack of overexpression of sorcin; (ix) increased total glutathione levels and overexpression of glutathione S-transferase pi. The fact that only certain of these features are considered characteristic of the 'classic' multidrug-resistant CHRC5 cell line supports our earlier proposal that exposure to fractionated X-irradiation results in the expression of a unique drug-resistance phenotype.

Cytogenetics and clinical correlations in breast cancer

We describe an ongoing study examining the relevance of cytogenetic changes in primary and metastatic breast cancer. Tumors samples from breast cancer patients are karyotype using G-banding techniques, and all chromosomal findings, including the presence of structural and numeric clonal abnormalities, are documented in a dynamic patient data base. Information on essential clinical characteristics is collected, and patients are followed longitudinally for disease recurrence, progression, and survival. Statistical analyses will examine potential correlations between specific abnormalities and clinical features of the disease, and survival differences between patients will be examined as a function of karyotypic differences. We anticipate that this research will provide insights on the natural history of breast cancer and help direct the search for the underlying molecular mechanisms of tumor genesis and progression.

Different mechanisms of decreased drug accumulation in doxorubicin and mitoxantrone resistant variants of the MCF7 human breast cancer cell line

We selected two drug resistant variants of the MCF7 human breast cancer cell line by chronic in vitro exposure to doxorubicin (MCF7/D40 cell line) and mitoxantrone (MCF7/Mitox cell line), respectively. The cell lines are similar in growth characteristics including doubling time, DNA synthetic phase and cell size. Resistance to mitoxantrone conferred only partial resistance to doxorubicin; whereas resistance selected for doxorubicin appeared to confer complete resistance to mitoxantrone. Both agents selected for cross resistance to the Vinca alkaloids. MCF7/D40 cells display a classic-multi-drug resistance phenotype with expression of P-glycoprotein, decreased drug accumulation relative to the parental line and reversal of drug accumulation and drug resistance by verapamil. MCF7/Mitox cells likewise display resistance to multiple drugs, but in contrast to MCF7/D40 cells do not express P-glycoprotein by immunoblot or RNA blot analysis. Net drug accumulation in MCF7/Mitox cells was decreased relative to the parental cells but there was no selective modulation of drug accumulation or in vitro drug resistance by the addition of verapamil. Efflux of mitoxantrone was enhanced in both the MCF7/D40 and MCF7/Mitox cell lines relative to the MCF7/S cell line. We conclude that the two drug resistant cell lines have different mechanisms of decreased drug accumulation.

Identification of a recurring translocation site involving chromosome 6 in human malignant melanoma

The recognition of recurring sites of chromosome change in human cancers has pinpointed the location in the genome of several important growth-regulatory sequences (e.g., cellular oncogenes). This report details the finding of a recurring translocation site involving the long arm of chromosome 6 (6q) in malignant melanoma. We have observed a translocation (t) between chromosomes 1 and 6 in five different cases of malignant metastatic melanoma. All five melanomas evidencing t(1;6) involved band regions 6q11-13, while two different regions of chromosome 1 (p22, q12-q21) were shown to be translocated to 6q. In reviewing previously published cases of melanoma, an additional two cases of t(1;6) and 13 cases of other translocations to 6q11-13 have been identified. Chromosome 6q contains several biologically important gene sequences including the proto-oncogenes ros, myb, and mas1. However, based on current mapping studies, the breakpoint of this translocation (6q11-13) is not within the region encoding these sequences. By analogy to other systems, molecular analysis of the translocation breakpoints may identify a gene(s) which plays a role in melanoma tumorigenesis.

Methods for chromosome banding of human and experimental tumors in vitro

Technological advances in the study of chromosomes from human and experimental cancers are occurring rapidly. Molecular cytogenetic techniques for in situ hybridization, as well as chromosome sorting and even karyotyping via flow cytometry (both described elsewhere within this volume), are important developing areas receiving considerable study. However, there currently remains a significant need for routine karyotyping of mammalian cells. It is hoped that the methods provided in this chapter will be of help in assisting somatic cell geneticists to identify chromosome changes in mammalian cell cultures.

Generation of clonal variants in a human ovarian carcinoma studied by chromosome banding analysis

We have utilized detailed chromosome banding analysis to document the selection of variant genetic clones existing in cell populations obtained from a patient with ovarian adenocarcinoma. Cytogenetic analysis was performed on two samples from the patient's malignant ascites obtained over a 9-month interval. Tumor cell lines were also established in monolayer culture from each ascites sample, analyzed by chromosome banding techniques, and compared to the clonogenic population grown from each ascites specimen. Appearance of karyotypically distinct populations were identified from both the in vivo tumor and the tumor cell lines. Tumor colony-forming units (TCFU) evidenced minimal karyotypic change between the original ascites tumor and the ascites sample obtained after a 9-month period in vivo. In contrast, the cell lines derived from these two ascites samples demonstrated markedly different karyotypic populations between samples and progressive chromosome change within each sample following prolonged in vitro growth.

Evidence for selection of homogeneously staining regions in a human melanoma cell line

Cytogenetic analysis of tumor cells from a human malignant melanoma was performed on both the primary tumor colony-forming cells and a cell line (HA-A) established subsequently from the clonogenic population. Chromosome-banding analysis demonstrated identical karyotypic alterations in both the tumor colony-forming cells and the HA-A cell line, documenting their origin from a common precursor. The most distinctive chromosome alterations shared between tumor colony-forming cells and the HA-A cell line were double-minute bodies (DMs) and a homogeneously staining region (HSR) on chromosome 7 at band p22. This represents the first observation of DMs or HSRs in cells from a human malignant melanoma. The frequency of HSR-bearing cells observed in the original tumor was less than 1%, while DM-containing cells were present in greater than 90% of all cells examined. In contrast, serial chromosome harvests at early passage of the HA-A cell line revealed positive selection for HSR-bearing cells with concomitant loss of DM-containing cells after increasing time in vitro. Following the ninth serial passage in vitro, HSRs were observed in 100% of cells with DMs no longer observed in the HA-A cell line. The finding of an HSR-bearing marker in the original tumor sample supports the view that HSRs are not an artifact of in vitro monolayer growth. However, our results demonstrate that the frequency of HSR-bearing cells within established cell lines may reflect in vitro selection and therefore not accurately reflect the frequency of this population in vivo.

Infiltrating ductal carcinoma of the breast in the postpubertal adolescent: a case report

Infiltrating ductal carcinoma is an extremely rare neoplasm in the teenage or pre-teenage child. Routine pediatric physical examination should include careful examination of the breast and all palpable masses should be excised. Carcinoma occurring in the prepubertal child carries an improved prognosis particularly if the tumor stains PAS-positive. Carcinoma occurring in the postpubertal teenager probably carries the same prognosis as that in the adult and should be treated in a similar manner. The authors discuss such a case occurring in a 13-year-old girl.