Detection of 1q polysomy in interphase nuclei of human solid tumors with a biotinylated probe

Expression analysis of mitotic spindle checkpoint genes in breast carcinoma: role of NDC80/HEC1 in early breast tumorigenicity, and a two-gene signature for aneuploidy

Background

Aneuploidy and chromosomal instability (CIN) are common abnormalities in human cancer. Alterations of the mitotic spindle checkpoint are likely to contribute to these phenotypes, but little is known about somatic alterations of mitotic spindle checkpoint genes in breast cancer.

Methods

To obtain further insight into the molecular mechanisms underlying aneuploidy in breast cancer, we used real-time quantitative RT-PCR to quantify the mRNA expression of 76 selected mitotic spindle checkpoint genes in a large panel of breast tumor samples.

Results

The expression of 49 (64.5%) of the 76 genes was significantly dysregulated in breast tumors compared to normal breast tissues: 40 genes were upregulated and 9 were downregulated. Most of these changes in gene expression during malignant transformation were observed in epithelial cells.

Alterations of nine of these genes, and particularly NDC80, were also detected in benign breast tumors, indicating that they may be involved in pre-neoplastic processes.

We also identified a two-gene expression signature (PLK1 + AURKA) which discriminated between DNA aneuploid and DNA diploid breast tumor samples. Interestingly, some DNA tetraploid tumor samples failed to cluster with DNA aneuploid breast tumors.

Conclusion

This study confirms the importance of previously characterized genes and identifies novel candidate genes that could be activated for aneuploidy to occur. Further functional analyses are required to clearly confirm the role of these new identified genes in the molecular mechanisms involved in breast cancer aneuploidy. The novel genes identified here, and/or the two-gene expression signature, might serve as diagnostic or prognostic markers and form the basis for novel therapeutic strategies.

An improved rapid procedure for fluorescence in situ hybridization that is applicable to intraoperative cancer cytodiagnosis

Fluorescence in situ hybridization (FISH) is among the most simple and useful methods for detecting numerical and structural aberration of chromosomes but it requires 12-24 h to complete. We devised a rapid FISH method that can be performed within 2 h. Here we describe the technique, which we have found to be extreme simple and as sensitive and specific as standard FISH, making it highly suitable for clinical use.

Frequent multiplication of chromosome 1q in non-invasive and papillotubular carcinoma of the breast

Carcinogenesis is considered to be a multistep process that may involve cumulative genetic alterations; one of these mechanisms, gain of chromosomal material, has the potential to activate tumor-promoting genes in breast carcinogenesis. Using 12 polymorphic microsatellite markers on the long arm of chromosome 1 (1q), we examined 130 sporadic breast carcinomas for abnormalities in the copy numbers of these loci in tumor cells using a differential PCR method. We also sought correlations between alterations on 1q and several clinicopathological parameters. At every locus examined, a 2-3-fold increase in copy number of an allele in tumor material was observed in one third of the tumors (46 of 130, 35%), indicating 'multiplication' of 1q. This multiplication involved the entire long arm in majority of those tumors (43 cases, 93%). The multiplication of 1q was observed more frequently in non-invasive ductal and papillotubular histological types than in solid-tubular and scirrhous types (13/25, 52% vs. 27/90, 30%) (P = 0.041). The predominant chromosomal alterations on 1q in breast carcinomas are found to be multiplications rather than losses. The multiplication represents polysomy of the entire region of 1q, and may confer a growth advantage during development and/or progression of non-invasive ductal and papillotubular histologic types of breast carcinomas.

Numerical aberrations of chromosomes 1 and 17 in tumor cell lines of the exocrine pancreas as determined by fluorescence in situ hybridization

The relationship between the copy numbers of chromosomes 1 and 17 and characteristics related to aggressiveness, histological grade, and doubling time was studied in 10 cell lines from pancreatic carcinomas (7 from primary tumors, 2 from ascites, and 1 from a liver metastasis). Fluorescence in situ hybridization with, respectively, the (peri-)centromeric pUC 1.77 (chromosome 1), and D17Z1 (chromosome 17) probes was applied to interphase nuclei. The results showed that most of these cell lines were hyperploid for both chromosomes studied in accordance with their chromosome counts in metaphase; moreover, there existed a statistically significant positive correlation between the results for both probes. Two of these cell lines had a higher mean copy number for chromosome 17 than for chromosome 1 (PaCa 44 and PaTu 2); two of them had a higher mean copy number for chromosome 1 than for chromosome 17 (Panc 1 and PSN 1). Although only a weak correlation was observed between the number of signals for either chromosomes 1 or 17 and the doubling time, lines of grade 1 and 2 showed a lower average number of spots per nucleus than grade 3 cell lines for both chromosomes studied.

FRAXF in a patient with chromosome 8 duplication

We report on a folate sensitive fragile site at Xq27-28 in a girl with a multiple congenital anomalies and mental retardation syndrome, who also carries a duplication of the long arm of chromosome 8. The fragile site was shown by FISH to be distal to both FRAXA and FRAXE. DNA hybridisation with probe OxF14 showed the amplification of the CGG repeats of locus FRAXF in the patient and in her clinically normal mother.

Identification of a supernumerary marker derived from chromosome 17 using FISH

We report on a 15-year-old girl with mental retardation, obesity, short stature and minor anomalies. She had 47 chromosomes with a minute extra ring which was identified by FISH to be derived from chromosome 17.

Study of numerical aberrations of chromosome 1 by fluorescent in situ hybridization and DNA content by densitometric analysis on (pre)-malignant cervical lesions

In an attempt to determine whether the fluorescent in situ hybridization (FISH) can be used as a rapid approach for the identification of aneuploidy in premalignant cervical smears, a centromeric probe for chromosome 1 was used. The results from the FISH experiments were compared with measurements of the overall DNA content obtained by means of an image analysis system. With progression to neoplasia, a decrease of the frequency of cells with two spots was observed, due to an increasing polysomy of chromosome 1. As far as the DNA content was concerned, an increasing DNA index and 5C-exceeding ratio (fraction of cells with a DNA content higher than 5C) was observed. Classification of the FISH results by a linear discriminant analysis revealed that 67.6% of the cases were classified in agreement with the CIN classification. These data suggest that chromosome 1 may be considered as a marker chromosome for pre-malignant cervical lesions and that the DNA content measurements are complementary to the FISH results.

Selection of adrenal tumor cells in culture demonstrated by interphase cytogenetics

Solid tumors often consist of an admixture of cell populations with different genome constitutions. Karyotyping of this material is complicated by the low mitotic index. Even when chromosome studies are feasible, altered representation of the original cell populations after cell cultivation is possible. We report a human adrenal carcinoma that exhibited a normal karyotype after cultivation but was shown to be highly aneuploid when investigated by fluorescence in situ hybridization (FISH) in direct preparations of uncultured cells with six different centromeric probes. The high frequencies of trisomy for the investigated chromosomes in these interphase cells indicate that most of the tumor cells were in the triploid range. Strong selection for disomic cells was detected in interphase preparations after one and two subcultures and was even stronger in the corresponding metaphase preparations. Trisomy for chromosome 15 appeared to be maintained independent of triploidy and might play a role in cultured cell survival. The number of chromosome 17 centromeres was not increased in polyploid cells, suggesting loss of this chromosome in the original cells of the tumor.

Improved detection of DNA aneuploidy in primary breast cancer using quantitative DNA image analysis in combination with fluorescent in situ hybridization technique

To obtain more information about the relationship between numerical aberrations of chromosome 1 and the overall DNA content of breast cancer cells, fluorescent in situ hybridization with a pericentromeric probe for this chromosome and image analysis based densitometry were carried out on imprints of benign (15 cases, mainly fibroadenomas) and malignant breast disease (31 invasive ductal carcinomas out of 45 cases). The most pronounced aneuploidy was observed in invasive ductal and lobular carcinoma cases both by in situ hybridization and DNA content (76.7 and 75.0% were aneuploid). The frequency of cells with two spots for chromosome 1 was 48.3 and 51.5%, respectively, as compared to 80.3% in control lymphocytes. There was a weak overall correlation (r2 = 0.83) between DNA content and copy number of chromosome 1 in the malignant samples, although some of the DNA diploid/near diploid carcinomas showed a marked aneusomy for this chromosome. Also, some aberrations were present in the benign breast disease samples. Classification of cases by a linear discriminant analysis was most accurate when both techniques were combined (77% of cases correctly classified, according to anatomo-pathological diagnosis). The variables which received the highest weight in the linear discriminant function are the percentage DNA-diploid cells and the fraction of cells with two spots for chromosome 1. The sensitivity and sources of error of both techniques is considered.

Aneuploidy for chromosome 1 and overall DNA content in benign and malignant breast disease

Fluorescence in situ hybridization (FISH) with a probe for the pericentromeric region of chromosome 1 and DNA content measurements by image-analysis-based densitometry have been carried out on imprints of benign and malignant breast tissue. In general, an increase in the number of spots per nucleus was observed in the invasive carcinomas, with a large intercellular variation. In comparison with lymphocytes from controls, some cases of benign breast disease already had an increased frequency of aneusomy of chromosome 1, although they were all (near)diploid by DNA-content. However, an overall concordance between the DNA content measurements and the results of FISH was observed, although some exceptions were seen. A statistically significant correlation between the DNA index and the mean number of spots for chromosome 1 per nucleus was found. A linear discriminant analysis was applied on the data; the resulting classification of patients was most accurate when parameters describing DNA content and FISH results were combined.

Detection of i(17q) chromosome by fluorescent in situ hybridization (FISH) with interphase nuclei in medulloblastoma

Medulloblastomas are the most frequent primitive neurectodermal tumors in children. An isochromosome for the long arm of 17, i(17q), is found in 30% of medulloblastomas. For some authors, this abnormality is observed in cases with a shorter survival time. In our cytogenetic studies of 30 medulloblastomas, we observed i(17q) in only three cases, a monosomy 17 in two cases, a monosomy 22 in four cases, nonspecific numerical or structural abnormalities in five cases, and normal karyotypes in 12 cases. We compared the results of karyotypic analysis after culture and FISH with a chromosome 17 alpha satellite DNA probe on interphase nuclei in five cases of medulloblastoma. In one case, i(17q) was only observed in four cells in karyotypic analysis, in three cases a normal karyotype was found, and in one case karyotypic analysis was impossible. In all of these cases, i(17q) was observed in a great number of nuclei by FISH on interphase nuclei. Our study shows that the FISH on interphase nuclei permitted us to observe i(17q) in the cases where it was not or could not be completely detected by karyotypic analysis. The association of these two techniques is required to detect i(17q), an abnormality whose prognosis value in medulloblastomas is now recognized.

Detection of premalignant stages in cervical smears with a biotinylated probe for chromosome 1

Fluorescence in situ hybridization with (peri-)centromeric probes is an easy method to detect numerical aberrations in nonmitotic and mitotic cells. In this study, cervical smears of premalignant and malignant stages (26 controls, 15 CIN I, 12 CIN II, and 15 CIN III cervical smears) were analyzed for the presence of numerical aberrations of chromosome 1 with a centromeric DNA probe (1q12). With more severe stages a decrease of disomy was observed, merely due to a gain of extra copies of chromosome 1; in some cases, however, monosomy was detected. The frequencies of disomy for chromosome 1 ranged from 65.3% to 95.0% in the controls, from 71.3% to 94.3% in CIN I, from 59.2% to 91.5% in CIN II, and from 23% to 96.2% in CIN III. Polysomy ranged from 0% to 5.7% in the controls, from 0% to 14.4% in CIN I, from 0.9% to 30.8% in CIN II, and from 0.8% to 69.6% in CIN III. Monosomy ranged from 2.6% to 34.1% in the controls, from 0% to 17.5% in CIN I, from 3.6% to 27.5% in CIN II, and from 0.9% to 31.4% in CIN III. The results show that screening for aneuploidy of chromosome 1 allows a good discrimination between control samples and dysplasia. These data suggest that chromosome 1 may be a marker chromosome. They are in accordance with previous cytodensitometric analyses, where already in the preneoplastic stages an increased DNA content (polyploidization with subsequent aneuploidization) is observed.

Chromosomal aneuploidy in proliferative breast disease

Although some forms of proliferative breast disease have been associated with increased risk of breast cancer, substantial confirmatory evidence that the lesions are biologically premalignant has not been presented. Our intent was to identify cytogenetic aberrations in proliferative breast disease using fluorescence in situ hybridization probes selected for their relationship to aberrations previously reported in breast cancer. Application of fluorescence in situ hybridization techniques to paraffin tissue sections using pericentromeric probes for chromosomes 1, 16, 17, 18, and X revealed chromosome aneuploidy in proliferative and malignant lesions of the breast. Sectioning artifact that may result in nuclear truncation was controlled by establishing expected baseline frequencies for gain and loss in normal tissues from the same breast. Localization of chromosomal aberrations to proliferative breast disease lesions with concomitant retention of a normal chromosome complement in corresponding normal breast tissues indicates biologic significance of the results. The similarities of losses involving chromosomes 16, 17, and 18 in hyperplastic lesions and in malignant breast lesions suggest that some hyperplasias may be part of a sequence of progression to malignancy in breast cancer. Gains of chromosome 1 in both in situ and invasive carcinoma are consistent with reports of polysomy 1q as a common cytogenetic change in breast cancer. Its localization to advanced lesions suggests that this trisomy is probably not the initial cytogenetic change in breast cancer tumorigenesis.

Detection of an i(17q) chromosome by fluorescent in situ hybridization with a chromosome 17 alpha satellite DNA probe

An isochromosome for the long arm of chromosome 17,i(17q), is frequently found as an additional chromosome aberration to the Ph with advanced disease in the chronic myelocytic leukemia (CML). We studied an i(17q) in blood samples from two patients with CML in blast crisis with a biotinylated chromosome 17 specific alpha satellite deoxyribonucleic acid probe. G-banded karyotypes of these patients showed a dicentric i(17q), dic(17)(p11.2). Fluorescence in situ hybridization (FISH) delineated one normal chromosome 17 and one i(17q) among metaphase chromosomes; the latter showed a dicentric pattern. In most interphase nuclei of both patients, two fluorescence spots were observed. In some interphase nuclei, including mature neutrophils, the dicentric chromosome was discernible by its size and shape of the fluorescent spots. Three fluorescent spots were observed in a small proportion of interphase cells, and existence of a subclone with two normal chromosome 17 and an i(17q) was confirmed by examining a large number of metaphase plates. The results of FISH provided us with information of numerical and structural aberrations of chromosome 17 in interphase cells.

Interphase cytogenetics on paraffin sections of malignant pleural mesothelioma. A comparison to conventional karyotyping and flow cytometric studies

We performed in situ hybridization (ISH) studies of malignant pleural mesotheliomas to detect numerical aberrations of chromosomes 1 and 7 in interphase nuclei of paraffin sections of 13 cases that had been analyzed previously by conventional karyotyping and flow cytometry. The hybridizations were performed with the biotin-labeled probes recognizing repetitive DNA sequences in the (peri)centromeric regions of chromosomes 1 (1q12) and 7(7cen). Application of histologic sections allowed us to analyze the tumor cells only. Comparison of the karyotype and ISH studies showed that the same chromosome copy numbers were detectable by both methods in 13 (chromosome 1) and in 12 (chromosome 7) cases evaluable by ISH. DNA indexes determined in the paraffin-embedded tumor material corresponded with the ISH findings. As compared with karyotype analysis, ISH showed a larger heterogeneity in chromosome copy numbers. The results can be divided into three groups: 1) Monosomy or disomy of chromosomes 1 and 7 was detected by both methods in two cases; 2) in four cases, disomy of both chromosome 1 and 7 was observed in most of the cells by ISH analysis, and karyotype analysis had shown clear polyploidization in three of these cases; 3) in seven cases, supernumerary copies of chromosomes 1 and/or 7 were present in an evident fraction (27-80%) of the cells analyzed by ISH, and karyotype analysis confirmed the aberrant copy numbers in five of these cases. On the other hand, ISH showed copy numbers not detected by karyotype analysis in six of the seven cases. Thus, by combining karyotype and interphase cytogenetic studies, complementary information about chromosomal aberrations in mesothelioma is obtained.

Uterine leiomyoma cytogenetics. III. Interphase cytogenetic analysis of karyotypically normal uterine leiomyoma excludes possibility of undetected trisomy 12

Uterine leiomyoma, a benign tumor that histopathologically is rather homogeneous, was recently characterized cytogenetically. About 40% of the investigated tumors are associated with clonal chromosome abnormalities and five different subgroups have been identified, characterized by trisomy 12, t(12;14)(q14-15;q23-24), del(7q), t(1;2)(p36;p24), and 6p rearrangements. In our survey of 76 cases, trisomy 12 was observed in 10% of the abnormal cases. To exclude a possible underscoring of this abnormality, we reexamined 15 of the cases with normal karyotype by interphase cytogenetics using a chromosome 12 alphoid DNA probe.

Nonradioactive in situ hybridization. A rapid approach for the identification of marker chromosomes: study of a case of acute leukemia with a Yq specific DNA probe

Nonradioactive in situ hybridization provides a rapid method for detecting specific nucleic acid sequences. In this study of a patient with acute leukemia, we applied in situ hybridization for identification of a marker chromosome and determination of the number of copies of this marker in interphase nuclei using a biotinylated Yq-specific DNA probe (pY3.4). We show that nonradioactive interphase in situ hybridization can be a useful method for karyotypic analysis in addition to routine cytogenetic techniques in neoplastic disorders.

Analysis of genes and chromosomes by nonisotopic in situ hybridization

Nonisotopic in situ hybridization is a powerful tool to analyze the organization of complex genomes. Current approaches utilizing this technique for the analysis of linear and spatial genome organizations are presented. Clinical applications of these approaches, which open new avenues for diagnosis of disease-related chromosomal changes, are also discussed.

Detection of monosomy in interphase nuclei and identification of marker chromosomes using biotinylated alpha-satellite DNA probes

Nonradioactive in situ hybridization with chromosome-specific highly repetitive DNA probes is a fast and easy method for the detection of the number of chromosome copies in nonmitotic cells. In this study, we report the use of four biotinylated probes of the human alpha-satellite family recognizing the (peri)centromeric regions of chromosomes 3, 10, 16, and 17. The reliability of the probes was tested by hybridizations to metaphase chromosomes and interphase nuclei of normal blood lymphocytes, which showed a two signal score in 85%-94% and 82%-86% of the cells, respectively. In situ hybridization experiments with nuclei and metaphase spreads derived from the LXFS-650 cell line indicated monosomy for chromosomes 10 and 16 and the presence of two derivative chromosomes 17. These results were in accordance with the cytogenetic data obtained with GTG-banding and confirmed the monoclonality of the cell line. Furthermore, with this method the origin of an unclassified marker chromosome could be identified as a derivative of chromosome 3. Our results show that fluorescence in situ hybridization can be a useful tool in cancer cytogenetics for the detection of numerical aberrations in interphase nuclei and for the classification of marker chromosomes in addition to conventional cytogenetic techniques.