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

Methodologies in cancer cytogenetics and molecular cytogenetics

Various types of cytogenetic and molecular cytogenetic approaches, including conventional banding, fluorescence in situ hybridization (FISH), fiber-FISH, comparative genomic hybridization (CGH), matrix array CGH, chromosome microdissection, and microcell-mediated chromosome transfer are summarized. The rationale, advantage, and limitations of each approach are discussed with respect to research and clinical applications in human neoplasia.

Overview of fluorescence in situ hybridization techniques for molecular cytogenetics

This unit presents an overview of the FISH methodology. It covers such topics as direct versus indirect methods, sensitivity, multiplicity, resolution, and applications.

Cytogenetic analysis of non Hodgkin's lymphomas by ratio-painting and comparative genomic hybridization reveals unsuspected chromosomal abnormalities

Cytogenetic analysis of cancer cells has proven to be a powerful tool in understanding malignant evolution and in providing clinically useful markers. In recent years the advent of new fluorescence in-situ hybridization (FISH) methods such as ratio-painting and comparative genomic hybridization (CGH) have enabled much more accurate karyotypes of malignant cells to be detected. In this study, we have examined the chromosomes present in malignant cells from a series of 6 low grade follicular centre and 2 high grade diffuse large cell non-Hodgkin's lymphomas (NHL) using conventional G-banding. In all cases chromosome abnormalities were observed, including the presence of marker chromosomes in six cases. The NHL cells were then subjected to the FISH method of ratio-painting. This provided a more accurate understanding of the origins of derivative chromosomes and identified the origins of all of the marker chromosomes. It also revealed hitherto unsuspected abnormalities. For example, in one case four abnormal chromosomes were demonstrated to contain material from chromosome 8, which had not been previously suspected from G-banding. Regions of amplification and deletion on the chromosomes were also investigated by CGH, which identified further unsuspected chromosomal abnormalities. For example, in case L124, trisomy of chromosome 7 was confirmed by CGH, but an unsuspected amplification of 3(p12) was also revealed. These approaches demonstrate the power of FISH technology in providing a more precise analysis of malignant cell chromosomes, and in doing so have produced comprehensive karyotypes of the NHL under study.

Comparative genomic hybridization as a tool in tumour cytogenetics

The quality of cytogenetic analysis of solid tumours has greatly improved in the past decade, but a number of technical difficulties remain which limit the characterization of solid tumour chromosomes by conventional cytogenetics alone. The identification of regions of chromosomal abnormality has been aided by the introduction of molecular cytogenetic techniques such as fluorescence in situ hybridization (FISH). Of these, a recently developed approach, comparative genomic hybridization (CGH), has had a particular impact on the cytogenetic analysis of solid tumours. It incorporates the sensitivity of in situ techniques and overcomes many of the drawbacks of conventional cytogenetic analysis. This review first outlines the CGH method, giving details for the preparation of DNA probes and target human metaphase chromosomes together with information on the in situ technique and data handling criteria used in our laboratory. It then presents an overview of some of the current applications of CGH, together with a discussion of future directions in the field.

Sequential G-banding FISH on human sperm chromosomes

A method that allows the performance of double-colour chromosome painting (FISH) on previously G-banded human sperm metaphases has been developed. Sperm chromosomes were obtained by using the fusion technique between zona-free hamster oocytes and human spermatozoa. Single- and double-colour chromosome painting was performed using DNA libraries specific for chromosomes X, Y and 21 on either unstained or G-banded preparations. The hybridization efficiency was very high (98%). The sequential staining technique is very useful for analyses of structural (stable) and numerical chromosome aberrations in human sperm and thus can increase the efficiency of the human sperm-hamster oocytes fusion system to assess the risk to human germ cells as a result of endogenous and exogenous factors.

Fluorescence in situ hybridization of old G-banded and mounted chromosome preparations

An improved method for fluorescence in situ hybridization (FISH) investigation of old, previously G-banded, mounted chromosome preparations with chromosome specific painting probes and centromere-specific probes is described. Before hybridization, the slides are incubated in xylene until the coverslips detach spontaneously; any mechanical manipulation will jeopardize the results. The success of chromosome painting is improved by excluding the regular RNase treatment step prior to hybridization. Additional changes compared with standard FISH protocols are that the 2 x SSC step is omitted, that the amount of added probe is increased approximately 2.5 times, and that the amplification of signals is performed twice. The applicability of the method, which allows double painting with two differently labeled probes using two differently fluorescing colors, was tested on 11 cases involving different chromosome abnormalities and different types of material, including short-term cultures of epithelial and mesenchymal tumors, blood, leukemic bone marrow, and long-term cultures of a cell line derived from an epithelial tumor. Success was achieved even with chromosome preparations that were several years old.

Reinterpretation of G-banded complex karyotypes by fluorescence in situ hybridization with chromosome-specific DNA painting probes and alpha-satellite centromere-specific DNA probes in malignant hematological disorders

In this study, we have performed fluorescence in situ hybridization (FISH) with chromosome-specific DNA painting probes 1, 2, 3, 4, 6, 8, and 12 and centromere-specific DNA probes 7,10,12,17,18, and X after G-banding on the same metaphase spreads from four patients with malignant hematological disorders to more precisely interpret their complex karyotypes. The findings demonstrated that the application of combined G-banding and FISH can more accurately explain complex karyotypes of hematological malignancies. FISH can detect not only the origin of marker chromosomes, but also the complex rearrangements that cannot be identified by routine banding techniques. This approach is very important to complement the cytogenetic analysis of malignant disorders and to evaluate the role of chromosome change in the development, progression, and prognosis of tumors.

FISHing chromosomes in endocrinology

Fluorescencein situ hybridization (FISH) is currently recognized as a reliable, sensitive, and reproducible technique for identification of copy number and structure of chromosomes providing information on the single-cell level. The technique permits cytogenetic investigation of metaphase spreads and interphase nuclei. Several protocols have been used for preparations from fresh samples or archival material. Alphoid or telomeric DNA probes can detect specific chromosomes, and cosmid probes can localize single copies of the segment of interest. FISH is a powerful tool in understanding physiologic mechanisms, in generating high-resolution physical genetic maps, and in resolving problems of the pathogenesis of several diseases. FISH may shed light on the cytogenetic background and chromosomal alterations in the field of endocrinology, resulting in a better understanding of functional activities and various endocrine disorders.

Analysis of 14q+ derivative chromosomes in non-Hodgkin's lymphomas by fluorescence in-situ hybridization

The most common chromosomal abnormality observed in non-Hodgkin's lymphomas (NHL) involves the structural alteration of the q arm of chromosome 14. It is not always possible, however, to fully analyse such derivative chromosomes by Giemsa-banding. Therefore, we have applied the fluorescence in-situ hybridization (FISH) technique of chromosome painting to elucidate the origins of the der(14) chromosomes in 8 cases of NHL. In 2 NHL the der(14) appeared to be the product of the t(14;18)(q32;q21) translocation, but were not accompanied by the reciprocal der(18) chromosome. In 3 cases the breakpoint was at 14q32 but the translocated material appeared not to be from chromosome 18 and in 2 cases the breakpoint was centromeric to 14q32. One case with a t(14;18)(q32;q21) was also analysed as a control. Dual painting was carried out with paints for chromosome 14 and either chromosome 3, 8, 10, 11, 18 or 19. In the control and 2 other cases the translocated material was demonstrated to be from chromosome 18, in two cases it was from chromosome 3 and in 1 case there was an unusual insertion of chromosome 11 material. We were unable to identify the origins of the translocated material in 1 NHL and in the final case the apparent der(14) was demonstrated not to contain chromosome 14 material. These data demonstrated the utility of the FISH technique for analysing malignant cell karyotypes, and in particular indicated the potential of this approach for identifying cases containing putative NHL associated oncogenes that may have been translocated adjacent to the immunoglobulin locus at 14q32.

Application of FISH to complex chromosomal rearrangements associated with chronic myelogenous leukemia

Identification of complex chromosomal rearrangements can be difficult, due either to the limited number and sometimes poor quality of metaphases in bone marrow preparations or to the nature of the rearrangements. Fluorescence in situ hybridization (FISH) using chromosome-specific DNA libraries in conjunction with a cosmid probe for the c-ABL oncogene was performed to substantiate the preliminary G-banded karyotypes of six patients with chronic myelogenous leukemia (CML). Our results indicate that FISH is sufficiently sensitive to detect complex and subtle rearrangements, even in bone marrow preparations with suboptimal metaphases, and can provide valuable corroborative information.

FISH in genome research and molecular diagnostics

Fluorescence in situ hybridization (FISH) has profoundly altered the aspect of genome research and molecular diagnostics. Deletions of only a few kilobases can be detected by hybridizing probes to naked DNA fibers. Loss or gain of chromosomal material in tumor cells can be visualized using comparative genome hybridization. Further diversification of FISH application will result from new ultrasensitive detection techniques.

Identification of chromosomal structural alterations in human ovarian carcinoma cells using combined GTG-banding and repetitive fluorescence in situ hybridization (FISH)

In order to identify chromosomal structural alterations in the ovarian carcinoma cell line MLS/P, fluorescence in situ hybridization with centromeric probes for chromosomes 1, 8, 9, 13/21, 14/22, 15, 17, and X and whole chromosome painting probes for chromosomes 1, 3, 4, 5, 7, 8, 9, 10, 12, 13, 14, 17, 19, 22, and X were performed subsequent to GTG-banding. This combined approach identified 14 of the 18 clonal structurally rearranged chromosomes, with the X chromosome involved in three aberrations. In contrast, only eight of the 14 rearrangements were identifiable by G-banding alone. These results indicate that the combined G-banding and FISH approach can significantly improve the cytogenetic analysis of human neoplasia.

Demonstration of i(17q) in metaphase and interphase of malignant hematopoietic cells by fluorescence in situ hybridization

In 10 patients with various hematopoietic disorders, i(17q) has been studied by the technique of fluorescence in situ hybridization (FISH) both in metaphase and interphase cells using an alpha-satellite centromere-specific probe #17. We observed some minor quantitative differences between metaphase and interphase cells with regard to the incidence of i(17q) in individual cases and considerable heteromorphism of the size of signal of i(17q) among different cases. Our results suggest that formation of i(17q) results from a break in the p-arm proximal to the centromere and that the breakpoints vary from case to case.

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.

Clarification of subtle reciprocal rearrangements using fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) using chromosome-specific DNA libraries as painting probes was applied in the analysis of six subtle, balanced chromosome rearrangements. Both fresh and older slides, some of which had been previously G-banded, were used to determine if FISH could identify unambiguously very small amounts of translocated material. Our results indicate that this procedure can clearly and precisely distinguish the specific components of extremely subtle translocations, in different cell types, such as leukocytes, aminocytes, and chorionic villus, and irregardless of preparation age. This ability makes FISH a valuable tool in clinical cytogenetics for the confirmation of preliminary G-banded karyotypes.

Chromosome painting as a supplement to cytogenetic banding analysis in non-Hodgkin's lymphoma

Chromosomal in situ suppression (CISS) hybridization with biotin labeled chromosome-specific libraries was performed on short-term cultures from five cases of non-Hodgkin's lymphoma (NHL). The painting analysis proceeded in three stages. First-stage CISS hybridization was done with libraries specific for chromosomes that seemed to be lost or rearranged as judged by banding analysis. Second-stage CISS included hybridization with probes specific for chromosomes that, because of banding pattern similarities, were considered to be likely candidates to have contributed unidentified chromatin blocks in the abnormal karyotype. The third and final stage was a confirmation hybridization with a library specific for the chromosome that, at the stage two analysis, was found to have donated the previously unknown chromosomal segment. The aberrant chromosomes were often more complex than the banding analysis had led us to believe. Among the rearrangements whose nature was determined by CISS hybridization were two add(1)(p36) which, in both cases, were shown to be a der(1)t(1;2)(p36;q31). This study illustrates the potential use of chromosome painting in resolving karyotypic uncertainties in NHL, and it shows that new cytogenetic subgroups may emerge when classical banding analysis is supplemented with fluorescence in situ hybridization techniques.

Unusual distribution of chromosome 12 in a testicular germ-cell tumor cell line (833K) and its cisplatin-resistant derivative (64CP9)

The distribution of chromosome 12 in a cisplatin-sensitive testicular germ-cell tumor (TGCT) cell line (833K), and its cisplatin-resistant derivative (64CP9), was studied by fluorescent in situ hybridization (FISH) using DNA alpha satellite and whole chromosome painting probes for chromosome 12. Chromosomes 12 and i(12p) in these cell lines were readily identified. However, chromosome 12-derived chromatin was also observed in acrocentric- and nonacrocentric-derived chromosomes. Several of the chromosome 12 painted regions resembled satellites and were separated from the chromosome by nonstaining stalk-like regions. In each cell line, different chromosomes were involved. In the 833K TGCT cell line these were a der(8), a der(14) with a 12-labeled "satellite" on the q arm and a der(14) with a 12-labeled "satellite" on the p arm. In the 64CP9 TGCT cell line, these were a der(5), a der(17), and a der(8). The der(8) observed in 64CP9 was different from the der(8) seen in 833K. These derived chromosomes were characterized using sequential FISH, Wright staining, and silver staining for nucleolar organizing regions (AgNORs). The non-staining stalk-like regions were AgNOR positive, indicating "ectopic" NORs. Chromosome 22 distribution in these cell lines was also studied. FISH, using a chromosome 22-specific painting probe, identified a small metacentric marker and a der(12)t(12;22) in each cell line. It is not known whether the differences in distribution of chromosome 12-derived chromatin between the two cell lines are related to cisplatin resistance. Our study shows that the distribution of chromosome 12 in the two TGCT cell lines is much more extensive than could be identified in GTG-banded karyotypes. FISH allows characterization of unidentified chromatin and thus is a valuable adjunct to traditional cytogenetic techniques.

Method for sequential staining of GTL-banded metaphases with fluorescent-labeled chromosome-specific paint probes

We describe a method for use of fluorescent-labeled whole chromosome-specific paint probes on GTL-banded metaphases to utilize the combined potential of these techniques for defining chromosome abnormalities. The efficacy of this method was tested on 6 cases involving different chromosome abnormalities and various tissues, including blood, amniotic fluid, skin fibroblasts, and bone marrow.

Identification of some marker chromosomes in acute leukemias by fluorescence in situ hybridization

Four patients with acute leukemia are presented in whom conventional karyotypic analysis had revealed complex numerical and structural changes including unidentifiable (marker) chromosomes. It is demonstrated that the application of fluorescence in situ hybridization (FISH) may contribute to the identification of such anomalies.

Establishment and characterization of 7 ovarian carcinoma cell lines and one granulosa tumor cell line: growth features and cytogenetics

The characteristics of 7 newly established ovarian carcinoma cell lines and one granulosa tumor cell line obtained from tumor samples of 7 patients with varying histology of the primary tumor are reported. The cell lines were isolated from 5 serous carcinomas, a mucinous carcinoma, an endometrioid carcinoma and a granulosa cell tumor. All cell lines were passaged at least 25 times and showed stable growth rates. Colony-forming efficiency varied on plastic from 2 to 57% and in agar from 0.01 to 9.30%. The DNA index of the granulosa tumor cell line was diploid, while the ovarian carcinoma cell lines were all aneuploid. In 2 cell lines polyploidisation occurred during culturing. A thorough cytogenetic analysis of 7 cell lines revealed that the granulosa tumor cell line has only minor cytogenetic abnormalities (+5, 22q+). In contrast, the epithelial ovarian-cancer cell lines gave very complex karyotypes with numerous markers and structurally rearranged chromosomes. The chromosomes most often in excess were 15 and 20. Structural rearrangements of chromosomes 1, 3, 7 and 11 were prominent in all ovarian cell lines. In addition, we found changes in chromosomes X, 5, 8 and 13 that have rarely been described before.

Orthotopic transplantation of histologically intact clinical specimens of stomach cancer to nude mice: correlation of metastatic sites in mouse and individual patient donors

Fresh surgical specimens derived from 36 patients with advanced stomach cancer were orthotopically transplanted in nude mice using histologically intact tissue. Twenty of 36 patient tumors gave rise to locally growing tumors in the mice. All 20 patients whose stomach tumors resulted in local growth in the nude mice had clinical lymph-node involvement, whereas 8 of the other 16 patients whose tumors were rejected had lymph-node involvement. There was a statistical correlation (p < 0.01) between local tumor growth in nude mice and clinical lymph-node involvement. Of the 20 cases resulting in local growth in the nude mice, 5 had clinical liver metastases and all 5 cases resulted in liver metastases in the nude mice. Of the 20 cases, 6 had clinical peritoneal involvement of their tumor, and of these 5 resulted in peritoneal metastasis in the nude mice. There were statistical correlations (p < 0.01) for both liver metastases and peritoneal involvement between patients and mice. These results indicate that, after orthotopic transplantation of histologically intact stomach cancers from patients to nude mice, the subsequent metastatic behavior of the tumors in the mice closely correlated with the course of the tumors in the patients.

Identification of a whole-arm translocation by in situ hybridization with directly fluorochrome-labeled probes in a myelodysplastic syndrome

A case of myelodysplasia was found to have a complex bone marrow karyotype, involving an apparent whole-arm translocation between 17q and 18q. The application of a simplified fluorescence in situ hybridization technique, using directly fluorochrome-labeled centromere-specific alpha-satellite DNA probes, demonstrated the presence of sequences from both chromosomes 17 and 18 in the centromere of the derivative chromosome. This proves that a true whole-arm translocation had occurred. The case exemplifies how in situ hybridization analysis can be used to resolve interpretation problems in cancer cytogenetics.

Cytogenetic analysis of a United Kingdom series of non-Hodgkins lymphomas

We describe cytogenetic analyses of cells derived from 40 non-Hodgkins lymphoma (NHL) node biopsies, 23 of which were from patients who had not been treated before biopsy. We noted that the chromosomes most frequently gained were X (32%), 12 (27%), and 3 (24%). Monosomies were much less common; loss of chromosome 13 (13.5%) was most frequent. Structural abnormalities primarily involved chromosomes 14 (70%), 1 (40.5%), 18 (38%), 6 (35%), and 17 (22%). Low-and high-grade disease showed similar patterns of structural changes; however, a markedly greater number of chromosome gains were associated with low-grade disease. Biopsy samples from patients who had previously been treated showed an increased frequency of structural abnormalities, as well as a significantly larger number of chromosome gains. The importance of these observations, particularly with regard to possible oncogene involvement in lymphoma evolution, is discussed.

YAC mapping by FISH using Alu-PCR-generated probes

Human genomic mapping has been greatly advanced by the independent development of three new methods: large DNA fragment cloning in yeast artificial chromosomes, amplification from complex DNAs of human specific segments by Alu-PCR, and high-resolution localization of complex DNA probes by fluorescent in situ hybridization. We describe here the combination of these three analytical tools for efficient and accurate localization of randomly screened or especially selected human YAC recombinants to chromosome 11. We map a YAC clone encompassing the pepsinogen A (PGA) locus to 11q13.1-11q13.3.