Hidden chromosome abnormalities in a primary central nervous system lymphoma detected by multicolor spectral karyotyping

Advanced molecular cytogenetics in human and mouse

Fluorescence in situ hybridization, spectral karyotyping, multiplex fluorescence in situ hybridization, comparative genomic hybridization, and more recently array comparative genomic hybridization, represent advancements in the field of molecular cytogenetics. The application of these techniques for the analysis of specimens from humans, or mouse models of human diseases, enables one to reliably identify and characterize complex chromosomal rearrangements resulting in alterations of the genome. As each of these techniques has advantages and limitations, a comprehensive analysis of cytogenetic aberrations can be accomplished through the utilization of a combination approach. As such, analyses of specific tumor types have proven invaluable in the identification of new tumor-specific chromosomal aberrations and imbalances (aneuploidy), as well as regions containing tumor-specific gene targets. Application of these techniques has already improved the classification of tumors into distinct categories, with the hope that this will lead to more tailored treatment strategies. These techniques, in particular the application of tumor-specific fluorescence in situ hybridization probes to interphase nuclei, are also powerful tools for the early identification of premalignant lesions.

Karyotypic evolution pathways in medulloblastoma/primitive neuroectodermal tumor determined with a combination of spectral karyotyping, G-banding, and fluorescence in situ hybridization

Medulloblastomas (MBs) or primitive neuroectodermal tumors (PNETs) represent 15%-30% of pediatric brain tumors and are the most common brain tumors in children; they are rare in adults. Classification of these tumors is based on tissue morphology and is often controversial and problematic. Karyotypic analysis of these tumors using conventional cytogenetic methods is often a difficult process that may be hindered by a limited number of metaphase cells and poor chromosome morphology, often leading to only partial characterization of the chromosomal abnormalities. We investigated three primary human tumors and four cell lines (CHO-707, DAOY, D-341, and PFSK) utilizing a combination of conventional G-banding, spectral karyotyping (SKY), and fluorescence in situ hybridization (FISH) techniques. A high level of intratumoral heterogeneity was seen, with multiple numerical and structural chromosomal aberrations. The chromosomes most frequently involved in structural aberrations were chromosomes 1 (14 rearrangements), 7 (9 rearrangements), and 21 (9 rearrangements). The chromosomes most frequently involved in numerical aberrations were chromosomes 1, 12, and 13 (four cases) and chromosomes 14, 17, 19, 21, 22, and X (three cases). Numerous aberrant chromosomes were characterized only with the SKY analysis, and based on these findings multiple clones were identified, facilitating analysis of karyotypic evolution. The most frequent evolution mechanism was via polyploidization, followed by acquisition of additional numerical or structural aberrations (or both); however, the results showed that the karyotypic evolution process in these tumors is typically divergent and complex.

Genomic imbalances in CML blast crisis: 8q24.12-q24.13 segment identified as a common region of over-representation

The acute phase of chronic myeloid leukemia (CML) is accompanied by secondary chromosomal changes. The additional changes have a non-random pattern; however, highly abnormal (marker) chromosomes are reported in some 20% of abnormal karyotypes. These marker chromosomes have proved to be beyond the resolution of conventional G-banding analysis. We used molecular cytogenetic techniques to determine the structure of complex chromosome markers in 10 CML-derived cell lines after our investigations of CML patients in blast crisis. Multicolor fluorescence in situ hybridization identified a multitude of structural chromosome aberrations. In addition, genomic gains identified by comparative genomic hybridization (CGH) were mapped to highly complex marker chromosomes in more than one cell line. The most common genomic loss detected by CGH affected chromosome 9, whereas the most common genomic gains affected, in order of frequency, the sequences of 8q, 6, and 13q. The smallest discrete amplification on 8q was identified in cell line MEG-01. This amplicon contains sequences represented by the marker D8S263/RMC08P029 but did not contain the proximal MYC gene or a more distal marker, D8S256/RMC08P025. We determined the size of the amplicon to be less than the chromosome segment 8q24.12-q24.13. The use of region- and locus-specific probes to analyze the organization of highly complex marker structures aided the identification of preferentially amplified genomic regions. The resultant amplifications could harbor gene(s) driving disease progression.

Characterization of chromosomal aberrations in a case of glioblastoma multiforme combining cytogenetic and molecular cytogenetic techniques

A case of glioblastoma multiforme (GBM) that was investigated with a broad spectrum of cytogenetic and molecular cytogenetic techniques is reported. The results of cytogenetic studies, interphase fluorescence in situ hybridization, comparative genomic hybridization, and spectral karyotyping (SKY) are reported. Various structural chromosomal aberrations were identified, among which aberrations involving chromosome arm 2p were especially frequent. Using SKY, six translocations not previously described in GBM are reported.

SKY detection of chromosome rearrangements in two cases of tMDS with a complex karyotype

In this study, we used spectral karyotyping (SKY) and fluorescence in situ hybridization (FISH) as complementary techniques for the analysis of two therapy-related secondary myelodysplastic syndrome (t-MDS) cases with complex karyotypes, previously analyzed by G-banding. Different types of SKY's cytogenetic contributions include confirmation of G-banding results, identification of partially characterized rearrangements, identification of marker chromosomes unidentified by G-banding, and detection of cryptic reciprocal translocations. In particular, the ability of SKY to clarify a number of markers led to the comprehension of clonal evolution. The common aberration found in these two t-MDS cases was the fragility of chromosome 5 and monosomy of chromosome 18. We clearly present that the use of SKY combined with conventional G-banding analysis and FISH has assisted in the identification of important chromosomal events that may play a key role in the development of t-MDS.

Interphase cytogenetic analysis of lymphoma-associated chromosomal breakpoints in primary diffuse large B-cell lymphomas of the central nervous system

Primary central nervous system lymphomas (PCNSLs) are germinal center-derived diffuse large B-cell lymphomas (DLBCLs) arising in and remaining confined to the brain, the pathogenesis of which is poorly understood. We investigated 13 PCNSLs from immunocompetent patients by means of interphase cytogenetics on cryopreserved cells derived from stereotactic biopsies. Interphase fluorescence in situ hybridization (FISH) was performed for the detection of structural alterations affecting the IGH (14q32), IGK (2p12), IGL (22q11), BCL6 (3q27), MYC (8q24), CCND1 (11q13), MLT, and BCL2 (both 18q21) loci. Signal constellations indicating breakpoints within the IGH and IGK locus were detected in 5 and 1 PCNSLs, respectively. There was no evidence for a t(8;14), t(11;14), or t(14;18) in this series of tumors. Breakpoints in the BCL6 locus were observed in 3 of the 13 cases, and nuclear Bcl-6 protein expression was detected in 6 of 9 PCNSLs, including those with genomic alterations of the encoding locus. Gains of 18q21 represented the most frequent imbalances present in more than one third of all cases. Interestingly, these gains included the MLT gene. Thus, this study provides the first evidence for recurrent chromosomal translocations in PCNSLs. While they share similarities with extracerebral DLBCL with respect to the presence of IGH translocations, they appear to differ in the usage of translocation partner genes, which remain to be identified.

Karyotypic similarity identified by multiplex-FISH relates four prostate adenocarcinoma cell lines: PC-3, PPC-1, ALVA-31, and ALVA-41

Recently developed molecular cytogenetic techniques for karyotyping are providing new and important insights regarding the chromosomal changes that occur in solid tumors. We used multiplex-FISH to analyze four adenocarcinoma cell lines, PC-3, PPC-1, ALVA-31, and ALVA-41, in which the characterization of a large number of rearranged chromosomes was partially or substantially inconclusive by G-banding. Although the original descriptions of these lines depict them as distinct entities established from different patients, this study demonstrates that these four lines share numerous, highly rearranged chromosomes, strongly supporting the conclusion that they are derived from the same patient material. Our analysis indicates that PPC-1, ALVA-31, and ALVA-41 were derived from PC-3 through mechanisms involving clonal progression represented by sequential changes and clonal diversion represented by differing patterns of changes. Extensive cellular heterogeneity was detected in all four lines, and most rearrangements included segments derived from multiple chromosomes. Each line also showed a set of unique derivative chromosomes. However, a limited number of metaphase cells (approximately 10) was analyzed for each line, and numerous single-cell abnormalities were detected in all of them. Therefore, it is plausible that the number of clonal, shared, and/or unique rearrangements has been underestimated. These cell lines have been utilized as models for understanding the biology of prostate cancer and reportedly differ in their cell physiology. Rather than detracting from their value, a complete understanding of the interrelationships of these lines to one another may provide the opportunity to define the molecular changes that have led to their individual malignant phenotypes.

Detection of unidentified chromosome abnormalities in human neuroblastoma by spectral karyotyping (SKY)

Spectral karyotyping (SKY) is a novel technique based on the simultaneous hybridization of 24 fluorescently labeled chromosome painting probes. It provides a valuable addition to the investigation of many tumors that can be difficult to define by conventional banding techniques. One such tumor is neuroblastoma, which is often characterized by poor chromosome morphology and complex karyotypes. Ten primary neuroblastoma tumor samples initially analyzed by G-banding were analyzed by SKY. In 8/10 tumors, we were able to obtain additional cytogenetic information. This included the identification of complex rearrangements and material of previously unknown origin. Structurally rearranged chromosomes can be identified even in highly condensed metaphase chromosomes. Following the SKY results, the G-banding findings were reevaluated, and the combination of the two techniques resulted in a more accurate karyotype. This combination allows identification not only of material gained and lost, but also of breakpoints and chromosomal associations. The use of SKY is therefore a powerful tool in the genetic characterization of neuroblastoma and can contribute to a better understanding of the molecular events associated with this tumor.

Analysis of secondary chromosomal alterations in 165 cases of follicular lymphoma with t(14;18)

Follicular lymphoma is characterized by the t(14;18) in up to 85% of cases. Almost all cases display evidence of secondary chromosomal alterations at initial diagnosis. The influence of recurrent secondary changes on disease progression has not been fully determined. The purpose of this study was to define the full spectrum of recurrent karyotypic events present at diagnosis in a large cohort of cases and to evaluate the sequence of cytogenetic evolution in relation to morphologic progression. A total of 165 cases of follicular lymphoma with t(14;18) were ascertained for which complete clinical information, histopathology, immunophenotype, and karyotype were available. One hundred sixty cases showed secondary alterations with an average of 7.9 additional changes per case. Recurrent alterations seen at the 10% or greater level included +X, +1q21-q44, +7, +12q, +18q, del(1)(p36), del(6q), del(10)(q22-q24), the development of polyploidy and sidelines, and the presence of extra marker chromosomes and chromosomal additions. Changes that correlated with morphologic progression included del(1)(p36), del(6q), del(10)(q22-q24), +7, the total number of abnormalities, the number of markers and additions, and the presence of polyploidy. The most frequent second event arising after the t(14;18) was duplication of the der(18)t(14;18). This study demonstrates that the number and type of secondary chromosomal alterations in follicular lymphoma is highly variable between cases, but that a relatively small number of changes are seen repeatedly in different combinations. A consistent pattern of cytogenetic evolution could not be identified. Potentially significant gene duplications or amplifications may be disguised within marker chromosomes and additions. Additional cytogenetic investigation is required to decipher the karyotypic complexity associated with the progression of follicular lymphoma.

Spectral karyotyping and multicolor fluorescence in situ hybridization reveal new tumor-specific chromosomal aberrations

Spectral karyotyping (SKY), multiple fluorescence in situ hybridization (M-FISH), cross-species color banding (Rx-FISH), multicolor chromosome banding, and other labeling techniques and strategies have been recent comprehensive technical developments in the field of molecular cytogenetics. The immediate goals of these methods are (1) to reliably characterize complex chromosomal rearrangements present in tumor karyotypes; (2) to screen for new tumor-specific chromosomal aberrations; (3) to improve genetic classification systems of different tumor types in correlation with clinical data, treatment regimens, detection of minimal residual disease, and prognosis; and (4) to identify new target regions for gene identification strategies. We present a brief overview of the different methods, including summaries of numerous published and submitted papers detailing specific cytogenetic aberrations associated with leukemias and lymphomas. To date, 640 tumor cases have been analyzed by SKY, including 410 hematologic malignancies, 146 solid tumors, and 45 mouse tumors.

Sensitivity of multiple color spectral karyotyping in detecting small interchromosomal rearrangements

Multiple color spectral karyotyping (SKY) has been proven to be a very useful tool for characterization of the complex rearrangements in cancer cells and the de novo constitutional structural abnormalities. The sensitivity of SKY in detecting interchromosomal alterations was assessed with 10 constitutional translocations involving subtelomeric regions. Among the 13 small segments tested, 9 were clearly visualized and 8 were unambiguously identified by SKY. Fluorescence in situ hybridizations (FISH) with subtelomeric probes confirmed the reciprocity in three of the four translocations in which a small segment was not detectable by SKY. On the basis of resolution level of G-banding and the information obtained from the FISH analysis, the minimum alteration that SKY can detect is estimated to be 1,000-2,000 kbp in size with the currently available probes. This study has demonstrated the power, but also the limitations, of SKY in detecting small interchromosomal alterations, particularly those in subtelomeric regions.

Cytogenetics of the chronic myeloid leukemia-derived cell line K562: karyotype clarification by multicolor fluorescence in situ hybridization, comparative genomic hybridization, and locus-specific fluorescence in situ hybridization

The transformation of chronic myeloid leukemia (CML) from a chronic phase to an acute phase is frequently accompanied by additional chromosome changes. Extensive chromosome G-banded studies have revealed the secondary changes are nonrandom and frequently include trisomy 8, isochromosome 17q, trisomy 19, or an extra copy of the Philadelphia chromosome. In addition to these secondary chromosome changes, complex structural rearrangements often occur to form marker structures that remain unidentified by conventional G-banded analysis. The CML-derived cell line, K562, has been widely used in research since it was originally established in 1975. The K562 karyotype however, has remained incomplete, and marker structures have never been fully described. Recent advances in fluorescence in situ hybridization (FISH) technology have introduced the possibility of chromosome classification based on 24-color chromosome painting (M-FISH). In this study, we report a clarified karyotype for K562 obtained by a combination of the following molecular cytogenetic techniques: comparative genomic hybridization (CGH), FISH mapping using locus-specific probes, and M-FISH. Multicolor FISH has identified the marker structures in this cell line. The characteristic marker chromosome in K562 has been confirmed by this study to be a der(18)t(1;18). Multicolor FISH confirmed the identity of marker structures partially identified by G-banding as der(6)t(6;6),der(17)t(9;17),der(21)t(1;21),der(5)t(5;6). In addition M-FISH has revealed a deleted 20q and a complex small metacentric marker comprised of material from chromosomes 1, 6, and 20. A cryptic rearrangement was revealed between chromosomes 12 and 21 that produced a structure that looks like a normal chromosome 12 homologue by G-banding analysis. Finally, M-FISH detected regions from chromosome 13 intercalated into two acrocentric markers.

Cytogenetics and cancer

Techniques based on fluorescence in situ hybridization (FISH) have bridged the gap between molecular genetics and conventional cytogenetics. Since its introduction in the late 1980s, advanced FISH-based methods have greatly enhanced the cytogenetic analysis of hematopoietic and solid tumors and are rapidly gaining ground in clinical cytogenetic diagnostics. As interest in FISH technologies has grown, it has inspired an era of new FISH-based technologies such as multiplex FISH, spectral karyotyping, and comparative genomic hybridization. In this review, the focus is on the impact of these technologies in the field of cancer genetics.