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. Copyright © 1999 John Wiley & Sons, Ltd.     

Chromosome painting in plants

The current 'state-of-art' as to chromosome painting in plants is reviewed. We define different situations described as painting so far: i) Genomic in situ hybridisation (GISH) with total genomic DNA to distinguish alien chromosomes on the basis of divergent dispersed repeats, ii) 'Chromosomal in situ suppression' (CISS) hybridisation with chromosome-derived DNA probes and blocking of interchromosomally dispersed repeats by total genomic or C₀ t-1 DNA in excess, iii) exceptional cases of single chromosome painting by probes containing chromosome-specific dispersed repeats, and iv) Fluorescence in situ hybridisation (FISH) with extended contigs of large insert clones for painting of those chromosomes of a euploid complement which harbour the cloned sequences. While GISH was successfully applied in most plant hybrids and/or their derivatives, painting of individual chromosomes by CISS hybridisations of chromosome-specific DNA probes have so far not revealed convincing results in plants. The reason for this failure and the use of possible alternative approaches are discussed. At least for small plant genomes, painting by large insert single sequence clones provides a promising alternative tool to solve cytogenetic questions, which up to now could not be tackled otherwise. An example of such a painting is described in detail for Arabidopsis thaliana.     

High-resolution fluorescencein situ hybridization ofRBM- andTSPY-related cosmids on released Y chromatin in humans and pygmy chimpanzees

Applying two-colour fluorescencein situ hybridization (FISH) we simultaneously hybridizedRBM- andTSPY-related cosmids to Y chromosomes in prophase and to released Y chromatin in interphase nuclei of man and pygmy chimpanzee. Whereas, even on prophasic Y chromosomes, no resolution of the overlappingRBM andTSPY signal clusters could be achieved, theRBM andTSPY signals are completely separated from each other in our maximum released Y chromatin stretches in interphase nuclei. These results unequivocally lend support to the view that theRBM andTSPY families have an interspersed organization on the Y chromosomes of man and higher apes. Thus, the distribution ofRBM andTSPY signals might well go back to a common organization of these genes next to each other on an ancient Y chromosome.accepted for publication by M. Schmid     

Nature of B chromosomes in the harvest mouse Reithrodontomys megalotis by fluorescence in situ hybridization (FISH)

Using fluorescence in situ hybridization, we examined the characteristics of two types of B chromosomes in harvest mice of the genus Reithrodontomys. B chromosomes were interrogated with rDNA, telomeric repeat, LINE element and centromeric heterochromatin probes. The two types of B chromosomes share the following features: (a) telomeres present on the ends of both arms; (b) hybridization to LINE probes; (c) absence of hybridization to the ribosomal gene probes; (d) C-band-positive centromeric regions; and (e) euchromatic arms. They differ as follows: (a) the larger B element hybridizes to the centromeric heterochromatin (pMeg-1) probe whereas the smaller B element does not; (b) the amount of C-band-positive material is reduced in the smaller B chromosome relative to that present on the larger B chromosome; and (c) the smaller element is reduced in size by about a third. It is concluded that the larger B chromosome arose as a leftover centromere from centric fusion, whereas the smaller element has a different origin — perhaps as an intact fragment or as an amplified region from the A chromosomes. The presence of euchromatic regions on B chromosomes may account for their survival in the karyotype.This revised version was published online in November 2005 with corrections to the Cover Date.     

Preparation of chromosomes from plant leaf meristems for karyotype analysis and in situ hybridization

A reliable method for preparing metaphase chromosomes from plant leaf tissues is described. The chromosomes are suitable for karyotype analysis and gene mapping by fluorescence in situ hybridisation (FISH). The method is based on enzymatic digestion of young leaf tissues (shoot-tips) after which the resulting protoplasts are treated hypotonically before being dropped onto microscopic slides. Compared to root-tip chromosomes, leaf chromosomes tend to be longer, or less condensed, and hence more karyotypically differentiated. Metaphase index in young leaf tissues is also very high. Metaphase spread consists of evenly and well-distributed chromosomes and this allows accurate counting. The plant used to demonstrate this method is birch (Betula L.), a group of tree species that has extremely small chromosomes. Root-tip chromosomes of these plants are difficult to obtain, as cutting does not produce roots readily. Seedling chromosomes do not represent the same genomic constitution as their mother trees due to introgressive hybridisation. Furthermore, sample collection in the field is convenient and actively growing leaf buds are available throughout the growing season. FISH experiments with these leaf chromosomes also give good results comparable to those obtained with root-tip chromosomes or even better as mapping on long or extended chromosomes has high resolution in general. Mapping of the 16S–28S ribosomal genes on birch leaf chromosomes has been shown to differentiate between birch species and therefore can accurately confirm their interspecific hybrids.     

Rapid detection of euchromatin by Alu-PRINS: use in clinical cytogenetics

Alu-PRINS was successful in providing positive identification of euchromatin when oligoprimers were used at either extremity of the consensus Alu sequence. This technique was sensitive, as shown by the ability to detect small regions of euchromatin translocated to the short arm of an acrocentric chromosome. Since the Alu-PRINS technique is rapid and relatively simple, it will be useful in the diagnostic cytogenetics laboratory for the assessment of aberrant short arms of acrocentric satellites. This technique was also useful in defining the structure of small accessory marker chromosomes.This revised version was published online in November 2005 with corrections to the Cover Date.     

Fluorescent in situ hybridization in plant polytene chromosomes

Polytene chromosomes are found in specialized tissues, with high metabolic activity, of a few angiosperm genera. They differ from Diptera polytenics in several aspects, mainly because their chromatids on each chromosome are not tightly paired, nor are they so highly endoreplicated as those of Diptera. In situ hybridization with isotopic and non-isotopic probes has been successfully used in plant polytene chromosomes, mainly in Phaseolus coccineus and Vigna unguiculata, where they have been best investigated. The results reported for mitotic and polytene chromosomes of these species, and a few others, are compared aiming to ascertain the efficiency and limitations of FISH in plant polytenics. In general, polytene chromosomes either from embryo suspensor cells of P. coccineus or from anther tapetal cells of V. unguiculata proved to be quite a suitable system for localizing DNA sequences by FISH. The partially unsynapsed chromatids, typically found in plant polytenics, seem to be the most important hindrance for a precise chromosome mapping. On the other hand, the interphase polytene nucleus is a valuable system for localizing FISH signals since they conserve a spatial organization similar to that of mitotic interphase and produce much amplified signals.     

Comparison of ribosomal DNA sites inLolium species by fluorescencein situ hybridization

The position of the 18S-5.8S-26S and 5S rRNA genes have been physically mapped on the chromosomes of sevenLolium taxa. 18S-5.8S-26S sites were seen on two pairs of chromosomes in the inbreeding taxa. In the outbreeding taxa six sites were found in theL. multiflorum, seven inL. perenne and nine inL. rigidum var.rigidum. Two 5S sites were found in each of the taxa. In the inbreeders, the 5S sites were found adjacent to the 18S-5.8S-26S sites on chromosome 2. InL. multiflorum andL. perenne the 5S sites were on the short arm of chromosome 3. However, inL. rigidum var.rigidum the 5S rDNA site was found in either of the two positions.accepted by J.S. (Pat) Heslop-Harrison     

Detection of chromosomal abnormalities of chromosome 12 in uterine leiomyoma using fluorescencein situ hybridization

Summary Fifty uterine leiomyomas were examined using conventional cytogenetic method and fluorescencein situ hybridization (FISH) for detection of chromosomal, abnormalities of chromosome 12. Of the 50 tumors, nine were examined using FISH on the non-cultured samples. Two (4.0%) of 50 tumor samples examined showed chromosomal abnormalities of chromosome 12 by the conventional cytogenetic analysis. For FISH, the whole-chromosome painting probe and D12Z3 probe specific for the centromeric region were used. Of the 50 cultured samples, 10 showed structural aberrations and four showed numerical aberrations of chromosome 12 by FISH analysis. Of the nine non-cultured samples, four showed structural abnormalities of chromosome 12, all of which also showed structural abnormalities of chromosome 12 on the cultured samples. These results indicate that chromosomal abnormalities of chromosome 12 are important in the biology of at least some types of uterine leiomyoma, and that FISH is a useful complement to the conventional cytogenetic analysis in the study of solid tumors.     

Insulin-like growth factor I in human thyroid tissue: Specific localization by immunohistochemistry andIn Situ hybridization

Insulin-like growth factor I and II (IGF-I and IGF-II) have been implicated in the replication of normal thyroid follicular cells in vitro. This study evaluates the distribution and abundance of immunoreactive IGF-I by histochemical analysis in human thyroid tissue with different histopathologic characteristics. We used two types of highly specific and sensitive polyclonal rabbit anti-IGF-I antibodies and one monoclonal antibody (MAb) with the immunoperoxidase technique on sections of 25 glands harboring adenomatous goiter; 11 glands with follicular adenoma (FA); 45 glands with thyroid carcinoma of papillary, follicular, and undifferentiated types; and 18 glands with Graves' disease. Immunoreactive IGF-I was present in some thyroid follicular cells of all thyroid tissues examined. The percentage of cells staining positively varies among the different processes, being lowest in normal thyroid tissues and highest in all thyroid carcinomas. The cytoplasmic pattern of IGF-I immunoreactivity also varied among the different thyroid conditions. Furthermore, using nonradioactivein situ hybridization (ISH) we detected IGF-I mRNA in the thyroid cells of adenomatous goiter. The expression was higher in the histologically hyperplastic areas. These findings provide further support for an autocrine and/or paracrine role of IGF-I in the function and/or growth of normal thyroid follicular cells and suggest that IGF-I may play a role in the dysfunctional growth of thyroid follicular cells in adenomatous goiter, thyroid carcinoma, and Graves' hyperthyroidism.     

Construction of novel Brassica napus genotypes through chromosomal substitution and elimination using interploid species hybridization

A synthetic Brassica napus rapeseed with genome composition of A(r)A(r)C(c)C(c), made by combining A(r) from B. rapa (A(r)A(r)) and C(c) from B. carinata (B(c)B(c)C(c)C(c)), is valuable for making new genes available to breeders and gaining heterosis in crosses. An intergenomic hybrid A(n)A(r)C(n)C(c) was made from a hybrid between natural Brassica napus (A(n)A(n)C(n)C(n)) and a synthetic rapeseed. To construct the synthetic Brassica napus, hexaploid plants (2n=54, A(r)A(r)B(c)B(c)C(c)C(c)) were first obtained through chromosome doubling of trigenomic hybrids (2n=27, A(r)B(c)C(c)) between Brassica carinata (2n=34) and B. rapa (2n=20). Pentaploid hybrids (2n=46, A(r)A(n)B(c)C(c)C(n)) were then produced by crossing the hexaploid with the pollen of natural B. napus (2n=38). Chromosomes with dual and single B(c) genomes were observed in somatic cells of hexaploid and pentaploid plants. About 80% of pollen mother cells of pentaploid hybrids had 19 or more bivalents, indicating that the bivalents from A(r)/A(n) and C(c)/C(n) chromosomes were normally formed. The occurrence of trivalents and quadrivalents at diakinesis suggested that B(c), A(n) and A(r) or B(c), C(n) and C(c) homologous pairing and exchange might happen. The variable number of laggards, 3 and 4 in most cases, were observed in the majority of PMCs at anaphase. Results from genomic in situ hybridization showed that the laggards belonged mainly to the B(c) genome, suggesting that the B(c) genome could be eliminated in the gametes of pentaploid hybrids. 16.15% of seeds derived from self-pollinated pentaploids have 38 chromosomes, and 90% of 38-chromosome seeds were completely excluded B(c) genome. The cytological results of this experiment suggested that it is possible to obtain new materials with genome composition of A(r)A(r)C(c)C(c) for rapeseed breeding.     

Karyotyping mouse chromosomes by multiplex-FISH (M-FISH)

Karyotyping of mouse chromosomes is a skillful art, which is laborious work even for experienced cytogeneticists. With the growing number of mouse models for human diseases, there is an increasing demand for automated mouse karyotyping systems. Here, such a karyotyping system for mouse chromosomes based on the multiplex-fluorescence in-situ hybridization (M-FISH) technology is shown. The system was tested on a number of individual mice with numerical and structural aberrations and its reproducibility and robustness verified. Mouse M-FISH should be a valuable tool for the analysis of chromosomal rearrangements in mice.     

Comparative genomic in situ hybridization (cGISH) analysis on plant chromosomes revealed by labelled Arabidopsis DNA

A new approach for comparative cytogenetic banding analysis of plant chromosomes has been established. The comparative GISH (cGISH) technique is universally applicable to various complex genomes of Monocotyledonae (Triticumaestivum, Agropyronelongatum, Secalecereale, Hordeumvulgare, Alliumcepa, Muscariarmenaticum and Liliumlongiflorum) and Dicotyledonae (Viciafaba, Betavulgaris, Arabidopsisthaliana). Labelled total genomic DNA of A. thaliana generates signals at conserved chromosome regions. The nucleolus organizing regions (NORs) containing the majority of tandemly repeated rDNA sequences, N-band regions containing satellite DNA, conserved homologous sequences at telomeres and additional chromosome-characteristic markers were detected in heterologous FISH experiments. Multicolour FISH analysis with repetitive DNA probes simultaneously revealed the chromosome assignment of 56 cGISH signals in rye and 61 cGISH signals in barley. Further advantages of this technique are: (1) the fast and straightforward preparation of the probe; (2) the generation of signals with high intensity and reproducibility even without signal amplification; and (3) no requirement of species-specific sequences suitable for molecular karyotype analysis. Hybridization can be performed without competitive DNA. Signal detection without significant background is possible under low stringency conditions. The universal application of this fast and simple one-step fluorescence banding technique for plant cytogenetic and plant genome evolution is discussed.     

Chromosomal integrity maintained in five human embryonic stem cell lines after prolonged in vitro culture

There have been recent reports of human embryonic stem cell (hESC) lines developing chromosomal aberrations after long-term culture, indicating an unstable genomic status due to the in vitro milieu. This raises concern, since it would limit their use in therapeutics. In this study the chromosomal status of five well-characterized hESC lines, SA002, SA002.5, AS034.1.1, SA121 and SA461, was monitored during long-term in vitro culture. The criteria of defined hESCs were met by all of the five hESC lines (four diploid and one trisomic for chromosome 13). The genomes were screened for chromosomal aberrations and rearrangements using comparative genomic hybridization (CGH), interphase fluorescence in situ hybridization (FISH) and traditional karyotyping on several occasions while in culture. The genomic integrity was shown to be maintained after repeated freeze-thaw procedures and continuous culture in vitro for up to 22 months (148 passages). We discuss the most common de novo chromosomal aberrations reported in hESCs, as well as their possible origin.     

Towards unlimited colors for fluorescence in-situ hybridization (FISH)

We describe a FISH protocol that allows rehybridization of complex DNA probes up to four times to the same specimen. This strategy, which we termed ReFISH, opens a wide range of new applications to conventional band pass filter epifluorescence microscopy. These include M-FISH karyotyping and cross-species color banding that emulate multiplex probe sets labeled with up to 12 fluorochromes in sequential hybridizations to the same specimen. We designed a human 24-color karyotyping probe set in combination with a 29-color cross-species color banding probe set using gibbon painting probes. Applying the ReFISH principle, 53 painting probes on individual metaphases were discriminated. This allowed simultaneous screening for inter- and intrachromosomal rearrangements on normal human diploid cells, a HeLa derived cell line, and highly rearranged gibbon chromosomes. Furthermore, the present ReFISH experiments successfully combine 24-color FISH with laser scanning confocal microscopy to study the 3D organization of all 46 human chromosome territories in individual interphase cell nuclei.     

Genealogical relationships of southern Ontario polyploid unisexual salamanders (genus Ambystoma) inferred from intergenomic exchanges and major rDNA cytotypes

North American unisexual salamanders in the genus Ambystoma are common around the Great Lakes region of North America. They contain an almost identical mitochondrial genome across their distribution that is unlike that of any of the four species whose genomes may be included in their nuclei. Thus, sequence-based phylogenies of unisexual populations are confusing. We used chromosomal intergenomic exchanges and major rDNA cytotypes as combined cytogenetic markers to tentatively construct a genealogy of unisexual Ambystoma in southern Ontario. We employed GISH and sequential/simultaneous GISH/FISH-rDNA to reveal intergenomic exchanges and rDNA cytotypes in unisexual A. laterale – 2 jeffersonianum (LJJ) triploids and their tetraploid derivative A. laterale – 3 jeffersonianum (LJJJ). We identified 10 different patterns of intergenomic exchanges from 18 isolated populations and used them as primary cytogenetic markers. Major rDNA cytotypes served as independent and supplementary markers. Our results suggest that current LJJ and LJJJ populations in southern Ontario are likely derived from a few unisexual individuals. Intergenomic exchanges are common phenomena and widely distributed in the salamanders of the A. laterale – A. jeffersonianum unisexual complex. Integration of GISH and FISH can exhibit multiple unrelated chromosomal markers on the same chromosome spread and demonstrate lineage relationships in unisexual populations. Similar methods may be applied for studying the molecular cytogenetics of other unisexuals to improve our understanding of their genealogical relationships and historical dispersal.     

Chromosome pairing in allotetraploid hybrids of <Emphasis Type="Italic">Festuca pratensis</Emphasis> × <Emphasis Type="Italic">Lolium perenne</Emphasis> revealed by genomic <Emphasis Type="Italic">in situ</Emphasis> hybridization (GISH)

Genomic in situ hybridization (GISH) was used to make a detailed study of chromosome pairing at metaphase I (MI) of meiosis in six F(1) hybrid plants of the allotetraploid Festuca pratensis x Lolium perenne (2n = 4x = 28; genomic constitution FpFpLpLp). The mean chromosome configurations for all hybrids analysed were 1.13 univalents + 11.51 bivalents + 0.32 trivalents + 0.72 quadrivalents, and the mean chiasma frequency was 21.96 per cell. GISH showed that pairing was predominantly intragenomic, with mean numbers of L. perenne (Lp/Lp) and F. pratensis (Fp/Fp) bivalents being virtually equal at 5.41 and 5.48 per cell, respectively. Intergenomic pairing between Lolium and Festuca chromosomes was observed in 33.3% of Lp/Fp bivalents (0.62 per cell), in 79.7% of trivalents - Lp/Lp/Fp and Lp/Fp/Fp (0.25 per cell), and in 98.4% of quadrivalents - Lp/Lp/Fp/Fp and Lp/Lp/Lp/Fp (0.71 per cell). About 4.0% of the total chromosome complement analysed remained as univalents, an average 0.68 Lp and 0.45 Fp univalents per cell. It is evident that in these hybrids there is opportunity for recombination to take place between the two component genomes, albeit at a low level, and this is discussed in the context of compromising the stability of Festulolium hybrid cultivars and accounting for the drift in the balance of the genomes over generations. We speculate that genotypic differences between hybrids could permit selection for pairing control, and that preferences for homologous versus homoeologous centromeres in their spindle attachments and movement to the poles at anaphase I could form the basis of a mechanism underlying genome drift.