Multiple colors by fluorescence in situ hybridization using ratio-labelled DNA probes create a molecular karyotype

History and evolution of cytogenetic techniques: Current and future applications in basic and clinical research

Chromosomes are the vehicles of genes, which are the functional units of a cell's nucleus. In humans, there are more than 20,000 genes that are distributed among 46 chromosomes in somatic cells. The study of chromosome structure and function is known as cytogenetics which is historically a field of hybrid science encompassing cytology and genetics. The field of cytogenetics has undergone rapid developments over the last several decades from classical Giemsa staining of chromosomes to 3-dimensional spatial organization of chromosomes with a high resolution mapping of gene structure at the nucleotide level. Improved molecular cytogenetic techniques have opened up exciting possibilities for understanding the chromosomal/molecular basis of various human diseases including cancer and tissue degeneration. This review summaries the history and evolution of various cytogenetic techniques and their current and future applications in diverse areas of basic research and medical diagnostics.

Development of Species-specific rDNA Probes for Giardia by Multiple Fluorescent In Situ Hybridization Combined with Immunocytochemical Identification of Cyst Wall Antigens

In this study, we describe the development of fluorescent oligonucleotide probes to variable regions in the small subunit of 16S rRNA in three distinct Giardia species. Sense and antisense probes (17–22 mer) to variable regions 1, 3, and 8 were labeled with digoxygenin or selected fluorochomes (FluorX, Cy3, or Cy5). Optimal results were obtained with fluorochome-labeled oligonucleotides for detection of rRNA in Giardia cysts. Specificity of fluorescent in situ hybridization (FISH) was shown using RNase digestion and high stringency to diminish the hybridization signal, and oligonucleotide probes for rRNA in Giardia lamblia, Giardia muris, and Giardia ardeae were shown to specifically stain rRNA only within cysts or trophozoites of those species. The fluorescent oligonucleotide specific for rRNA in human isolates of Giardia was positive for ten different strains. A method for simultaneous FISH detection of cysts using fluorescent antibody (genotype marker) and two oligonucleotide probes (species marker) permitted visualization of G. lamblia and G. muris cysts in the same preparation. Testing of an environmental water sample revealed the presence of FISH-positive G. lamblia cysts with a specific rDNA probe for rRNA, while negative cysts were presumed to be of animal or bird origin.

Pseudoisodicentric Xp chromosome [46,X,psu idic(X)(q21.1)] and its effect on growth and pubertal development

BACKGROUND

Most isodicentric (Xp) and (Xq) chromosomes occur as a mosaic with a 45,X cell line. Patients with a nonmosaic 46,X,idic(Xq) are rare.

CASES

The first girl was referred at 13 years with a short stature and pubertal delay (M1, P2, A1). Her height was 141.6 cm (-3.1 SDS). Ovarian failure was present. The second girl was referred because of her short stature at 12.5 years. Her height was 142.2 cm (-2.4 SDS). She had spontaneous puberty (M3, P1, A1).

RESULTS

In both girls, conventional karyotyping of lymphocytes revealed an aberrant X chromosome consisting of twice the short arm and a small part of the long arm of the X chromosome [nonmosaic 46,X,psu idic(X)(q21.1)]. FISH analysis of the aberrant X chromosome showed the presence of two centromeres, two copies of the XIST gene and two copies of the SHOX gene.

CONCLUSIONS

The presence of two XIST genes on the isodicentric X chromosome with Xq deletion indicates the inactivation of this chromosome. This inactivation also concerned the pseudoautosomal regions which caused haploinsufficiency of the SHOX genes. The girls were treated with growth hormones. The critical region (Xq23 to Xq28) for the ovarian function was deleted in both patients, but the gonadal function was variable. .

Fluorescence in situ hybridization for cancer-related studies

Cytogenetic analysis of tumour material has been greatly enhanced over the past 30 years by the application of a range of techniques based around fluorescence in situ hybridization (FISH). Fluorescence detection for in situ hybridization has the advantage of including the use of a multitude of fluorochromes to allow simultaneous specific detection of multiple probes by virtue of their differential labelling and emission spectra. FISH can be used to detect structural (translocation/inversion) and numerical (deletion/gain) genetic aberrations. This chapter will deal with FISH methods to detect and localize one or more complementary nucleic acid sequences (probes) within a range of different cellular targets including metaphase chromosomes, nuclei from cell suspension, and formalin-fixed paraffin-embedded FFPE tissue sections. Methods for the efficient localization of probes to FFPE tissue cores in tissue microarrays (TMAs) are also described.

'Chromosomal Rainbows' Detect Oncogenic Rearrangements of Signaling Molecules in Thyroid Tumors

Altered signal transduction can be considered a hallmark of many solid tumors. In thyroid cancers the receptor tyrosine kinase (rtk) genes NTRK1 (Online Mendelian Inheritance in Man = OMIM *191315, also known as 'TRKA'), RET ('Rearranged during Transfection protooncogene', OMIM *164761) and MET (OMIM *164860) have been reported as activated, rearranged or overexpressed. In many cases, a combination of cytogenetic and molecular techniques allows elucidation of cellular changes that initiate tumor development and progression. While the mechanisms leading to overexpression of the rtk MET gene remain largely unknown, a variety of chromosomal rearrangements of the RET or NTKR1 gene could be demonstrated in thyroid cancer. Abnormal expressions in these tumors seem to follow a similar pattern: the rearrangement translocates the 3'- end of the rtk gene including the entire catalytic domain to an expressed gene leading to a chimeric RNA and protein with kinase activity. Our research was prompted by an increasing number of reports describing translocations involving ret and previously unknown translocation partners.We developed a high resolution technique based on fluorescence in situ hybridization (FISH) to allow rapid screening for cytogenetic rearrangements which complements conventional chromosome banding analysis. Our technique applies simultaneous hybridization of numerous probes labeled with different reporter molecules which are distributed along the target chromosome allowing the detection of cytogenetic changes at near megabasepair (Mbp) resolution. Here, we report our results using a probe set specific for human chromosome 10, which is altered in a significant portion of human thyroid cancers (TC's). While rendering accurate information about the cytogenetic location of rearranged elements, our multi-locus, multi-color analysis was developed primarily to overcome limitations of whole chromosome painting (WCP) and chromosome banding techniques for fine mapping of breakpoints in papillary thyroid cancer (PTC).

Probe labeling and fluorescence in situ hybridization

This unit describes in detail basic protocols for probe labeling, denaturing of in situ target DNA, in situ hybridization, and post-hybridization washes. Support protocols for probe labeling cover probe purification and quality control.

Digital fluorescence microscopy

Fluorescence microscopy is a valuable tool for biomedical research, providing good sensitivity and high multiplicity. Specialized techniques (anisotropy measurement, resonance energy transfer) can provide information on cell spatial arrangement or label microenvironment. The unit discusses camera selection strategy, microscope hardware, and image acquisition and processing.

COmbined Binary RAtio fluorescence in situ hybridiziation (COBRA-FISH): development and applications

The ability to probe for the location of DNA sequences in morphologically preserved chromosomes and nuclei by fluorescence in situ hybridization (FISH) provided for cytogenetics a quantum leap forward in resolution and ease of detection of chromosomal aberrations. COBRA-FISH, an acronym for COmbined Binary RAtio-FISH is a multicolor FISH methodology, which enables recognition of all human chromosome arms on the basis of color, thus greatly facilitating cytogenetic analysis. It also permits gene and viral integration site mapping in the context of chromosome arm painting. Here we review the principle, practice and applications of COBRA-FISH.

Multiplex-FISH (M-FISH): technique, developments and applications

Multiplex FISH (M-FISH) represents one of the most significant developments in molecular cytogenetics of the past decade. Originally designed to generate 24 colour karyotyping, the technique has spawned many variations and an equally diverse range of applications. In tumour and leukaemia cytogenetics, the two groups that have been targeted represent both ends of the cytogenetic spectrum: those with an apparently normal karyotype (suspected of harbouring small rearrangements not detectable by conventional cytogenetics) and those with a complex aberrant karyotype (which are difficult to karyotype accurately due to the sheer number of aberrations). In research, mouse M-FISH provides a powerful tool to characterize mouse models of a disease. In addition, the ability to accurately karyotype single metaphases without selection makes M-FISH the perfect tool in chromosome breakage studies and for characterizing clonal evolution of tumours. Finally, M-FISH has emerged as the perfect partner for the developing genomic microarray (array CGH) technologies, providing a powerful approach to gene discovery.

Preimplantation genetic diagnosis of numerical abnormalities for 13 chromosomes

Several types of FISH protocols for PGD have been used to maximize results from a limited number of fluorochomes to study as many chromosomes as possible. The major purpose of the present study was to optimize the use of three sequential hybridizations to analyse up to 15 chromosome types in single cells. A secondary purpose was to study the frequency of aneuploidy of other chromosomes not yet extensively studied in preimplantation embryos. Patients underwent PGD of aneuploidy, and the biopsied cells were analysed with three sequential hybridizations, the first for chromosomes 13, 16, 18, 21 and 22, the second for X, Y, 15 and 17 and the third for 2, 3, 4 and 11. Overall, only 27% of embryos were normal. The chromosomes most involved in aneuploidy were, in order, chromosome 16, 15, 21, 22, 13, 18, 17, 3, 2, 4, 11, and gonosomes. Of the abnormal embryos, only 3% would have been missed without the third set of probes. This protocol allows the simultaneous analysis of up to 15 chromosomes although only 13 were analysed in this study. Results so far show that the chromosomes most involved in abnormalities are those already covered with the two first sets of probes.

A 10-Mb paracentric inversion of chromosome arm 2p inactivates MSH2 and is responsible for hereditary nonpolyposis colorectal cancer in a North-American kindred

Genomic deletions of the MSH2 gene are a frequent cause of hereditary nonpolyposis colorectal cancer (HNPCC), a common hereditary predisposition to the development of tumors in several organs including the gastrointestinal and urinary tracts and endometrium. The mutation spectrum at the MSH2 gene is extremely heterogeneous because it includes nonsense and missense point mutations, small insertions and deletions leading to frameshifts, and larger genomic deletions, the latter representing approximately 25% of the total mutation burden. Here, we report the identification and molecular characterization of the first paracentric inversion of the MSH2 locus known to cause HNPCC. Southern blot analysis and inverse PCR showed that the centromeric and telomeric breakpoints of the paracentric inversion map within intron 7 and to a contig 10 Mb 3' of MSH2, respectively. Pathogenicity of the paracentric inversion was demonstrated by conversion analysis. The patient's lymphocytes were employed to generate somatic cell hybrids to analyze the expression of the inverted MSH2 allele in an Msh2-deficient rodent cellular background. The inversion was shown to abolish MSH2 expression by both northern and western analysis. This study confirms that Southern blot analysis still represents a useful and informative tool to screen for and identify complex genomic rearrangements in HNPCC. Moreover, monoallelic expression analysis represents an attractive approach to demonstrate pathogenicity of unusual mutations in autosomal dominant hereditary conditions.

Molecular cytogenetics

Refinements in cytogenetic techniques over the past 30 years have allowed the increasingly sensitive detection of chromosome abnormalities in haematological malignancies. In particular, the advent of fluorescence in situ hybridization techniques has provided significant advances in both diagnosis and research of leukaemias. The application of new multicolour karyotyping techniques has allowed the complete dissection of complex chromosome rearrangements and provides the prospect of identifying new recurrent chromosome rearrangements. Both comparative genomic hybridization and interphase fluorescence in situ hybridization avoid the use of metaphase chromosomes altogether and have allowed the genetic analysis of previously intractable targets. Recent developments in comparative genomic hybridization to DNA microarrays provide the promise of high resolution and automated screening for chromosomal imbalances. Rather than replacing conventional cytogenetics, however, these techniques have extended the range of cytogenetic analyses when applied in a complementary fashion.

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.

Simultaneous molecular karyotyping and mapping of viral DNA integration sites by 25-color COBRA-FISH

Combined binary ratio labeling (COBRA) fluorescence in situ hybridization (FISH) allows 24-color FISH karyotyping of human metaphase chromosomes utilizing only four fluorochromes, instead of the five required for combinatorial labeling procedures. Here we show that by introduction of a fifth fluorochrome, COBRA-FISH permits molecular cytogenetic mapping of viral integration sites in complex karyotypes in the context of a 24-color hybridization. We were able to detect a single copy of the human papillomavirus 16 in the SiHa cell line and to confirm the site of integration at 13q21-31. We also demonstrate the gene mapping possibility of 25-color hybridization by detecting a MYC cosmid on normal metaphase chromosomes. The possibility of mapping single-copy probes in the background of 24-color hybridization expands the tools for cytogenetic mapping of DNA sequences and will contribute to the understanding of the role of viral integration and chromosome rearrangement in virus-mediated carcinogenesis.

Multiplex fluorescence in situ hybridization and cross species color banding of a case of chronic myeloid leukemia in blastic crisis with a complex Philadelphia translocation

Exciting new techniques in molecular cytogenetics--namely, spectral karyotyping, multiplex fluorescence in situ hybridization (M-FISH), and cross species color banding--have been recently developed. An increasing number of reports demonstrate the success of these procedures in providing additional cytogenetic information--identifying marker chromosomes and revealing the presence of previously undetected chromosomal changes. However, these procedures have their limitations, and their absolute sensitivity in the accurate identification of subtle chromosomal abnormalities remains to be established. M-FISH and color banding have been applied to a case of chronic myeloid leukemia with a complex Philadelphia translocation involving chromosomes 9, 17, and 22, which had initially been identified from G-banded chromosome analysis. The abnormalities were confirmed by chromosome "painting" and specific probes. Although M-FISH and color banding revealed no additional cryptic chromosomal changes, this study has clearly demonstrated the success of these multiple color FISH approaches in the accurate characterization of a complex rearrangement with subtle abnormalities.

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.

Multipaint FISH: a rapid and reliable way to define cryptic and complex abnormalities

We present the use of a multipaint fluorescence in situ hybridisation (FISH) approach for the detection and interpretation of chromosome abnormalities that could not be resolved by conventional cytogenetics alone. In case 1, a de novo add(Xp) was shown to be an unbalanced X;12 translocation; in case 2, a complex rearrangement involving a deletion of 5p was shown to include a previously undetected cryptic 5;6 translocation. In addition, in case 3, this technique defined additional complexities and nine breakpoints in an acquired rearrangement of chromosomes 2, 9, 11, 16 and 22 in a patient with myelodysplasia. The technique allows the simultaneous identification of up to 24 chromosomes on a single slide using FISH with directly labelled whole chromosome paints. This simple and rapid method does not require image enhancement, produces results within 48 h and, therefore, offers an alternative to other recent developments, such as combinatorial multifluor FISH, spectral karyotyping or comparative genomic hybridisation.

Signal to noise analysis of multiple color fluorescence imaging microscopy

BACKGROUND

Various approaches that were recently developed demonstrate the ability to simultaneously detect all human (or other species) chromosomes by using combinatorial labeling and fluorescence in situ hybridization (FISH). With the growing interest in this field, it is important to develop tools for optimizing and estimating the accuracy of different experimental methods.

METHODS

We have analyzed the principles of multiple color fluorescence imaging microscopy. First, formalism based on the physical principles of fluorescence microscopy and noise analysis is introduced. Next, a signal to noise (S/N) analysis is performed and summarized in a simple accuracy criterion. The analysis assumes shot noise to be the dominant source of noise.

RESULTS

The accuracy criterion was used to calculate the S/N of multicolor FISH (M-FISH), spectral karyotyping, ratio imaging, and a method based on using a set of broad band filters. Spectral karyotyping is tested on various types of samples and shows accurate classifications. We have also tested classification accuracy as a function of total measurement time.

CONCLUSIONS

The accuracy criterion that we have developed can be used for optimizing and analyzing different multiple color fluorescence microscopy methods. The assumption that shot noise is dominant in these measurements is supported by our measurements.

Advances in fluorescence in situ hybridization

The techniques of in situ hybridization (ISH) are widely applied for analyzing the genetic make-up and RNA expression patterns of individual cells. This review focusses on a number of advances made over the last 5 years in the fluorescence ISH (FISH) field, i.e., Fiber-FISH, Multi-colour chromosome painting, Comparative Genomic Hybridization, Tyramide Signal Amplification and FISH with Polypeptide Nucleic Acid and Padlock probes.

Spectral imaging in preconception/preimplantation genetic diagnosis of aneuploidy: multicolor, multichromosome screening of single cells

PURPOSE

Our purpose was to evaluate the utility of spectral imaging for multicolor, multichromosome enumeration in human interphase cell nuclei.

METHODS

Chromosome-specific probes labeled with different fluorochromes or nonfluorescent haptens were obtained commercially or prepared in-house. Metaphase spreads, interphase lymphocytes, or blastomeres cells were hybridized with either 7 or 11 distinctly different probes. Following 46 hr of hybridization, slides were washed and detected using either a filter-based quantitative image processing system (QUIPS) developed in-house or a commercial spectral imaging system.

RESULTS

The filter-based fluorescence microscope system is preferred for simultaneous detection of up to seven chromosome targets because of its high sensitivity and speed. However, this approach may not be applicable to interphase cells when 11 or more targets need to be discriminated. Interferometer-based spectral imaging with a spectral resolution of approximately 10 nm allows labeling of chromosome-specific DNA probes with fluorochromes having greatly overlapping emission spectra. This leads to increases in the number of fluorochromes or fluorochrome combinations available to score unambiguously chromosomes in interphase nuclei.

CONCLUSIONS

Spectral imaging provides a significant improvement over conventional filter-based microscope systems for enumeration of multiple chromosomes in interphase nuclei, although further technical development is necessary in its application to embryonic blastomeres. When applied to preconception/preimplantation genetic diagnosis, presently available probes for spectral imaging are expected to detect abnormalities responsible for 70-80% of spontaneous abortions caused by chromosomal trisomies.

Yeast nuclei display prominent centromere clustering that is reduced in nondividing cells and in meiotic prophase

Chromosome arrangement in spread nuclei of the budding yeast, Saccharomyces cerevisiae was studied by fluorescence in situ hybridization with probes to centromeres and telomeric chromosome regions. We found that during interphase centromeres are tightly clustered in a peripheral region of the nucleus, whereas telomeres tend to occupy the area outside the centromeric domain. In vigorously growing cultures, centromere clustering occurred in approximately 90% of cells and it appeared to be maintained throughout interphase. It was reduced when cells were kept under stationary conditions for an extended period. In meiosis, centromere clusters disintegrated before the emergence of the earliest precursors of the synaptonemal complex. Evidence for the contribution of centromere clustering to other aspects of suprachromosomal nuclear order, in particular the vegetative association of homologous chromosomes, is provided, and a possible supporting role in meiotic homology searching is discussed.

Detection of phosphatidylinositol glycan class A gene transcripts by RT in situ PCR hybridization. A comparative study using fluorescein, Texas Red, and digoxigenin-11 dUTP for color detection

Gene-specific probes labeled with fluorescein, Texas Red, and digoxigenin-11 dUTP (DIG) were used for RT in situ PCR hybridization to detect PIG-A gene (phosphatidylinositol glycan class A) transcripts. The PIG-A gene is responsible for biosynthesis of the glycosylphosphatidyl-inositol (GPI) anchor. Lack of GPI anchor expression due to mutations can cause an acquired clonal hematologic disorder called paroxysmal nocturnal hemoglobinuria (PNH). In this RT in situ PCR study, two types of labeling methods, a direct method (using fluorescein and Texas Red) and an indirect method (using DIG-11 dUTP) were compared. Both were successfully applied to detect and localize the PIG-A gene transcripts within single cells of the cell lines AA2, H9, and JY. Furthermore, similar results for sensitivity and reproducibility were obtained. Advantages and disadvantages of the different labeling techniques are discussed. In addition, peripheral blood mononuclear cells from PNH patients were also included in this study.

Multicolor FISHing: what's the catch?

Recent advances in protocols for multicolor fluorescence in situ hybridization (FISH) mark a major milestone in the field of molecular cytogenetics. Brilliant chromosome images have been presented, where each chromosome homolog is depicted in a different color. The easy recognition of chromosomes seems to simplify karyotype analysis considerably and the procedure is meant to open new avenues for scanning human and other genomes for chromosomal rearrangements. How will this development change the field of cytogenetics? In this review the current applications that benefit from the new protocols are summarized and future perspectives are discussed.

Seven-color time-resolved fluorescence hybridization analysis of human papilloma virus types

Identification of human papilloma virus (HPV) types is important in order to determine the risk of cervical carcinoma in women. This requires a technique to probe individual samples for multiple virus specificities. Here we describe simultaneous multicolor analysis of amplification products for any of seven amplified HPV types 16, 18, 31, 33, 35, 39, and 45, associated with cancer of the cervix. A seminested polymerase chain reaction was performed in a single tube using a biotinylated inner primer. Sets of amplification products, immobilized on a 96-pronged manifold solid support, were rendered single stranded and probed with a mix of seven type-specific, differentially labeled oligonucleotides. These probes contained 10 or 20 lanthanide chelates at the 5' ends with seven distinct combinations of europium, terbium, and samarium ions. The seven viral strains were correctly identified by time-resolved fluorescence measurement of the specifically hybridized probes. Using this assay format, simultaneous detection of any of seven or even more target variants is possible.

MLL/ENL fusion in congenital acute lymphoblastic leukemia with a unique t(11;18;19)

To elucidate the events leading to a unique complex translocation involving chromosomes 11, 18, and 19 in a congenital progenitor B-cell acute lymphoblastic leukemia, we have performed comprehensive cytogenetic and fluorescence in situ hybridization (FISH) analyses as well as molecular genetic studies on the DNA and RNA level. We were able to confirm the cytogenetic interpretation of this complex t(11;18;19)(q23;q22;p13.3) by chromosome painting. Involvement of the MLL gene on 11q23 became evident by Southern blot analysis as well as by FISH with a YAC clone containing the respective gene. Despite the fact that the additional signals of the split YAC clone were observed on the abnormal chromosome 18, reverse transcription polymerase chain reaction (RT-PCR) revealed a MLL/ENL hybrid mRNA, which is specific for a t(11;19)(q23;p13.3). This gene fusion most probably represents the critical part of this rearrangement. The transfer of the translocated part of the split YAC clone onto chromosome 18 indicates that the second break must have occurred in the vicinity of the first one, at a distance too close to be resolved by FISH. Whether this break took place within chromosome 11 or 19 sequences, up- or downstream of the MLL/ENL fusion, and whether this translocation results from a concerted simultaneous exchange of material or from two separate sequential events in consecutive cell generations remains open.

Instability of chromosomes 1, 3, 16, and 17 in primary breast carcinomas inferred by fluorescence in situ hybridization

Abnormalities of chromosomes 1, 3, 16, and 17 were examined in 203 metaphase cells from 12 cases of primary breast carcinoma using fluorescence in situ hybridization with chromosome painting probes. The most common structural abnormalities were chromosomal rearrangements, especially translocations, and chromosome 17 was most frequently involved in these types of changes. Chromosome 16 was preferentially involved in the losses and deletions, while chromosomes 1 and 17 were more involved in the gains, including amplifications, than other chromosomes. This approach has revealed a different profile of abnormalities from those normally shown by G-banding analysis. Some of these changes are likely to be novel and may be biologic or clinical importance in breast cancer.

Karyotyping human chromosomes by combinatorial multi-fluor FISH

We have developed epifluorescence filter sets and computer software for the detection and discrimination of 27 different DNA probes hybridized simultaneously. For karyotype analysis, a pool of human chromosome painting probes, each labelled with a different fluor combination, was hybridized to metaphase chromosomes prepared from normal cells, clinical specimens, and neoplastic cell lines. Both simple and complex chromosomal rearrangements could be detected rapidly and unequivocally; many of the more complex chromosomal abnormalities could not be delineated by conventional cytogenetic banding techniques. Our data suggest that multiplex-fluorescence in situ hybridization (M-FISH) could have wide clinical utility and complement standard cytogenetics, particularly for the characterization of complex karyotypes.

Fluorescence in situ hybridization on human metaphase chromosomes detected by near-field scanning optical microscopy

Fluorescence in situ hybridization on human metaphase chromosomes is detected by near-field scanning optical microscopy. This combination of cytochemical and scanning probe techniques enables the localization and identification of several fluorescently labelled genomic DNA fragments on a single chromosome with an unprecedented resolution. Three nucleic acid probes are used: pUC1.77, p1-79 and the plasmid probe alpha-spectrin. The hybridization signals are very well resolved in the near-field fluorescence images, while the exact location of the probes can be correlated accurately with the chromosome topography as afforded by the shear force image.

Detection of fluorescence in situ hybridization on human metaphase chromosomes by near-field scanning optical microscopy

Fluorescence in situ hybridization signals on human metaphase chromosomes are detected by a near-field scanning optical microscope. This makes it possible to localize and identify several fluorescently labeled genomic DNA fragments on a single chromosome with a resolution superior to traditional fluorescence microscopy. Several nucleic acid probes have been used. The hybridization signals are well resolved in the near-field fluorescence images, and the exact location of the probes can be correlated to the topography as it is afforded by the shear-force feedback.

Low-efficiency (macro-)pinocytic internalization of non-pathogenic Escherichia coli into HEp-2 cells

HEp-2 cells internalize non-pathogenic Escherichia coli bacteria by a low-efficiency internalization mechanism which is upregulated in Pho-derepressed strains (as shown by Sinai and Bavoil in 1993), and is independent of microfilament integrity but requires functional microtubules. Here, we further characterize the microtubule requirement of this pathway using various effectors of microtubule integrity and function. Furthermore, we show that internalization is enhanced upon treatment with monodansylcadaverine, a specific inhibitor of receptor mediated endocytosis, and is insensitive to brefeldin A, which promotes the microtubule-dependent reorganization of the endosome. An assay system is also described to directly evaluate the contribution of pinocytosis to this pathway based on the ability of the bacteria to cointernalize and consequently colocalize with the fluid-phase marker, Texas-red-conjugated dextran (TRD). Using this assay, Hoescht-stained bacteria were observed in TRD-containing vesicles in numbers that are consistent with their observed internalization rate. Overall, these data are strongly supportive of the existence of a low-efficiency macropinocytic mechanism of entry for these non-pathogenic bacteria. Moreover, the observed requirements for host tyrosine kinase and protein kinase C activities suggest that it is inducible.

Robert Feulgen Prize Lecture 1995. Electronic light microscopy: present capabilities and future prospects

Electronic light microscopy involves the combination of microscopic techniques with electronic imaging and digital image processing, resulting in dramatic improvements in image quality and ease of quantitative analysis. In this review, after a brief definition of digital images and a discussion of the sampling requirements for the accurate digital recording of optical images, I discuss the three most important imaging modalities in electronic light microscopy--video-enhanced contrast microscopy, digital fluorescence microscopy and confocal scanning microscopy--considering their capabilities, their applications, and recent developments that will increase their potential. Video-enhanced contrast microscopy permits the clear visualisation and real-time dynamic recording of minute objects such as microtubules, vesicles and colloidal gold particles, an order of magnitude smaller than the resolution limit of the light microscope. It has revolutionised the study of cellular motility, and permits the quantitative tracking of organelles and gold-labelled membrane bound proteins. In combination with the technique of optical trapping (optical tweezers), it permits exquisitely sensitive force and distance measurements to be made on motor proteins. Digital fluorescence microscopy enables low-light-level imaging of fluorescently labelled specimens. Recent progress has involved improvements in cameras, fluorescent probes and fluorescent filter sets, particularly multiple bandpass dichroic mirrors, and developments in multiparameter imaging, which is becoming particularly important for in situ hybridisation studies and automated image cytometry, fluorescence ratio imaging, and time-resolved fluorescence. As software improves and small computers become more powerful, computational techniques for out-of-focus blur deconvolution and image restoration are becoming increasingly important. Confocal microscopy permits convenient, high-resolution, non-invasive, blur-free optical sectioning and 3D image acquisition, but suffers from a number of limitations. I discuss advances in confocal techniques that address the problems of temporal resolution, spherical and chromatic aberration, wavelength flexibility and cross-talk between fluorescent channels, and describe new optics to enhance axial resolution and the use of two-photon excitation to reduce photobleaching. Finally, I consider the desirability of establishing a digital image database, the BioImage database, which would permit the archival storage of, and public Internet access to, multidimensional image data from all forms of biological microscopy. Submission of images to the BioImage database would be made in coordination with the scientific publication of research results based upon these data.(ABSTRACT TRUNCATED AT 400 WORDS)

Molecular cytogenetics: unraveling of the genetic composition of individual cells by fluorescence in situ hybridization and digital imaging microscopy

Molecular biology techniques allow the unraveling of the genetic alterations that cause or accompany malignant disease. Since tumors are often heterogeneous, biochemical analysis of tissue homogenates is of limited diagnostic value. This paper gives examples of methods that are presently operational to analyze the genetic composition of individual cells. They are based on fluorescence in situ hybridization (FISH) and digital imaging microscopy. First, the current status of indirect and direct FISH staining methods with respect to probe labeling, detection sensitivity, multiplicity, and DNA resolution is summarized. Microscope hardware as well as charge-coupled device (CCD) cameras required for FISH analysis are then described. Applications potentially important for the analysis of urological malignancies, such as the automated enumeration of chromosomal abnormalities (counting of dots in interphase cells) and high-resolution DNA mapping on highly extended chromatin, are described in detail. Finally, the limitations of the present methodology and its future prospects are discussed.

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.

New epi-fluorescence optical system for independent analysis of two different fluorochromes in microscopy

A new epi-fluorescence optical system is described that uses splitting of the primary excitation and emission light beams, independent modification of the separated beams, and their reunification. The optical system was constructed for analysis of two different fluorochromes, e.g., DAPI and TRITC. Modifications in the separated beams comprise: (1) isolation of specific wavelengths (365 nm, 546 nm, 435-500 nm, and 590-750 nm), (2) wavelength switching without image displacement and blur by means of a light chopper alternating between ultraviolet-excitation/blue-detection and green-excitation/red-detection at frequencies of up to 140 Hz for observation by eye without image flicker, and (3) separate positioning of lenses for compensation of chromatic aberrations. This system demonstrates a good transmission of the chosen wavelengths. A high specificity of double fluorescence analysis with minimal effects of spectral overlap was obtained with good temporal resolution. It has been shown that it is feasable to obtain separate chromatic compensations for the use of a microscope objective in spectral regions outside the range for which the objective is corrected.

A comparative study of karyotypes of muntjacs by chromosome painting

We have used a combination of chromosome sorting, degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), chromosome painting and digital image capturing and processing techniques for comparative chromosome analysis of members of the genus Muntiacus. Chromosome-specific "paints" from a female Indian muntjac were hybridised to the metaphase chromosomes of the Gongshan, Black, and Chinese muntjac by both single and three colour chromosome painting. Karyotypes and idiograms for the Indian, Gongshan, Black and Chinese muntjac were constructed, based on enhanced 4', 6-diamidino-2-phenylindole (DAPI) banding patterns. The hybridisation signal for each paint was assigned to specific bands or chromosomes for all of the above muntjac species. The interspecific chromosomal homology was demonstrated by the use of both enhanced DAPI banding and comparative chromosome painting. These results provide direct molecular cytogenetic evidence for the tandem fusion theory of the chromosome evolution of muntjac species.

Assessment of numeric abnormalities of X, Y, 18, and 16 chromosomes in preimplantation human embryos before transfer

OBJECTIVE

Our purpose was to determine the feasibility of ascertaining aneuploidy for chromosomes X, Y, 18, and 16 by use of multiple-probe fluorescence in situ hybridization in blastomeres from preimplantation human embryos.

STUDY DESIGN

A short fluorescence in situ hybridization procedure involving the simultaneous use of four deoxyribonucleic acid probes detected with red, green, blue, or a mixture of red and green fluorochromes was developed to determine numeric abnormalities of chromosomes X, Y, 18, and 16. Embryos underwent biopsy, and all or most cells were analyzed to distinguish true aneuploidy from mosaicism and to assess technique variations within the same embryo (n = 64).

RESULTS

The analysis of all the blastomeres of an embryo was achieved in 91% of the embryos. Successful analyses including biopsy, fixation, and fluorescence in situ hybridization were achieved in 87.8% of the blastomeres. Of the four chromosomes tested, numeric aberrations were found in 23% and 42% of normally and abnormally developing embryos, respectively, including aneuploidy, polyploidy, haploidy, and mosaicism. When diploid embryos containing one or several tetraploid cells are counted as chromosomally abnormal, then 49% and 61% of normally and abnormally developing embryos, respectively, were chromosomally abnormal. Aneuploid embryos consisted of two monosomies for chromosome 16, one for chromosome 18, and a trisomy for chromosome 16. There was a tendency for aneuploidy to increase with maternal age.

CONCLUSIONS

Fluorescence in situ hybridization is a more efficient method than cytogenetic analysis to study specific aneuploidies at preimplantation stages of development in human embryos. In addition, the preimplantation genetic diagnosis of two blastomeres per eight-cell embryo may be sufficient to ensure successful analysis of polyploidy, haploidy, and specific aneuploidies without endangering the survival of the embryo. The technique can be easily modified to consider other chromosomes, including 13 and 21. Because most chromosomally abnormal embryos do not develop to term, the use of this technique may increase the delivery rate per embryo by allowing only transfer of embryos normal for the tested chromosomes. This technique would be most useful for older women undergoing in vitro fertilization, because aneuploidy appears to increase with advancing maternal age.

Analysis of antifading reagents for fluorescence microscopy

The utility of p-phenylenediamine, 1,4-di-azobicyclo-(2.2.2.)-octane, and the commercial products Citifluor, Slowfade, and Vectashield, antifading agents frequently used as mounting media for fluorescence in situ hybridization, was investigated. Fading curves for bound fluorochromes were recorded with digital microscopy, and relative fluorescence intensities of fluorochromes in solution were measured with an aperture defined measurement system. The three commonly used fluorochromes, fluorescein, tetramethyl rhodamine, and coumarin, were studied. Vectashield offered the best antifading properties for all three fluorochromes, although their relative fluorescence intensity was slightly less in Vectashield in comparison with other antifading agents. In Vectashield, fluorescein, tetramethyl rhodamine, and coumarin showed half-life times of 96, 330, and 106 s, respectively, whereas in 90% glycerol in PBS (pH 8.5), these half-life time values were 9, 7, and 25 s, respectively. Vectashield is particularly recommended as a mounting medium for quantitative digital imaging microscopy and for multicolor applications, where it is easy to have errors due to differences in fading rates of the fluorochromes.

CCD microscopy and image analysis of cells and chromosomes stained by fluorescence in situ hybridization

This paper reviews methods and applications of CCD microscopy for analysing cells and chromosomes subjected to fluorescence in situ hybridization (FISH). The current status of indirect and direct FISH staining methods with respect to probe labelling, detection sensitivity, multiplicity and DNA resolution is summarized. Microscope hardware, including special multi-band pass filters and CCD cameras required for FISH analysis, is described. Then follows a detailed discussion of current and emerging applications such as the automated enumeration of chromosomal abnormalities (counting of dots in interphase cells), comparative genomic hybridization, automated evaluation of radiation-induced chromosomal translocations, and high-resolution DNA mapping on highly extended chromatin. Finally, the limitations of the present methodology and future prospects are discussed.

Mosaicism of autosomes and sex chromosomes in morphologically normal, monospermic preimplantation human embryos

We have previously detected chromosome abnormalities in human embryos whilst identifying the sex for preimplantation diagnosis of X-linked disease. In this study we assess the incidence of these abnormalities, both for sex chromosomes and autosomes 1 and 17, using dual fluorescent in situ hybridization (FISH). Sixty-nine normally fertilized embryos of good morphology at the 6-10 cell stage (day 3 post-insemination) were examined. The embryos were spread whole using HCl and Tween 20 to dissolve the cytoplasm. Thirty-four embryos were analyzed for the sex chromosomes and 35 for autosomes 1 and 17. All probes were directly labelled with fluorochromes allowing analysis in 2 h. Control lymphocytes demonstrated that the probes were of high specificity. For the sex chromosomes, five embryos were mosaic (15 per cent) with the remaining 29 being uniformly XX or XY. In no case was an XX nucleus found in an otherwise XY embryo, indicating that even though mosaicism for the sex chromosomes is present, such abnormalities would not lead to a misdiagnosis of sex. For the autosomes, 16 embryos were abnormal (46 per cent); one embryo was triploid, one was monosomic for chromosome 1, and ten others were diploid mosaics (three diploid/aneuploid, three diploid/polyploid, and four diploid/haploid). A further four embryos had variable chromosome numbers in the majority of nuclei which appeared to be the result of uncontrolled mitotic division. The presence of haploidy or double monosomy, which occurred in 15 per cent of nuclei, has important implications for the diagnosis of trisomies and dominant disorders.