New methods in cytogenetics

α-Thalassemia, mental retardation, and myelodysplastic syndrome

This article describes three rare syndromes in which the presence of α-thalassemia provided an important clue to the molecular basis of the underlying condition. It exemplifies how rare diseases allied with careful clinical observation can lead to important biological principles. Two of the syndromes, ATR-16 and ATR-X, are characterized by α-thalassemia in association with multiple developmental abnormalities including mental retardation. The third condition, ATMDS, is an acquired disorder in which α-thalassemia arises in the context of myelodysplasia. Intriguingly, mutations in the chromatin remodeling factor, ATRX, are common to both ATR-X syndrome and ATMDS.

In situ genetic analysis of cellular chimerism

Copy number variants are a recently discovered source of large-scale genomic diversity present in all individuals. We capitalize on these inherent genomic differences, focusing on deletion polymorphisms, to develop informative fluorescence in situ hybridization probes with the ability to unequivocally distinguish between donor and recipient cells in situ. These probes are accurate, specific, highly polymorphic and, notably, can be used to assign genetic identity in situ in a completely gender-independent fashion. We anticipate that these polymorphic deletion probes will be useful in further understanding the dynamics of cellular chimerism after transplantation, including the details of chronic organ rejection, post-transplant lymphoproliferative disorder and graft-versus-host disease, and in optimizing future tissue engineering and pluripotent stem cell therapies.

Fluorescence in situ hybridization in cardiovascular disease

Many human diseases are associated with cytogenetic abnormalities or chromosomal disorders including translocations, deletions, duplications, inversions, and other complicated chromosomal changes. Fluorescence in situ hybridization (FISH), a technique involving hybridization of labeled probes to chromosomes and detection of hybridization via fluorochromes, has become a popular method for identification and characterization of cytogenetic abnormalities. For FISH analysis, metaphase chromosomes are prepared by mitotic arrest and hypotonic shock, and denatured. Hybridization of digoxigenin- or biotin-labeled probes to these chromosomes is visualized using fluorochromes like fluorescein isothiocyanate and Texas Red. We have successfully applied FISH technology to the characterization of chromosome breakpoints involved in disease-associated cytogenetic abnormalities to identify candidate gene(s) for the disease. FISH is also widely used in clinical diagnosis of chromosomal disorders.

[Research into the human genome driven by improved methods]

The enormous progress made by research of the human genome is mainly driven by newly established or improved methods for the analysis of nucleic acids and proteins. Among the methods that have gained a wide-spread use within a comparably short time are fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR) including methods for quantitative PCR, and the use of short interfering RNA (siRNA) molecules aimed at gene silencing. The increasing significance of the analysis of secondary modifications of nucleic acids and proteins (genomic imprinting by DNA methylation, posttranslational protein modification) is reflected by an increasing use of mass spectrometry for the analysis and characterization of these biomolecules. Overall, in the future the research into the human genome and the interpretation of data will further benefit from these and other refined tools.

The role of protein elongation factor eEF1A2 in ovarian cancer

Frequent gains of chromosome 20q12-13 in ovarian tumors indicate that at least one important oncogene is found at that locus. One of the genes there is EEF1A2, which maps to 20q13.3 and encodes protein elongation factor eEF1A2. This review will focus on recent evidence indicating that EEF1A2 is an important ovarian oncogene and that the protein elongation network can activate tumorigenesis and inhibit apoptosis.

High resolution FISH to delineate contiguous and small DNA sequences

Somatic and meiotic metaphase, and pachytene chromosomes were subjected to DNA: DNA in situ hybridization to elucidate relative resolution of FISH signals for weak/contiguous hybridization sites. Hybridization with a '350 family' rye repetitive DNA probe pSc 200 characteristically differentiated the rye chromosome 5 from the rest of the complement on account of two small terminal homologous sites in the long arm, resolution of which is substantially improved using pachytene. Higher resolution of the two weak hybridization sites; a very small distal and a small proximal, is unequivocally demonstrated in the FISH painted 5RL examined at pachytene in the 5AS/5RL wheat background. Additionally this probe exhibits a large block of distal telomeric hybridization site in 5RS, followed by a more prominent proximal site homologous to '610 family' rye repetitive probe pSc 250. Precise denaturation - hybridization incubation and post hybridization stringency washing facilitates spatial resolution of contiguous repetitive rye probes pSc 200 and pSc 250, and physical localisation of small RFLP probe xpr 115 of wheat on barley chromosomes.

The chromosome: cytogenetic analysis and its clinical application

PURPOSE

Chromosomes are highly structured, dynamic complexes of DNA and protein. The human genome consists of 46 chromosomes (22 paired autosomes and 2 sex chromosomes). Cytogenetic analysis provides a means to identify, as well as describe, chromosomes and disorder-related aberrations. The purpose of this article is to 1) introduce chromosome structure and alterations, 2) describe the technical fundamentals of cytogenetic analysis, and 3) provide a brief overview of the clinical applications of this technology.

A single-center population-based consecutive series of 1500 cytogenetically investigated adult hematological malignancies: karyotypic features in relation to morphology, age and gender

During the 18-yr period 1976-93, a population-based series of 1586 adults with suspected or confirmed hematological malignancies were successfully cytogenetically investigated at a single center. Eighty-six cases were excluded due to unretrievable medical records or if analyzed only in remission or at relapse. The remaining 1500 medical records were reviewed regarding morphology and clinical parameters in order to investigate possible associations between karyotypic pattern (normal, 1, 2 or complex anomalies; specific abnormalities) and gender, age and morphological subgroups. The impact of time-period, i.e. 1976-87 vs. 1988-93, and referring center on cytogenetic findings was also studied. A total of 372 acute myeloid leukemias (AML), 389 myelodysplastic syndromes (MDS), 64 acute lymphoblastic leukemias (ALL) and 262 chronic myeloid leukemias (CML) were identified, altogether 1087 cases. Patients with other (n=261) or no hematological malignancies (n = 152) were excluded from the present analysis. Cytogenetic abnormalities were detected in 52% AML, 51 % MDS, 68% ALL and 97% CML, frequencies that did not differ significantly between the 2 time periods or referring centers. No significant age- or gender-related differences in karyotypic patterns were discerned in AML, MDS, ALL or CML, whereas the karyotypic patterns varied among the FAB groups in both AML (p= 0.001) and MDS (p < 0.001). The specific abnormalities t(8;21), t(15;17) and inv(16) were more common (p < 0.001) in younger AML patients and 5q- was more frequent in females with MDS (p<0.001). These findings indicate, in contrast to previous series, that neoplasia-associated karyotypic aberrations are not more common among older patients or in males.

Rapid denaturation improves chromosome morphology and permits multiple hybridizations during fluorescence in situ hybridization

Denaturation of chromosomal DNA for fluorescence in situ hybridization (FISH) is an essential step in a procedure associated with a number of variables. In our experience, shorter denaturation time in 70% formamide/2 x SSC at 72 C provides sufficient denaturation, where the hydrogen bonds are broken between the purines and pyrimidines of the double helix. This shortened exposure improves retention of morphology of human chromosomes from lymphocytes, aminocytes, fibroblasts and bone marrow, and allows the same metaphases to be denatured repeatedly and rehybridized with different probes. This approach is useful in investigations where sample volume is limited.

Molecular genetics and cytogenetics of breast carcinomas: comparison of the two methods

Molecular genetics and cytogenetics are two different approaches to studying genetic changes in breast carcinoma. We have used karyotype analysis, fluorescence in situ hybridization, and molecular analysis of allelic imbalance on chromosomes 7q and 16q and on both arms of chromosome 17, to study 85 breast carcinomas. Twenty-five of these samples gave results that could be used to compare the two methods. Sixty-nine chromosome arms were compared, of which 48 (70%) gave concordant molecular and cytogenetical results. Samples were processed for karyotyping both by harvesting directly from the fresh tissue and after selective culture for a few days. Karyotypes among the direct harvest samples matched significantly better with the molecular genetics results than karyotypes among the cultured cell preparations.

A method to codetect introduced genes and their products in gene therapy protocols

To monitor the presence of introduced genes and the distribution of the encoded proteins in host tissues after gene transfer, we combined fluorescence in situ hybridization (FISH) and immunohistochemistry in two separate gene therapy paradigms. In brain tissue sections from animals injected with pHSVlac vector, we localized nuclei containing vector DNA both in cells expressing and not expressing beta-galactosidase (beta-gal). This suggests that the efficiency of gene transfer is affected not only by gene delivery, but also by cellular controls on gene expression. In a second paradigm, following myoblast transplantation, we detected donor nuclei in the muscle of a patient with Duchenne's muscular dystrophy. The donor nuclei were either surrounded by host nuclei or apparently fused in the patient's muscle fiber producing dystrophin. The combined FISH and immunohistochemistry assay offers greater sensitivity and more information than currently used polymerase chain reaction and protein detection methods.

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.