Spontaneous chromosome fragility in chorionic villus cells

Cloning of genetically tagged chromosome break sequences reveals new fragile sites at 6p21 and 13q22

Fragile sites are specific genomic loci that are especially prone to chromosome breakage. For the human genome there are 31 rare fragile sites and 88 common fragile sites listed in the National Center for Biotechnology Information database; however, the exact number remains unknown. In this study, unstable DNA sequences, which have been previously tagged with a marker gene, were cloned and provided starting points for the characterization of two aphidicolin inducible common fragile sites. Mapping of these unstable regions with six-color fluorescence in situ hybridization revealed two new fragile sites at 6p21 and 13q22, which encompass genomic regions of 9.3 and 3.1 Mb, respectively. According to the fragile site nomenclature they were consequently entitled as FRA6H and FRA13E. Both identified regions are known to be associated with recurrent aberrations in malignant and nonmalignant disorders. It is conceivable that these fragile sites result in genetic damage that might contribute to cancer phenotypes such as osteosarcoma, breast and prostate cancer.

Common fragile site FRA11G and rare fragile site FRA11B at 11q23.3 encompass distinct genomic regions

Fragile sites are specific genomic loci that are particularly prone to chromosomal breakage. Based on their incidence in the human population, they are divided into rare fragile sites occurring in less than 5% of all individuals and common fragile sites being a constitutional feature of the genome of probably all individuals. In this study, cloning of unstable DNA sequences, which have been previously genetically tagged with a marker gene, was the basis for defining the genomic localization of the common fragile site FRA11G at 11q23.3. Mapping of the fragile site with six-color fluorescence in situ hybridization (FISH) resulted in the precise genomic localization of FRA11G to a 4.5 Mb region. The chromosomal subband 11q23.3 harbors both the common fragile site FRA11G and the rare fragile site FRA11B. Here, we show that FRA11G maps 0.8 Mb proximal to the genomic region previously defined to be affected by expression of FRA11B; thus, the common and the rare fragile sites at 11q23.3 encompass distinct genomic regions. The region of FRA11G is known to be involved in somatic and germline recurrent aberrations, and it is conceivable that genetic damage resulting from this fragile site might contribute to clinical phenotypes.

Immunodeficiency, centromeric region instability, facial anomalies syndrome (ICF)

The Immunodeficiency, Centromeric region instability, Facial anomalies syndrome (ICF) is a rare autosomal recessive disease described in about 50 patients worldwide and characterized by immunodeficiency, although B cells are present, and by characteristic rearrangements in the vicinity of the centromeres (the juxtacentromeric heterochromatin) of chromosomes 1 and 16 and sometimes 9. Other variable symptoms of this probably under-diagnosed syndrome include mild facial dysmorphism, growth retardation, failure to thrive, and psychomotor retardation. Serum levels of IgG, IgM, IgE, and/or IgA are low, although the type of immunoglobulin deficiency is variable. Recurrent infections are the presenting symptom, usually in early childhood. ICF always involves limited hypomethylation of DNA and often arises from mutations in one of the DNA methyltransferase genes (DNMT3B). Much of this DNA hypomethylation is in 1qh, 9qh, and 16qh, regions that are the site of whole-arm deletions, chromatid and chromosome breaks, stretching (decondensation), and multiradial chromosome junctions in mitogen-stimulated lymphocytes. By an unknown mechanism, the DNMT3B deficiency that causes ICF interferes with lymphogenesis (at a step after class switching) or lymphocyte activation. With the identification of DNMT3B as the affected gene in a majority of ICF patients, prenatal diagnosis of ICF is possible. However, given the variety of DNMT3B mutations, a first-degree affected relative should first have both alleles of this gene sequenced. Treatment almost always includes regular infusions of immunoglobulins, mostly intravenously. Recently, bone marrow transplantation has been tried.

Characteristic chromosomal fragility of human embryonic cells exposed in vitro to aphidicolin

The frequency and distribution of aphidicolin (APC)-induced common fragile sites (cfs) were analyzed in human embryonic cells of different origins. Embryonic lung fibroblasts (MRC-5), amniocytes (AMINO) and embryonic retina cells (HERO790) are as sensitive to the APC-induced clastogenic effect as peripheral lymphocytes, whereas embryonic kidney cells (HEK) seem more resistant to the induction of chromosomal gaps and breaks by the drug. Analysis of the distribution of fragile sites confirmed that the expression of specific APC-induced cfs varies in different cells and that the embryonic cell strains show a greater similarity among themselves than to lymphocytes. In addition, HEK, MRC-5, HERO790 and AMINO cells show specific APC induction of the cfs at the 1p31.2 chromosomal band, which seems to be a distinctive feature of the embryonic stage of cells.

Appraisal of fluorescence in situ hybridization (FISH) techniques in prenatal diagnosis

The reliability of FISH was appraised using probes for the X and Y chromosome and for chromosomes 12 and 18 in prenatal and adult interphase nuclei. Detection of a single hybridization spot proved to be quite reliable (80-92% positive nuclei). Detection of two hybridization spots was more difficult; percentages of nuclei showing two signals varied between 62-72%. The percentages of nuclei with the correct number of spots was higher in the metaphases occasionally found. Thus, FISH may complement but not replace cytogenetic analysis. For sex determination and for the detection of mosaicism, we suggest the use of two different probes in separate regions of the same preparation.