Method for sequential staining of GTL-banded metaphases with fluorescent-labeled chromosome-specific paint probes

Gene expression profile of an adenomyoepithelioma of the breast with a reciprocal translocation involving chromosomes 8 and 16

Myoepithelium is an integral part of the mammary ductal and lobular architecture, positioned between luminal cells and the basement membrane. We describe the first report on cytogenetic findings in an adenomyoepithelioma of the breast with a balanced t(8;16)(p23;q21), and provide gene expression profile using Affymetrix GeneChip U95AV2 (Affymetrix, Santa Clara, CA). Differential analysis identified 857 genes with 2-fold or more mRNA change in comparison to pooled normal breast control; immunohistochemical analysis was used to confirm these results in a limited number of genes. Expression results were grouped based on the chromosomal location of the genes and associated protein function, and identified several potential pathogenetic mechanisms (autocrine and paracrine growth stimuli) in the development of myoepithelial tumors.

Detailed genome-wide screening for inter- and intrachromosomal abnormalities by sequential G-banding and RxFISH color banding of the same metaphase cells

While the now-classic chromosome banding methods, such as G-banding, remain the techniques of choice for the initial screening for karyotypic abnormalities, sometimes chromosomal rearrangements involve segments too small or too similarly banded to be detected or described adequately by these techniques. The necessity to use a genome-wide, fluorescence in situ hybridization (FISH)-based screening technique as a complement to G-banding is especially obvious in cases where the information obtained by the latter analysis does not provide an adequate guide to the choice of probes for chromosome-specific FISH. Furthermore, the same metaphase cells should ideally be used for both G-banding and FISH analysis to overcome the scarcity of metaphases observed in many cases and to ensure the correct interpretation of chromosomal aberrations in cytogenetically unstable neoplasms with massive cell-to-cell karyotypic variability. We describe a protocol which enables cross-species color banding (RxFISH), a new FISH-based screening technique that simultaneously imparts specific color banding patterns on all chromosomes, of preparations that have been G-banded and mounted for up to several years, as well as a procedure allowing chromosome-specific painting of the same metaphase cells to resolve whatever doubts persist after the preceding G-banding and RxFISH analyses. This approach makes possible a detailed, genome-wide screening for inter- and intrachromosomal abnormalities including archival cases whose karyotypic rearrangements had been incompletely identified by G-banding.

Ring chromosome 8 syndrome: further characterization

We describe two de novo cases of extra r(8) confirmed by fluorescent in situ hybridization (FISH). Based on these two and eight additional cases of extra r(8) confirmed by FISH, the phenotype is better documented. One of our patients had minor facial anomalies, near-normal growth, and neurological development. She had a ring in each cell analyzed. The second had minor craniofacial anomalies and growth and mental retardation. He had a small or double-sized ring in each cell. The phenotype of these 10 cases ranges from almost normal in an adult with 10% mosaicism to variable degrees of minor anomalies, growth retardation, and mental retardation overlapping the mosaic +8 syndrome.

Utility of multicolor fluorescent in situ hybridization in clinical cytogenetics

PURPOSE

Multicolor FISH (M-FISH) was introduced in 1996 to scan all 24 chromosomes in different fluorescent colors by use of a specific filter set and computer software. However, the clinical utility of M-FISH has been limited because of the lack of commercial availability of reagents and hardware. We have evaluated M-FISH for identification of markers, derivative chromosomes, and complex karyotypes.

METHODS

We present our findings based on a representative sample of one normal and six abnormal cases from a variety of tissue types. The results of M-FISH were confirmed by other well-established FISH probes.

RESULTS

M-FISH analyses were successful in all six cases. The derivative chromosomes, ring, and a complex karyotype were resolved.

CONCLUSIONS

We find M-FISH to be an invaluable tool for a high degree of accuracy and efficiency for chromosome identification. The limitations similar to spectral karyotyping system (SKY) include the inability to detect intrachromosomal anomalies, abnormalities involving the p-arms of acrocentrics and areas rich in highly repetitive DNA. In addition, there are some concerns of misinterpretation due to overlap of fluorophore combinations of different chromosomes, especially for subtle insertional translocations.

Sequential G-banding FISH on human sperm chromosomes

A method that allows the performance of double-colour chromosome painting (FISH) on previously G-banded human sperm metaphases has been developed. Sperm chromosomes were obtained by using the fusion technique between zona-free hamster oocytes and human spermatozoa. Single- and double-colour chromosome painting was performed using DNA libraries specific for chromosomes X, Y and 21 on either unstained or G-banded preparations. The hybridization efficiency was very high (98%). The sequential staining technique is very useful for analyses of structural (stable) and numerical chromosome aberrations in human sperm and thus can increase the efficiency of the human sperm-hamster oocytes fusion system to assess the risk to human germ cells as a result of endogenous and exogenous factors.

Fluorescence in situ hybridization of old G-banded and mounted chromosome preparations

An improved method for fluorescence in situ hybridization (FISH) investigation of old, previously G-banded, mounted chromosome preparations with chromosome specific painting probes and centromere-specific probes is described. Before hybridization, the slides are incubated in xylene until the coverslips detach spontaneously; any mechanical manipulation will jeopardize the results. The success of chromosome painting is improved by excluding the regular RNase treatment step prior to hybridization. Additional changes compared with standard FISH protocols are that the 2 x SSC step is omitted, that the amount of added probe is increased approximately 2.5 times, and that the amplification of signals is performed twice. The applicability of the method, which allows double painting with two differently labeled probes using two differently fluorescing colors, was tested on 11 cases involving different chromosome abnormalities and different types of material, including short-term cultures of epithelial and mesenchymal tumors, blood, leukemic bone marrow, and long-term cultures of a cell line derived from an epithelial tumor. Success was achieved even with chromosome preparations that were several years old.

Characterization of human SHC p66 cDNA and its processed pseudogene mapping to Xq12-q13.1

SHC is an adapter protein in the Ras-MAPkinase pathway that is involved in the regulation of cell growth and differentiation. The p46 and p52 isoforms are thought to be produced by the use of two alternative translation initiation sites in a 3.4-kb transcript from the SHCA gene, which maps to chromosome 1q21. The p66 isoform could be encoded by a different 3.8- or 2.8-kb transcript of the same gene or alternatively by a SHC-related gene. To characterize other putative genes coding for SHC-like proteins, primers from the 3' UTR of the SHCA gene were used to screen a yeast artificial chromosome (YAC) library by polymerase chain reaction (PCR). Two YAC clones, 20D11B and 36D1D, were isolated and used as probes for fluorescence in situ hybridization analysis. Both these probes hybridized to chromosome Xq12-q13.1. This novel SHC-related sequence was characterized by direct sequencing of vectorette library PCR products produced from clone 20D11B. A transcript of 3.2 kb that was 85% identical to the mouse Shc cDNA encoding the p66 isoform was identified. Sequence analysis demonstrated the presence of multiple stop codons identifying this isoform of SHC as a processed pseudogene. Using primers designed on the basis of the nucleotide sequence of the pseudogene, we have now amplified and sequenced a human cDNA that encodes the SHC p66 protein. Thus, we have characterized the human SHC p66 isoform cDNA and identified a processed SHC pseudogene that maps to chromosome Xq12-q13.1.

Acute promyelocytic leukemia with t(15;16;17;19) and unusual fluorescence in situ hybridization pattern with PML and RARA probes

We report a 58-year-old female with typical morphological and clinical features of acute promyelocytic leukemia in whom a complex translocation involving chromosomes 15, 16, 17 and 19 was detected using conventional cytogenetics and fluorescence in situ hybridization (FISH) with chromosome specific paints. RARA-PML fusion was not evident by FISH, but the RARA signal was split in 74.5% of cells. GTL-banding and FISH with probes for PML, RARA and chromosome 15 specific paint raise the possibility of PML-RARA fusion on the abnormal chromosome 19 in the complex translocation. The unusual PML-RARA fusion may be related to this patient's poor response to induction therapy with all-trans-retinoic acid.

Characterization of a human ubiquitin-conjugating enzyme gene UBE2L3

Ubiquitin-conjugating enzymes (E2s) are essential components of the post-translational protein ubiquitination pathway, mediating the transfer of activated ubiquitin to substrate proteins. We have identified a human gene, UBE2L3, localized on Chromosome (Chr) 22q11. 2-13.1, encoding an E2 almost identical to that encoded by the recently described human L-UBC (UBE2L1) gene present on Chr 14q24.3. Using chromosome-specific vectorette PCR, we have determined the intron/exon structure of UBE2L3. In contrast to the intronless UBE2L1 gene, the coding sequence of UBE2L3 is interrupted by three large introns. UBE2L3-derived mRNA appears to be the predominant species in most tissues rather than the transcript from UBE2L1 or another homologous gene UBE2L2, which maps to Chr 12q12. We also present additional evidence that these genes are members of a larger multigene family. The primary sequence of the protein encoded by UBE2L3 is identical to partial peptide sequence derived from the rabbit E2 'E2-F1,' suggesting that we have identified the human homolog of this protein. This latter E2 has been demonstrated to participate in transcription factor NF-kappaB maturation, c-fos degradation, and human papilloma virus-mediated p53 degradation in vitro.

Yeast artificial chromosome cloning and chromosomal localization of the abundant odontogenic keratocyst protein elafin

An imbalance in human leucocyte elastase (HLE) activity is widely recognized to play an important pathological role in a number of human diseases. An earlier report has described greater transcription of elafin, an endogenous inhibitor of HLE, in epithelia of odontogenic keratocysts of the jaw than in normal oral mucosa. The elafin gene was now localized to chromosome 20q11.2-13.1 using a combination of somatic cell-hybrid panel screening and fluorescence in situ hybridization using a biotinylated DNA probe prepared from isolated yeast artificial chromosomes. No other positive fluorescent signals were observed. This eliminates the elafin gene as a candidate gene for naevoid basal-cell carcinoma syndrome, as the gene for this syndrome localizes to chromosome 9q23.1-31. The elafin yeast artificial chromosome DNA is to be subcloned to identify polymorphic microsatellite markers that will establish whether this gene is frequently amplified in oral neoplastic tissue.

Cytogenetic and clinical characteristics of a case involving complete duplication of Xpter-->Xq13

True isochromosomes for Xp probably do not exist in a liveborn. We describe a rare case of complete Xp duplication and retention of the inactivation centre at Xq13. Cytogenetically, it is described as a nonmosaic 46,X,psu idic(X)(q13). Complete duplication of Xpter-->Xq13 was confirmed by banded analysis and FISH probes for X centromere, Xp21, XIST locus, and whole chromosome paints for X and Y. The abnormal X was always late replicating. Clinically, the patient was short statured, had primary amenorrhoea, and incomplete development of secondary sexual characteristics, but otherwise was phenotypically normal. There are no non-mosaic reported cases with complete duplication of i(Xp) confirmed by FISH or molecular techniques. Those cases with partial duplication of Xp and presence of the inactivation centre share the traits of amenorrhoea and poor secondary sexual development. To develop a clinical profile of duplication of Xp (in presence of Xq13) there is a need to study more cases.

Partial monosomy of chromosome 1p36.3: characterization of the critical region and delineation of a syndrome

We describe 5 patients ranging in age from 3 to 47 years, with karyotypic abnormalities resulting in monosomy for portion of 1p36.3, microcephaly, mental retardation, prominent forehead, deep-set eyes, depressed nasal bridge, flat midface, relative prognathism, and abnormal ears. Four patients have small hands and feet. All exhibited self-abusive behavior. Additional findings in some of the patients include brain anomalies, optic atrophy, hearing loss and skeletal deformities. The breakpoints within chromosome 1 were designated at 1p36.33 (1 case). Thus, the smallest region of deletion overlap is 1p36.33-->1pter. Detection of the abnormal 1 relied on high resolution G-band analysis. Fluorescence in situ hybridization (FISH) utilizing a DNA probe (Oncor D1Z2) containing the repetitive sequences in distal 1p36, confirmed a deletion of one 1 homologue in all 5 cases. The abnormal 1 resulted from a de novo deletion in only one patient. The remaining patients were either confirmed (3 cases) or suspected (1 case) to have unbalanced translocations. Despite the additional genetic imbalance present in these four cases, monosomy of 1p36.33 appears to be responsible for a specific clinical phenotype. Characterization of this phenotype should assist in the clinical diagnosis of this chromosome abnormality.

A human ubiquitin conjugating enzyme, L-UBC, maps in the Alzheimer's disease locus on chromosome 14q24.3

We have identified a novel ubiquitin conjugating enzyme gene, L-UBC, which maps to human Chromosome (Chr) 14q24.3. This is also the location of the major early onset familial Alzheimer's disease gene (FAD3). L-UBC encodes a protein that demonstrates homology to the yeast ubiquitin conjugating enzyme, UBC-4, and human UbcH5. Their functions are to ubiquitinate specific proteins targeted for degradation. The protein also exhibits very strong homology to a rabbit protein, E2-F1, which mediates p53 degradation driven by papilloma virus E6 protein in vitro. The accumulation of specific proteins that have undergone aberrant processing in neurofibrillary tangles and amyloid plaques is the classic pathological feature in brains of Alzheimer's disease patients. Abnormal ubiquitination has previously been suggested to play a role in the etiology of Alzheimer's disease. This gene therefore represents a plausible candidate gene for FAD3.

Partial trisomy 13q identified by sequential fluorescence in situ hybridization

We report on a 19-month-old boy with partial trisomy 13q resulting from a probable balanced translocation involving chromosomes 1 and 13. The infant presented with omphalocele, malrotation, microcephaly with overriding skull bones, micrognathia, apparently low-set ears, rocker-bottom feet, and congenital heart disease, findings suggestive of trisomy 13. Karyotypic studies from peripheral blood lymphocytes documented an unbalanced karyotype 46,XY,-1,+der(1). The mother's chromosomes were normal, and the father was not available. Conventional cytogenetic techniques were unable to identify the extra material on the terminal 1q. Using fluorescence in situ hybridization (FISH) on the GTL-banded metaphases, the extra material on 1q was identified as the terminal long arm of 13, thus resulting in partial trisomy 13 (q32-qter).

Yeast artificial chromosome cloning of the beta-catenin locus on human chromosome 3p21-22

beta-Catenin has emerged as an important component of the adherens junctions between epithelial cells. As a result of studies of its interaction with the APC gene product, it has been implicated in the development of colorectal cancer. alpha-Catenin, beta-catenin, E-cadherin and APC appear to mediate contact inhibition in epithelia. As part of the study of the organization of the beta-catenin gene, we have isolated yeast artificial chromosomes (YACs) to characterize its intron/exon structure. YAC fluorescence in situ hybridization analysis and polymerase chain reaction analysis of somatic cell hybrid DNAs show that beta-catenin maps in the 3p21-22 region, the location of tumour-suppressor genes deleted in small-cell lung cancer (SCLC) and other disorders. beta-Catenin YACs will provide a source of microsatellite markers useful in loss of heterozygosity studies to assess the importance of beta-catenin deletions in SCLC.

Diagnosis of microdeletion syndromes: high-resolution chromosome analysis versus fluorescence in situ hybridization

Contiguous gene syndromes are characterized by deletions or duplications of specific chromosomal segments involving clusters of single genes. Although these syndromes are associated with distinct clinical phenotypes, these features are difficult to distinguish in the newborn and early childhood periods. In such cases, demonstration of chromosomal involvement through cytogenetic studies is of vital importance in arriving at an accurate diagnosis. In this article results of microdeletion analysis of 31 cases comprising 16 cases of Prader-Willi syndrome, 3 of Angelman syndrome, 7 of Miller-Dieker syndrome, and 5 of DiGeorge syndrome are reported. All patients were studied with both high-resolution chromosome analysis and fluorescence in situ hybridization. In the majority of cases there is 100% concordance between the two techniques. However, in one patient suspected of having DiGeorge syndrome with a normal karyotype at the 750 band level, fluorescence in situ hybridization identified a deletion within the critical region. Without fluorescence in situ hybridization studies on this patient, it would not have been possible to confirm the diagnosis of DiGeorge syndrome cytogenetically. Based on these results and other studies reported in the literature, it is recommended that all suspected cases of microdeletion syndromes should be studied using fluorescence in situ hybridization, irrespective of high-resolution chromosome results. However, because of the difficulties associated with clinical diagnosis of these syndromes, fluorescence in situ hybridization should not replace standard chromosome analysis.

Malignant rhabdoid tumor of the kidney: involvement of chromosome 22

Cytogenetic and molecular studies have demonstrated that involvement of 22q is a non-random finding in malignant rhabdoid tumors (MRTs) of the brain. We present an MRT of the kidney with the karyotype 47,XY, + i(1)(q10), der(8)t(8;22)(q12;q11.2),der(22)t(8;22)(q23 or q24.1;q11.2). This unbalanced reciprocal translocation was confirmed by fluorescence in situ hybridization (FISH) with chromosome-specific paints for chromosomes 8 and 22. Molecular analysis demonstrated a partial deletion of 22q in the BCR region at q11.2, strengthening the suspicion that this is a critical region for the initiation or progression of these highly malignant neoplasms. Establishing non-random cytogenetic changes in MRTs arising from the kidney may be of value in distinguishing these rare, but often fatal tumors from other renal neoplasms that mimic them histologically. The similarity in cytogenetic and molecular abnormalities between renal and extra-renal MRTs argues against the concept that extra-renal MRTs are only representative of a rhabdoid phenotype, rather than being true rhabdoid tumors.