Molecular Cytogenetic Investigations Research Articles

The natural history of Cri du Chat Syndrome. A report from the Italian Register

The aim of this report is to provide an update on the natural history of the Cri du Chat Syndrome by means of the Italian Register (I.R.). Two hundred twenty patients were diagnosed by standard cytogenetic methods and 112 of these were also characterised by molecular-cytogenetic investigation (FISH). FISH analysis showed interstitial deletions, short terminal deletions and other rare rearrangements not previously correctly diagnosed by standard cytogenetics. The diagnosis was made in the first month of life in 42% and within first year in 82% of cases. The remaining 18% were diagnosed at an age ranging from 13 months to 47 years. At the last follow-up, patient age ranged from 8 months to 61 years. Mortality, already low, has decreased over time as it is lower between 1984–2002 compared to 1965–1983. Mortality was higher in patients with unbalanced translocations resulting in 5p deletions. Our data confirm that the cat-like cry and peculiar timbre of voice are the most typical signs of the syndrome, not only at birth but also later and these are the only signs which might suggest the diagnosis in patients with small deletions and mild clinical picture. A cytogenetic and clinical variability must be underlined. Cardiac, cerebral, renal and gastrointestinal malformations were more frequent in the patients with unbalanced translocations resulting in 5p deletions. Sucking and feeding difficulties and respiratory infections are frequent in the first months or years of life. Intubation difficulties linked to larynx anomalies must be considered. Psychomotor development is delayed in all patients but there is a variability related to deletion size and type as well as other genetic and environmental factors. However, the results showed an improvement in the acquisition of the development skills and progress in social introduction which should encourage caregivers and parents to work together in carrying out the rehabilitative and educational interventions.

T(14;22)(q32;q11) in non‐Hodgkin lymphoma and myeloid leukaemia: molecular cytogenetic investigations

Two non-Hodgkin lymphomas (NHL), one chronic lymphocytic leukaemia/small lymphocytic lymphoma and one diffuse large B-cell lymphoma and three cases of myeloid leukaemia, two chronic (CML) and one acute (AML), showed, by G-banding analysis, apparently identical chromosomal translocations t(14;22)(q32;q11), in three of the cases as the sole abnormality. Fluorescence in situ hybridisation (FISH) analysis with locus-specific probes for ABL at 9q34 [bacterial artificial chromosomes (BACs) 835J22 and 1132H12], IGH at 14q32 [P1 artificial chromosome (PAC) 998D24] and IGL (PAC 1019H10) and BCR (BAC 74M14) at 22q11, as well as multicolour in situ hybridisation (M-FISH) analyses were performed. A three-way variant translocation of the classical t(9;22)(q34;q11), t(9;22;14)(q34;q11;q32), involving both BCR and ABL, was unravelled by the molecular cytogenetic investigations in the three myeloid leukaemia cases; a similar variant translocation has previously been reported in seven CML. The two cases of NHL (one NHL with a similar 14;22-translocation has been reported previously) had no involvement of BCR or ABL, but instead the IGH and IGL genes were shown to be juxtaposed by the t(14;22)(q32;q11). How such a rearrangement with recombination of IGH and IGL might elicit a pathogenetic effect is completely unknown.

Concurrent translocation of BCL2 and MYC with a single immunoglobulin locus in high-grade B-cell lymphomas

B-cell leukaemia or lymphoma with a combination of t(8;14)(q24;q32) of Burkitt leukaemia/lymphoma and t(14;18)(q32;q21) of follicular lymphoma may present clinically as de novo acute lymphoblastic leukaemia or transformation of follicular lymphoma to aggressive histology diffuse lymphoma. A number of cell lines have been reported with a complex t(8;14;18) with fusion of MYC, IGH and BCL2 on the same derivative 8 chromosome. The objective of this study was to determine the frequency and chromosomal features of this der(8)t(8;14;18) in a series of acute leukaemias and malignant lymphomas. A database of 1350 leukaemia and lymphoma karyotypes was searched for cases with structural alterations affecting both 8q24 and 18q21. A total of 55 cases were identified, of which eight revealed a complex der(8)t(8;14;18) with an MYC-IGH-BCL2 rearrangement resulting from translocation of BCL2 and MYC with a single disrupted IGH allele. Molecular cytogenetic investigation is essential to identify cases of high-grade leukaemia/lymphoma with concurrent translocations affecting the BCL2 and MYC loci.

Duplication of Xq26.2-q27.1, includingSOX3, in a mother and daughter with short stature and dyslalia

Duplications of the distal long arm of the X chromosome are rare and carrier females are usually phenotypically normal. We report on a 14-year-old short statured (height and weight <3rd centile) girl with dup(X)(q26.2q27.1) inherited from a short mother. The proband has minor dysmorphic features, lordosis, lack of menarche, late signs of puberty, low prepuberal levels of gonadotrophins and steroids, but borderline low IGF-1 and normal IGF-Bp3 serum levels. Both the proposita and her mother have severe speech problems with stuttering and dyslalia. The 44-year-old mother with a strikingly aged face and a prominent nose, had menarche at 15 years. Both maternal sisters and the grandmother of the proposita are also short. Karyotyping revealed an additional band at Xq26 in all metaphases from the proband, her mother, and two maternal aunts. Molecular cytogenetic investigations revealed an Xq26.2-q27.1 direct duplication of approximately 7.5 Mb that encompasses or disrupts the SOX3 gene, which maps at the distal border of the duplicated segment. A similar chromosomal duplication was reported recently in five families and in each was associated with an abnormal phenotype in males with short stature [Hol et al., 2000; Solomon et al., 2002, 2004]. Using an androgen-receptor (HUMARA) gene methylation assay and FISH, we show that despite preferential inactivation of the dup(Xq) chromosome a significant proportion of lymphocytes in both mother and daughter carry an active duplicated X chromosome. Our findings further suggest that a dosage effect of SOX3 may to be responsible for a speech disorder in addition to short stature secondary to hypopituitarism.

Evaluation of Focal Adhesion Kinase Gene Expression in Leukemia and Cancer Cell Lines Using Combined Molecular Cytogenetic Investigations and Quantitative Real Time RT-PCR.

FAK (Focal Adhesion Kinase) is a non-receptor tyrosine kinase protein implicated in integrin-mediated signal pathways. The human gene fak is located on chromosome 8q near c-myc. Cells that overexpress FAK show increased migration and increased cell survival with apoptosis inhibition. The aim of the present study was to investigate the genomic or post-genomic origin of this overexpression in seven tumor cell lines with different levels of FAK expression: K562, an erythroblastic cell line; U937, a monoblastic cell line; KG1a, a poorly differenciated myeloblastic cell line; HL 60, a promyelocytic cell line; Jurkat, a lymphoblastic cell line; A549, a bronchial adenocarcinoma cell line; M4Beu, a lymph node metastasis melanoma cell line. Total or partial chromosome 8 qualitative or quantitative abnormalities and the presence of double minute chromosomes bearing coding genomic DNA fragments were investigated using both conventional cytogenetic (standard karyotype after R- and G- banding) and molecular cytogenetic such as multicolor karyotype (M-FISH), FISH and comparative genomic hybridization (CGH). The mRNA expression was investigated using quantitative real time RT-PCR and the protein level using immunocytochemistry and western blot (immunoblot) analysis. Except for the Jurkat cell line, karyotypes revealed complex modifications. FISH and M-FISH allowed to precisely identify the chromosomal origin of the genomic material on each chromosome and CGH allowed to characterize relative loss and gain of coding genomic DNA and to identify their chromosomal origin. Summarized results are shown in the following table:No detectable RT-PCR product was observed for HL60 and U937 cell lines. The preliminary results show that there was usually a good correlation between PCR data and western blot analysis. However, FAK overexpression for KG1a cell line most probably has a genomic origin, while in K562 and A549 cell lines the origin is most probably at the transcription or post-transcription level without any abnormality of chromosome 8. Dysregulation of fak gene is observed in hematopoietic as well as solid tulor cell lines, and may contribute to leukemogenesis.</CENTER>Cell lineFISH 8q24-qterCGH Chr. 8RT-PCRRT-Q-PCRWestern blotK562NormalNormal+130.1++++KG1aAmplifiedenh(8)(q11qter)+37.5++++JurkatNormalNormal+8.7+ (low)U937Normalenh(8)(pterqter)000HL60Amplifiedamp(8)(q23-24)000M4BeuNormalNormal+43.50A549NormalNormal+46++++RT-Q-PCR results in copy number ratio

Cytogenetic characterization of seven human cancer cell lines by combining G- and R-banding, M-FISH, CGH and chromosome- and locus-specific FISH

Leukemia cell lines K562, KG1a, U937, HL60, Jurkat and solid tumor cell lines A549 and M4Beu are widely used in studies of cell cycle, apoptosis and adhesion mechanisms in cancer cells. Although the K562 and U937 cell lines were previously subjected to a detailed cytogenetic characterization, only a few molecular cytogenetic investigations have been performed on the other five cell lines. We combined several molecular cytogenetic techniques, such as fluorescence in situ hybridization (FISH), multicolor FISH (M-FISH), and comparative genomic hybridization (CGH) to demonstrate the precise genetic aberrations in tumor genomes of these seven cell lines. This information may be useful for multiple studies on these cell lines, providing a genetic basis for the interpretations of experimental findings.

Cytogenetic and molecular cytogenetic analyses in diffuse astrocytomas

Diffuse astrocytomas are highly variable tumors and show complex biologic behavior that is based on multi-step oncogenesis. We report cytogenetic and molecular cytogenetic investigations in 23 cases of diffuse astrocytomas. The results of conventional karyotyping, interphase fluorescence in situ hybridization (FISH), comparative genomic hybridization, multicolor FISH, and spectral karyotyping are reported. Various numerical and structural chromosomal aberrations were identified. Clustering of structural alterations in the short arm of chromosome 2 (2p) and the long arm of chromosome 7 (7q) were detected. Using spectral karyotyping, additional chromosome rearrangements not detectable by conventional methods were found. Some of these anomalies have not been previously described in diffuse astrocytomas. An independent validation of these discrepant findings is required.

Comprehensive conventional and molecular cytogenetic characterization of B-CPAP, a human papillary thyroid carcinoma-derived cell line

Cell lines derived from different thyroid tumor histotypes are useful for the in vitro study of both the phenotypic and genetic features of these cancers. Although karyotypic changes are known to be associated with thyroid lesions, the chromosome patterns of only a few cell lines have been published. Herein, we report an extensive conventional and molecular cytogenetic investigation of the human papillary thyroid carcinoma derived cell line B-CPAP. Morphological studies and expression of tumor markers in this cell line have been reported previously, but no detailed characterization on the origin of the chromosome markers is available. B-CPAP cells have a rather stable hypertriploid karyotype, with chromosome polysomies and structural chromosome abnormalities featuring whole chromosome arm imbalances. Chromosome banding revealed a main clone with nine chromosome markers, and fluorescence in situ hybridization (FISH) with whole chromosome paint (wcp), partial chromosome paint (pcp), and centromeric probes clarifyied their origin. The use of centromeric probes provided accurate refinement of the rearrangements classified as whole-arm translocations by banding and FISH with wcp probes. Both chromosomal and array-based comparative genomic hybridization experiments confirmed the cytogenetic characterization of this cell line. Moreover, the use of fluorescence immunophenotyping and interphase cytogenetics as a tool for the investigation of neoplasms (FICTION) technique, which simultaneously shows nuclear ploidy and cytoplasmic immunofluorescence, detailed the oncocytic feature of the cells. Intriguingly, despite their origin, they lack most of the features expressed in papillary thyroid tumor cells and have a chromosomal pattern reminiscent of that of a subgroup of oncocytic malignant thyroid tumors.

Molecular cytogenetic investigations of synchronous bilateral breast cancer

Background: Bilaterality in breast cancer is a rare event and together with an early onset of disease points towards inheritance of the disease. However, most cases seem to occur sporadically,...

Sequential FISH analysis of oocytes and polar bodies reveals aneuploidy mechanisms.

Constitutional aneuploidy occurs in at least 5% of recognised pregnancies, with apparent preferential involvement of the X chromosome and the smaller autosomes. Molecular cytogenetic investigations of cleavage-stage embryos have revealed anomalies affecting all sizes of chromosomes. The aim was to investigate the variety of anomalies arising during maternal meiosis I by analysis of unfertilised oocytes and polar bodies to gain insight into aneuploidy mechanisms. Sequential FISH analysis was carried out with specific probes derived from eight chromosomes, representing all sizes. Only imbalance due to a gain of a whole chromosome or chromatid, represented by extra signals, was counted to avoid artefact. Data were obtained on 236 eggs from 124 patients of average age 32.5 years (range 22-44). Ten patients (average 32.6 years) had abnormal eggs. The abnormality rate for oocytes and for polar bodies was close to 4% for each. Fourteen hyperploidies were found, seven involving additional single chromatids. The abnormalities affected chromosomes 13,16,18, 21 and X but not chromosomes 1, 9 or 12. The data provide evidence for several mechanisms leading to aneuploidy, including classical non-disjunction of whole univalents; pre-division of chromatids prior to anaphase I, leading to imbalance detected at metaphase II; gonadal mosaicism for a trisomic cell line and preferential involvement of the smaller chromosomes. Monosomy for the large autosomes is not uncommon in cleavage-stage embryos and may additionally arise from anaphase lag preferentially affecting such chromosomes.

X chromosomal abnormalities in Indian adolescent girls.

In girls of adolescent age, primary amenorrhea is a major problem and it is often suspected as Turner syndrome (TS), with complete or partial absence of one of the two X chromosomes. The girls who are unable to menstruate are primarily investigated by the gynecologists with the help of a physical examination, sonogram of the pelvis, endocrinologic tests, and ultimately cytogenetic analysis. Chromosomal analyses have been carried out in 280 such cases that were referred from different parts of the country. The standard protocol for peripheral blood lymphocyte culture was followed for metaphase chromosome preparation and conventional analysis of G-banded chromosomes. A total of 29% cases were found to have some chromosomal abnormality, including TS and testicular feminization syndrome involving sex chromosomes. Amongst those with sex chromosomal anomaly, 34% had evidence of a 46,XY karyotype in phenotypic females and 51% had pure line 45,X or mosaic with normal XX or other aberrations in X. The classification of the TS group further showed the spectrum of variant TS in Indian adolescent girls who suffered from absence or delayed menarche to correspond well with the Belgian, Danish, or Russian population. However, it has been reported that only 1% of the pure line 45,X conception is viable, indicating the necessity of mosaicism with X or Y chromosome. It has been understood that conventional banding analysis is absolutely necessary for segregating the variant nature of TS. In addition, molecular genetic or molecular cytogenetic investigations can determine the nature of mosaicism. The present study further indicated the involvement of autosomes in causing improper sexual development in girls of adolescent age.

Multiple telomeric aberrations in a telomerase-positive leukemia patient

Bone marrow samples from a pancytopenia/leukemia patient were routinely analyzed at first and second admission. At the first presentation, the karyotype was normal, whereas 17 months later several chromosome aberrations were recognized including presumed additions to the short arms of chromosomes 1 and 16 in all cells, and numerous other aberrations in subpopulations of cells. From the predominance of aberrations at chromosome ends, we suspected insufficient telomere maintenance as an underlying mechanism behind the karyotype changes, in particular as an interstitial deletion in the region harboring the gene for the RNA component ( hTERC) of the telomerase enzyme was also noticed; however, while molecular cytogenetic investigation confirmed the terminal aberrations, we found the malignant cells positive for telomerase activity and the presence of an hTERC gene on both chromosomes 3. A presumed chromosome 1 addition turned out to reflect an amplification of a tandemly repeated sequence element. Labeling of multiple tandem repeat sequences in situ by a novel multicolor primed in situ hybridization showed no evidence of instability of other repeated DNA elements.

Frequent loss of chromosome 3p and hypermethylation of RASSF1A in cholangiocarcinoma

Background/Aims : Cholangiocarcinoma comprises 5–20% of all primary malignant tumors of the liver. However, the lack of information about the genetic basis of cholangiocarcinoma has impeded characterization and understanding of its biological behavior. Methods : In this study, genome-wide aberrations in 13 cases of cholangiocarcinoma were examined by the molecular cytogenetic technique, comparative genomic hybridization. Results : Frequent gains of 1q, 3q, 8q, 15q and 17q, and common losses on 3p, 4q, 6q, 9p, 17p and 18q were found. The finding of common chromosome 3p loss (∼40%) with a minimal deleted region of 3p13-p21 has prompted our further investigation on the tumor suppressor gene RASSF1A , located at 3p21.3. Using bisulphite modification followed by methyl-specific PCR, a high incidence of methylated RASSF1A promoter region was detected in our current series (9/13 cases; 69%). Further expression analysis on the nine cases with promoter hypermethylation indicated much reduced RASSF1A expression compared to normal livers. Conclusions : Our current molecular cytogenetic investigation on primary cholangiocarcinoma provided overall karyotypic information and represents the first report on the methylation status of RASSF1A in cholangiocarcinoma. The high incidence of 3p loss and RASSF1A promoter hypermethylation detected may have implications for this tumor suppressor gene in the malignant progression of cholangiocarcinoma.

Comprehensive molecular cytogenetic investigation of chromosomal abnormalities in human medulloblastoma cell lines and xenograft

Comprehensive molecular cytogenetic investigation of chromosomal abnormalities in human medulloblastoma cell lines and xenograft

Comprehensive molecular cytogenetic investigation of chromosomal abnormalities in human medulloblastoma cell lines and xenograft.

Cell lines and xenografts derived from medulloblastomas are useful tools to investigate the chromosomal changes in these tumors. Here we used G-banding, fluorescence in situ hybridization (FISH), spectral karyotyping (SKY), and comparative genomic hybridization to study 4 medulloblastoma cell lines and 1 xenograft. Cell line D-425 Med had a relatively simple karyotype, with a terminal deletion of 10q and amplification of MYC in double-minutes (dmins). FISH demonstrated that an apparent isochromosome (17q) by routine karyotyping was actually an unbalanced translocation between 2 copies of chromosome 17. Cell line D-556 Med also had a simple near-diploid stemline with an unbalanced 1;13 translocation resulting in a gain of 1q, an isochromosome (17q), and dmins. These findings were initially described using routine G-banded preparations, and FISH showed that the dmins were an amplification of MYC and the i(17q) was an isodicentric 17q chromosome. The other finding was confirmed by FISH, SKY, and comparative genomic hybridization. Cell lines D-721 Med and D-581 Med had complex karyotypic patterns that could be completely characterized only when FISH and SKY were used. Xenograft D-690 Med also had a complex pattern that FISH and SKY were helpful in completely elucidating. Interestingly, balanced reciprocal translocations were seen as well as complicated unbalanced translocations and marker chromosomes. Comparative genomic hybridization demonstrated only a deletion of 10q22-10q24, supporting the idea that despite the complexity of the chromosomal rearrangements, minimal alterations in the overall chromosomal content had occurred. This study demonstrates that routine cytogenetic preparations are adequate to describe chromosomal abnormalities in occasional medulloblastoma samples, but a broader spectrum of molecular cytogenetic methods is required to completely analyze most of these tumor samples.

Comprehensive molecular cytogenetic investigation of chromosomal abnormalities in human medulloblastoma cell lines and xenograft

Comprehensive molecular cytogenetic investigation of chromosomal abnormalities in human medulloblastoma cell lines and xenograft

Molecular-cytogenetic investigation of skewed chromosome X inactivation in Rett syndrome

We have developed an approach to differentiate homologous X chromosomes in metaphase chromosomes and interphase nuclei by a fluorescence in situ hybridization (FISH) technique with chromosome X-specific alpha-satellite DNA probe. FISH analysis of metaphase chromosomes in a cohort of 33 girls with Rett syndrome (RTT) allowed us to detect eight girls with structurally different X chromosomes, one X chromosome with a large and another one with a small centromeric heterochromatin (so-called chromosomal heteromorphism). Step-wise application of differential replication staining and the FISH technique to identify the inactivation status of paternal and maternal chromosome X in RTT girls was applied. Skewed X inactivation in seven RTT girls with preferential inactivation of one X chromosome over the other X chromosome was detected in 62–93% of cells. Therefore, non-random or skewed X inactivation with variable penetrance in blood cells could take place in RTT.

Identification of a small supernumerary marker chromosome, r(2)(p10q11.2), and the problem of determining prognosis

The identification of small supernumerary marker chromosomes (SMCs) and the elucidation of their clinical significance remain two of the problems in classical human cytogenetics. We observed a small supernumerary ring in amniotic fluid cell cultures and identified its origin as r(2)(p10q11.2) and its extent by means of fluorescent in situ hybridisation (FISH). Uniparental disomy (UPD) was excluded by microsatellite analysis using polymorphic markers localised in the same region. On the basis of normal ultrasonographic checks, the patient decided to continue the pregnancy. A normal female was delivered at term and subsequent neonatal follow-ups confirmed the normal phenotype and development. In the present case, genetic counselling was not helpful because of the absence of reference cases. Detailed characterisation made it possible to correlate the normal baby phenotype with the trisomic 2p10-2q11.2 genomic region. Further molecular cytogenetic investigations of SMCs classified by DNA content and pregnancy outcome data should improve genetic counselling and risk evaluation.

Fluorescence in situ Hybridization General Principles and Clinical Application with Special Emphasis to Interphase Diagnostics

Fluorescence in situ hybridization (FISH) is a molecular-cytogenetic investigation method and thus cov- ers a gap between classical cytogenetic and molecular-ge- netic techniques. By the broad spectrum of application pos- sibilities it leads to important new developments in basic and applied cytogenetics. It enables the labeling of whole chromosomes and defined chromosome regions and fur- thermore gene localization with single copy probes. FISH is a technique that allows DNA sequences to be detected on metaphase chromosomes, in interphase nuclei, in a tis- sue section, or in blastomeres and gametes. In basic scien- tific research special fields of application comprise charac- terization of somatic cell hybrids, analyses of meiosis and of karyotype evolution. In clinical and tumor cytogenetic it helps to identify chromosome rearrangements, marker chromosomes, chromosome mosaicism and specific tumor cell lines. Fluorescence in situ hybridization receives a spe- cial importance for interphase cytogenetics, which mainly covers the development in this field.

Molecular cytogenetic investigations define a subgroup of thyroid adenomas with 2p21 breakpoints clustered to a region of less than 450 kb

Structural rearrangements involving chromosome band 2p21 characterize a cytogenetic subgroup of benign thyroid tumors. To narrow down the breakpoints of these aberrations, we established two cell lines from benign thyroid tumors showing translocations involving 2p21. These two cell lines and one additional primary tumor were used for FISH-studies with 18 BAC clones. All breakpoints were mapped to a cluster of about 450 kb.