Multiplex Fluorescence In Situ Hybridization Research Articles

Abstract 1189: Chromosomal aberrations reveal novel genes with prognostic significance in esophageal adenocarcinoma

Abstract INTRODUCTION: The incidence of esophageal adenocarcinoma (EAC) has increased 6-fold in the west over the last 30 years, with a dismal survival rate of about 10%. Understanding the genomic aberrations and molecular pathogenesis in this cancer may enhance disease interventions. AIMS: To identify novel molecular targets with prognostic significance and to better characterize EAC by analyzing chromosomal aberrations across the whole genome. METHODS: An in-house oligonucleotide array comparative genomic hybridization (CGH) was performed on 89 chemo-naive EAC resection samples with long-term clinical follow-up data to identify regions of copy number gains/losses: good quality data obtained for 56 samples. Illumina Human Cyto Single-nucleotide Polymorphism (SNP)-12 Beadarray was carried out to map genomic boundaries of regions with aberrations. Touch-imprinting fluorescence in situ hybridization (FISH) assays were carried out using bacterial artificial chromosome probes on interphase nuclei of frozen samples to confirm findings. Regions with potential homozygous deletions (HDs) were investigated by multiplex nested PCR using microdissected DNA of frozen samples. The degree and pattern of genomic gains were studied using different FISH probes. RESULTS: 19 minimal regions with gains and 12 regions with losses (cut off=2 standard deviations (SD) above/below mean log2 ratios) were identified. Potential HDs (cut off=3 SD) were identified in 4 samples (7.1%) at 9p21. Nested multiplex PCR and FISH (quantitative: 100 nuclei per sample counted) confirmed a p16 deletion in all 4 samples. SNP analysis suggested another region of potential HD that involves a novel gene, ELAVL2. Amplifications (cut off=3 SD) in 6 samples (10.7%) at 8p23.1 were confirmed by analyses from the SNP array, which narrowed down the width of amplicon to 2 regions involving: (a) SOX7/PINX1 (5/6 samples) and (b) GATA4, NEIL2, FDFT1 and CTSB (4/6 samples). FISH assays confirmed amplifications of GATA4, NEIL2, FDFT1, CTSB, SOX7 (6 or more copies/centromere) and gains of PINX1 (3-6 copies/centromere). Unsupervised K means clustering (50 iterations) of the array CGH data generated 5 groups and survival analyses identified a group (32.1% of cohort) with significantly worse prognosis (median survival=500 days, p=0.0149). Modified T test with adjusted Bonferroni correction identified 17 clones with different log2 ratios (p<0.05), implicating 4 regions of gains and including 6 novel genes, between this group and the other 4 combined. The only clinical difference between this group and the others was an increased male:female ratio (Fishers exact test; p=0.01). CONCLUSIONS: 9p deletions and 8p amplifications are present in 7-11% of samples. The use of array CGH has identified copy number gains with prognostic significance in EAC. Further work is required to determine whether the genes involved have a causative role. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1189.

22q11.2 Microduplication in Two Patients with Bladder Exstrophy and Hearing Impairment

Purpose Bladder exstrophy is a congenital malformation of the bladder occurring in about 1 in 35 000 newborns. A few cases of bladder exstrophy patients have been described to carry chromosomal aberrations and in addition the recurrence risk in higher among relatives of bladder exstrophy cases than in the general population. This speaks in favour of a genetic contribution to the pathogenesis of bladder exstrophy. Material and Methods We have performed array-CGH analysis of 36 Swedish bladder exstrophy patients in order to look for submicroscopic chromosomal aberrations. Results The analysis revealed a 22q11.21 microduplication in two unrelated cases with bladder exstrophy and hearing impairment consistent with the recently described 22q11.2 microduplication syndrome. This finding was confirmed by multiplex ligation-dependent probe amplification (MLPA) and FISH analysis. Subsequent MLPA analysis of this chromosomal region in 33 bladder exstrophy patients did not reveal any deletion/duplication within this region. MLPA analysis of 171 anonymous control individuals revealed one individual carrying this microduplication. Conclusions Chromosomal rearrangements of 22q11.2 are implicated in several genomic disorders i.e. DiGeorge/velocardiofacial- and cat-eye syndrome. Deletions within this chromosomal region are relatively common while duplications of 22q11.2 are much less frequently observed. An increasing number of reports of microduplications of this region describe a highly variable phenotype. This is the first report of 22q11.2 microduplication associated with bladder exstrophy and hearing impairment. The finding of one carrier among a cohort of normal controls further highlights the variable phenotype linked to this microduplication syndrome.

Applications of fluorescence in situ hybridization (FISH) in detecting genetic aberrations of medical significance

Fluorescence in situ hybridization (FISH) is a powerful technique used in the detection of chromosomal abnormalities. The high sensi- tivity and specificity of FISH and the speed with which the assays can be performed have made FISH a pivotal cytogenetic technique that has provided significant advances in both the research and diagnosis of haematological malignancies and solid tumours. From a medical perspective, FISH can be applied to detect genetic abnormalities such as characteristic gene fusions, aneuploidy, loss of a chromosomal region or a whole chromosome or to monitor the progression of an aberration serving as a technique that can help in both the diagnosis of a genetic disease or suggesting prognostic outcomes. FISH can also be applied to such research applications as gene mapping or the identification of novel oncogenes or genetic aberrations that contribute towards various cancers. FISH is based on DNA probes annealing to specific target sequence of sample DNA. Attached to the probes are fluorescent reporter molecules which under fluorescence microscopy confirm the presence or absence of a particular genetic aberration when viewed under fluorescence microscopy. The tech- nique has recently evolved to allow screening of the whole genome simultaneously through multicolour whole-chromosome probe techniques such as multiplex FISH or spectral karyotyping, or through an array-based method using comparative genomic hybridization. This simple, yet effective, technique has revolutionized cytogenetics and has become well established in its potential as a diagnostic and discovery tool in the fight against cancer.

Multiplex fluorescence in situ hybridization in identifying chromosome involvement of complex karyotypes in de novo myelodysplastic syndromes and acute myeloid leukemia

Complex chromosomal aberrations (CCA) can be detected in a substantial proportion of myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), which are associated with very poor prognosis. Conventional cytogenetics (CC) cannot accurately define the specific alterations in CCA. Multiplex fluorescence in situ hybridization (M-FISH) allows the comprehensive identification of CCA. In this study, M-FISH was used in 16 patients with de novo MDS and 22 with AML with CCA detected by R-banding CC, and revealed 206 aberrations involved all 24 chromosomes, including 73 numerical chromosomal abnormalities and 133 structural abnormalities. The chromosomes most often involved were, by decreasing incidence, 5, 17, 8, 11, 7 and 21 in 57.9%, 55.3%, 44.7%, 36.8%, 34.2% and 34.2% of the cases, respectively. There were 98 unbalanced translocations, which were the most frequently observed aberrations in our study. Derivative chromosome 5 and 8 were implicated most often. The other derivatives were der(11), der(12), der(7), der(14), der(15) and der(17). Fourteen balanced translocations were detected in our series, and the most frequent reciprocal translocations was t(8;21). Fifty-five monosomies, 15 partial deletions, and 18 trisomies were found in all patients. The most frequently observed were -5/5q-, -17/17q-, -7, -18, -21, -19, and trisomy of chromosome 8 and 6. There were some abnormalities that have not been previously described, including two complex t(8;21) and seven unbalanced translocations. M-FISH could refine CCA, find or correct the missed or misidentified aberrations by CC analysis. Our findings confirmed that M-FISH was a powerful molecular cytogenetic tool to characterize complex karyotypes in MDS and AML.

22q11.2 microduplication in two patients with bladder exstrophy and hearing impairment

Bladder exstrophy is a congenital malformation of the bladder and urethra. The genetic basis of this malformation is unknown however it is well known that chromosomal aberrations can lead to defects in organ development. A few bladder exstrophy patients have been described to carry chromosomal aberrations. Chromosomal rearrangements of 22q11.2 are implicated in several genomic disorders i.e. DiGeorge/velocardiofacial- and cat-eye syndrome. Deletions within this chromosomal region are relatively common while duplications of 22q11.2 are much less frequently observed. An increasing number of reports of microduplications of this region describe a highly variable phenotype. We have performed array-CGH analysis of 36 Swedish bladder exstrophy patients. The analysis revealed a similar and approximately 3 Mb duplication, consistent with the recently described 22q11.2 microduplication syndrome, in two unrelated cases with bladder exstrophy and hearing impairment. This finding was confirmed by multiplex ligation-dependent probe amplification (MLPA) and FISH analysis. Subsequent MLPA analysis of this chromosomal region in 33 bladder exstrophy patients did not reveal any deletion/duplication within this region. MLPA analysis of 171 anonymous control individuals revealed one individual carrying this microduplication. This is the first report of 22q11.2 microduplication associated with bladder exstrophy and hearing impairment. Furthermore the finding of one carrier among a cohort of normal controls further highlights the variable phenotype linked to this microduplication syndrome.

In situ Visualization of Gene Expression Using Polymer‐Coated Quantum–Dot–DNA Conjugates

Imaging of specific mRNA targets in cells is of great importance in understanding gene expression and cell signaling processes. Subcellular localization of mRNA is known as a universal mechanism for cells to sequester specific mRNA for high production of required proteins. Various gene expressions in Drosophila cells are studied using quantum dots (QDs) and the fluorescence in situ hybridization (FISH) method. The excellent photostability and highly luminescent properties of QDs compared to conventional fluorophores allows reproducible obtainment of quantifiable mRNA gene expression imaging. Amine-modified oligonucleotide probes are designed and covalently attached to the carboxyl-terminated polymer-coated QDs via EDC chemistry. The resulting QD-DNA conjugates show sequence-specific hybridization with target mRNAs. Quantitative analysis of FISH on the Diptericin gene after lipopolysaccharide (LPS) treatment shows that the intensity and number of FISH signals per cell depends on the concentration of LPS and correlates well with quantitative real-time PCR results. In addition, our QD-DNA probes exhibit excellent sensitivity to detect the low-expressing Dorsal-related immunity factor gene. Importantly, multiplex FISH of Ribosomal protein 49 and Actin 5C using green and red QD-DNA conjugates allows the observation of cellular distribution of the two independent genes simultaneously. These results demonstrate that highly fluorescent and stable QD-DNA probes can be a powerful tool for direct localization and quantification of gene expression in situ.

Multi‐color FISH assays for characterization of marker chromosomes and epigenetic changes

Multicolor fluorescence in situ hybridization (mFISH) assays are essential for a precise description of chromosomal rearrangements. Routine application on human chromosomes started in 1996 with the simultaneous use of all 24 human whole chromosome painting probes in multiplex‐FISH (M‐FISH) and spectral karyotyping (SKY), even though the principle of mFISH was already described in 1989. Numerous approaches for chromosomal differentiation based on mFISH assays were reported recently. Predominantly, these have been established to characterize marker chromosomes, but also in many other fields mFISH is applied nowadays (for overview see the mFISH homepage http://www.med.uni‐jena.de/fish/mFISH/mFISHlit.htm). Here we review the recent developments and applications of mFISH including variants of M‐FISH, FISH‐banding techniques and applications in 2‐D and 3‐D‐FISH. Also a recently invented possibility to do sort of 'microsatellite analyses' in situ on human chromosomes called parental origin determination FISH (pod‐FISH) is presented. Overall, mFISH approaches are and will be essential scientific and diagnostic tools irrespective of being called death due to recent chip‐ and array‐technology developments. Supported in parts by the Stiftung Leukämie, Stefan‐Morsch‐Stiftung, DAAD 415‐br‐probal/po‐D/07/09624 and D07/00070 and the DFG (LI 820/11‐1, LI 820/13‐1, LI 820/17‐1).

Molecular Cytogenetic Studies of Complex Karyotypes in Myelodysplastic Syndromes (MDS): Conventional Cytogenetics, FISH and Multiplex FISH (mFISH/mBAND)

Karyotype represents one of the most valuable prognostic markers for MDS patients with profound impact on differential diagnosis and therapeutic decisions despite of the fact that it is a heterogenous patient population with diverse pathogenesis and clinical course. In approximately 10–20% of MDS patients complex chromosomal aberrations (CCA; three or more numerical/structural cytogenetic aberrations) are present at diagnosis and this finding is associated with the treatment resistance and poor outcome. Precise identifications of chromosomal regions involved in CCA could help in detection of cryptic, recurrent, prognostically relevant aberrations and in identification of candidate genes involved in leukemogenesis and progression of the disease. In this study we used various modifications of molecular cytogenetic techniques to specify CCA more precisely and to determine exact localization and frequency of chromosomal breakpoints. During the last seven years we examined bone marrow samples of 630 adults with MDS and in 81 of them (12,9%) complex karyotypes were found (in 73 patients at diagnosis and in 8 cases during the disease progression). Out of 73 patients with CCA at diagnosis were 43 males and 30 females, age range 22 to 82 years (median 65,5 years). Primary MDS was diagnosed in 63 (86.3%) of them, in 10 cases therapy related MDS was ascertained. Diagnoses according to the WHO classifications: MDS NS 3x, RA 2x, RA/RCMD 6x, RCMD 5x, RAEB I 20x, RAEB II 20x, MDS-AML 16x and RARS 1x. 63 patients died, 10 patients are still alive (four of them after stem cell transplatation). Chromosomal aberrations found by G-banding were verified by FISH with appropriate locus specific probes (Abbott-Vysis, Des Plaines, Illinois, USA), and by multiplex FISH (mFISH/mBAND) with the “XCyte” probe kits (MetaSystems, Altlussheim, Germany).Deletion of 5q31 region was proved in 63 patients (86.3%). In 29 cases mFISH analyses showed that parts of deleted No. 5 were translocated into other chromosomes. The most recurrent chromosomal partners of No. 5 in unbalanced translocations were Nos. 17 (9x), 12 (5x), 7 (5x), 2 (4x) and 3 (4x). Monosomy of No. 5 was confirmed in one case only, thus it was proved that monosomy 5 is not separated diagnostic unit in CCA. Except No. 5 the most frequently involved in CCA were chromosomes 7 (36x), 3 (33x), 12 (31x), 17 (31x) and 11 (23x). Presence of CCA at diagnosis was connected with poor response to the therapy and with short overall survival. For survival analysis patients were classified into three groups according to the molecular cytogenetic findings:del(5)(q31) and additional CCA – 33 cases,deleted chromosome 5 involved in CCA – 29 cases,CCA without deletion of 5q – 10 cases.The worst overall survival was found in group 2 (median 3 months), followed by group 1 (median 5 months) and 3 (median 6 months).Patients with MDS and CCA should be considered as a unique entity with extremely poor prognosis. Exact molecular cytogenetic analysis by multiplex FISH of all chromosomal aberrations which are involved in CCA will lead to selection of the patients into new prognostic groups. Exploring the underlying mechanism of leukemogenesis could improve the therapeutic outcome for these patients and could contribute to the development of a new targeted treatment strategy.

An analysis of complex chromosomal aberrations in seven cases of myelodysplastic syndromes by M-FISH and whole chromosome painting

Complex chromosomal aberrations (CCAs) can be detected in a substantial proportion of myelodysplastic syndrome (MDS). Comprehensive analysis of the chromosomal rearrangements in these CCAs has been hampered by the limitations of conventional cytogenetics (CC). Multiplex fluorescence in situ hybridization (M-FISH) is a new generation FISH technique which allows simultaneous identification of all the 24 human chromosomes. So it is very useful in clarifying CCAs, identifying cryptic interchromosomal rearrangements and characterizing marker chromosomes. But it also has some limitations. We used M-FISH and whole chromosome painting (WCP) to accurately refine the CCAs revealed by R-banding CC in seven cases with MDS. The composition and origin of 6 kinds of marker chromosomes, nine kinds of chromosomes with additional material undetermined and five kinds of derivative chromosomes undefined by CC were defined after M-FISH analysis. Four kinds of cryptic translocations overlooked by CC were found on derivative chromosomes and previously normal appearing chromosomes. In addition, M-FISH revealed some nonrandom aberrations which most frequently involved chromosome 17 (5/7) and -5/5q-(4/7). Fluorescence flaring is a main factor leading to misinterpretations. Some misclassified and missed chromosomal aberrations by M-FISH were corrected by WCP. M-FISH is a powerful molecular cytogenetic tool in clarification of CCAs. Complementary WCP can further identify misclassified and missed chromosomal aberrations by M-FISH. CC in combination with molecular cytogenetic techniques including M-FISH and WCP can more precisely unravel CCAs.

Establishment and characterization of a new human acute myelocytic leukemia cell line SH-2 with a loss of Y chromosome, a derivative chromosome 16 resulting from an unbalanced translocation between chromosomes 16 and 17, monosomy 17, trisomy 19, and p53 alteration

To report here a new acute myelocytic leukemia (AML) cell line SH-2 and describe its biological characteristics. Mononuclear cells isolated from a patient with AML-M2 subtype were passaged by liquid culture medium. Interleukin-3 and bone marrow stromal cells were used to support cell proliferation at the first 3 months. Various methods, including cytogenetic analysis, fluorescence in situ hybridization (FISH), multiplex FISH (M-FISH), reverse transcriptase polymerase chain reaction (RT-PCR), multiplex RT-PCR, short tandem repeat (STR)-PCR, direct sequencing of DNA, clonogenic assay, and tumorigenicity in nude and severe combined immunodeficient (SCID) mice were employed to identify and characterize SH-2 cell line. SH-2 cells were maintained without cytokine and stromal cells for 3 years. It had no Epstein-Barr virus or mycoplasma contamination. The SH-2 cell line showed typical myelocytic features in morphology and simultaneous strongly expressed myeloid antigens (CD13, 99.6% and CD33, 99.26%) and natural killer (NK)-related antigens (CD56, 99.5% and CD16/56, 99.62%) suggesting that SH-2 is an AML cell line with NK-antigen expression. SH-2 cell line initially showed a karyotype of 45, X, -Y, der(16)t(16;17)(q24;q12), -17, +19. During the passage period, the cells with a hypodiploid karyotype gradually decreased and were replaced by the near-tetraploid cells with a karyotype of 71-105(86), XX, -Y, -Y, der(16)t(16;17)x2, -17, -17, +19, +19. FISH and M-FISH delineated all abnormalities. SH-2 cells had the approximately same morphological, immunophenotypical, and cytogenetic features as the patient's leukemia cells had. STR-PCR provided powerful evidence for the derivation of SH-2 cell line from the patient's leukemia cells. SH-2 cells showed multiple drug resistance (MDR), which may be related to the p53 gene alteration, including the loss of one p53 allele due to the monosomy 17 and a point mutation of CAG to CAT at codon 576 of exon 5 in another p53 allele resulting in the loss of p53 gene function. In addition, SH-2 cell line did not express MDR-related genes, such as MDR1, multidrug resistance-related protein, and lung resistance protein, but expressed apoptosis-related genes, such as Bcl-2, Fas, glutathione S-transferase-pi, and p21, which were also related to the MDR. SH-2 cell line had tumorigenic capacities in nude and SCID mice. Because SH-2 cell line had a clear biology background, it will provide a useful tool for the study of the pathogenesis and treatment strategy of AML with MDR.

A Multichannel Watershed-Based Segmentation Method for Multispectral Chromosome Classification

Multiplex fluorescent in situ hybridization (M-FISH) is a recently developed chromosome imaging technique where each chromosome class appears to have a distinct color. This technique not only facilitates the detection of subtle chromosomal aberrations but also makes the analysis of chromosome images easier; both for human inspection and computerized analysis. In this paper, a novel method for segmentation and classification of M-FISH chromosome images is presented. The segmentation is based on the multichannel watershed transform in order to define regions of similar spatial and spectral characteristics. Then, a Bayes classifier, task-specific on region classification, is applied. Our method consists of four basic steps: 1) computation of the gradient magnitude of the image, 2) application of the watershed transform to decompose the image into a set of homogenous regions, 3) classification of each region, and 4) merging of similar adjacent regions. The method is evaluated using a publicly available chromosome image database and the obtained overall accuracy is 82.4%. By introducing the classification of each watershed region, the proposed method achieves substantially better results compared to other methods at a lower computational cost. The combination of the multichannel segmentation and the region-based classification is found to improve the overall classification accuracy compared to pixel-by-pixel approaches.

The Multicolor Fluorescence in Situ Hybridization (mFISH) Homepage

The Multicolor Fluorescencein SituHybridization (mFISH) HomepageMulticolor fluorescencein situhybridization (mFISH) assays are essential for a precise description of chromosomal rearrangements. Routine application of such techniques on human chromosomes started in 1996 with the simultaneous use of all 24 human whole chromosome painting probes in multiplex-FISH (M-FISH) and spectral karyotyping (SKY), even though the principle of mFISH was reported in 1989. Numerous approaches for chromosomal differentiation based on mFISH assays have been established, predominantly, to characterize marker chromosomes, but also in evolutionary biology, nuclear architecture, zoology and botany. The mFISH Homepage, which reviews all available literature at http://www.med. uni-jena.de/fish/mFISH/mFISHlit.htm will be introduced here.

Cryptic telomere imbalance: A 15‐year update

It has been 15 years since we proposed that assays of telomere integrity might reveal cryptic translocations and deletions as a significant cause of mental retardation (MR) in patients with normal G-banded karyotypes. Development of unique genomic probes adjacent to the subtelomeric repeats of each chromosome arm allowed multiplex FISH analyses that confirmed such cryptic telomeric imbalances in 3-6% of all unexplained MR. Although such "telomere FISH" analysis quickly became standard of care, limitations of this technology platform included a lack of information on the size and gene content of the deleted/duplicated segments and the failure to detect interstitial deletions not involving the most distal unique clone. The development of "molecular ruler" clone sets for every human telomere provided the foundation for accurate determination of size and gene content of each imbalance, as well as the detection of interstitial deletions within these regions. Array comparative genomic hybridization (aCGH) has emerged as a powerful technology to assess single copy changes (monosomy or trisomy) at targeted loci such as telomeres or across the whole genome. This technology now replaces multiplex FISH for the assessment of telomere integrity in unexplained MR and has the advantage of efficiently determining the size and gene content of the imbalance, as well as detecting interstitial deletions near telomeres or anywhere else in the genome covered by the array design. The application of aCGH in several studies of unexplained MR has confirmed that telomere imbalances are overrepresented compared to "average" chromosomal regions, although this is likely due to random chromosome breakage rather than specific molecular mechanisms associated with the genomic architecture of human telomeres. Telomere imbalances are significantly larger than initially envisioned ( approximately 40% are >5 Mb in size), and indicate the analytic sensitivity of the G-banded karyotype is much lower than previously thought. Finally, experience with smaller benign variants compared to larger pathogenic imbalances at telomeres serves as a model for approaching whole-genome aCGH in a clinical setting.

The in vivo dynamics of Streptococcus spp., Actinomyces naeslundii, Fusobacterium nucleatum and Veillonella spp. in dental plaque biofilm as analysed by five-colour multiplex fluorescence in situ hybridization

The formation and composition of dental plaque biofilm in vivo are important factors which influence the development of gingivitis, caries and periodontitis. Studying dental plaque biofilm in in vitro models can cause an oversimplification of the real conditions in the oral cavity. In this study, bovine enamel slabs were fixed in an individual acrylic appliance in situ to quantify dental plaque formation and composition using multiplex fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy. Each of the five oligonucleotide probes used for FISH was specific for either eubacteria or one of four frequently isolated bacterial constituents belonging to early and late colonizers of tooth surfaces. The thickness of formed biofilm increased from 14.9+/-5.0 microm after 1 day to 49.3+/-11.6 microm after 7 days. Streptococcus spp. were predominant in 1-day-old dental plaque and decreased significantly after 7 days (P=0.0061). Compared to the first day, Fusobacterium nucleatum decreased after 2 days and increased significantly after 7 days (P=0.0006). The decreases of Actinomyces naeslundii content on day 2 and day 7 were significant (P=0.0028). Changes in Veillonella spp. were not significant during the study period (P >0.05). The results showed that an in vivo observation period of 7 days was required to detect significant changes in Streptococcus spp. and F. nucleatum. The multiplex FISH used is suitable for analysing the dynamics of four important bacterial constituents in the oral biofilm in epidemiological studies.

Retrospective Species Identification of Microsporidian Spores in Diarrheic Fecal Samples from Human Immunodeficiency Virus/AIDS Patients by Multiplexed Fluorescence In Situ Hybridization

In order to assess the applicability of multiplexed fluorescence in situ hybridization (FISH) assay for the clinical setting, we conducted retrospective analysis of 110 formalin-stored diarrheic stool samples from human immunodeficiency virus (HIV)/AIDS patients with intestinal microsporidiosis collected between 1992 and 2003. The multiplexed FISH assay identified microsporidian spores in 94 of 110 (85.5%) samples: 49 (52.1%) were positive for Enterocytozoon bieneusi, 43 (45.8%) were positive for Encephalitozoon intestinalis, 2 (2.1%) were positive for Encephalitozoon hellem, and 9 samples (9.6%) contained both E. bieneusi and E. intestinalis spores. Quantitative spore counts per ml of stool yielded concentration values from 3.5 x 10(3) to 4.4 x 10(5) for E. bieneusi (mean, 8.8 x 10(4)/ml), 2.3 x 10(2) to 7.8 x 10(4) (mean, 1.5 x 10(4)/ml) for E. intestinalis, and 1.8 x 10(2) to 3.6 x 10(2) for E. hellem (mean, 2.7 x 10(2)/ml). Identification of microsporidian spores by multiplex FISH assay was more sensitive than both Chromotrope-2R and CalcoFluor White M2R stains; 85.5% versus 72.7 and 70.9%, respectively. The study demonstrated that microsporidian coinfection in HIV/AIDS patients with intestinal microsporidiosis is not uncommon and that formalin-stored fecal samples older than 10 years may not be suitable for retrospective analysis by techniques targeting rRNA. Multiplexed FISH assay is a reliable, quantitative fluorescence microscopy method for the simultaneous identification of E. bieneusi, E. intestinalis, and E. hellem, as well as Encephalitozoon cuniculi, spores in fecal samples and is a useful tool for assessing spore shedding intensity in intestinal microsporidiosis. The method can be used for epidemiological investigations and applied in clinical settings.

Multipoint interphase FISH in childhood T-acute lymphoblastic leukemia detects subpopulations that carry different chromosome 3 aberrations

We examined chromosome 3 in 32 childhood acute lymphoblastic leukemia (ALL) bone marrow samples. Using interphase multipoint FISH (mp-FISH), which was developed by our group, with 42 chromosome 3–specific probes, we detected clonal chromosome 3 aberrations in 4 T-cell ALL (T-ALL) cases. Four out of seven T-ALL cases carried 3q trisomies. One T-ALL case carried either trisomy 3 (in 15% of the cells) or a 23-megabase (Mb) 3p13∼p12 deletion in a different subpopulation of cells of 32%. Another T-ALL case had either 3q trisomy in 11% or a 12-Mb 3p12∼p13 deletion in 19% of the cells. The deletions were overlapping. In both cases, the majority of the bone marrow cells (47 and 70%, respectively) were normal chromosome 3 disomics. The interstitial deletions detected harbor a known homozygous deletion region between 72.6 and 78.8 Mb, which has been described in lung and breast tumors and contains the DUTT1/ROBO1 tumor suppressor gene. These deletions detected by mp-FISH would have remained unnoticed by conventional cytogenetics and multiplex FISH, as well as by current methods based on total tumor DNA analysis such as comparative genomic hybridization (CGH), array CGH, and loss of heterozygosity (LOH).

Spectral karyotyping analysis of human and mouse chromosomes.

Classical banding methods provide basic information about the identities and structures of chromosomes on the basis of their unique banding patterns. Spectral karyotyping (SKY), and the related multiplex fluorescence in situ hybridization (M-FISH), are chromosome-specific multicolor FISH techniques that augment cytogenetic evaluations of malignant disease by providing additional information and improved characterization of aberrant chromosomes that contain DNA sequences not identifiable using conventional banding methods. SKY is based on cohybridization of combinatorially labeled chromosome-painting probes with unique fluorochrome signatures onto human or mouse metaphase chromosome preparations. Image acquisition and analysis use a specialized imaging system, combining Sagnac interferometer and CCD camera images to reconstruct spectral information at each pixel. Here we present a protocol for SKY analysis using commercially available SkyPaint probes, including procedures for metaphase chromosome preparation, slide pretreatment and probe hybridization and detection. SKY analysis requires approximately 6 d.

Whole Chromosome Painting and Multiplex Fluorescence In Situ Hybridization in Detecting Complex Chromosomal Aberrations in Myelodysplastic Syndromes.

Objective To explore the value of the technique of whole chromosome painting (WCP) and multiplex fluorescence in situ hybridization (M-FISH) in the detection of complex chromosomal aberrations (CCAs) of myelodysplastic syndromes (MDS).Methods M-FISH was used in seven MDS patients with CCAs detected by R-banding technique to refine CCAs, and to identify cryptic translocations and characterization of marker chromosomes. Dual-color WCP procedures were further performed in 7 cases to confirm some rearrangements detected by M-FISH.Results In all cases, M-FISH confirmed all results of R-banding.The composition and origin of 6 kinds of marker chromosomes, 9 kinds of chromosomes with additional material undetermined and 5 kinds of derivative chromosomes undefined by CC were defined after M-FISH analysis; 4 kinds of cryptic translocations overlooked by CC were found on derivative chromosomes and previously normal appearing chromosomes. In addition, M-FISH revealed some nonrandom aberrations: aberrations involving chromosome 17 (5/7) and -5/5q- (4/7) were the two most frequent aberrations. Fluorescence flaring is a main factor leading to misinterpretations. Some misclassified and missed chromosomal aberrations by M-FISH were corrected by WCP.Conclusions M-FISH is a powerful molecular cytogenetic tool in clarification of CCAs. Complementary WCP helped us identify misclassified and missed chromosomal aberrations by M-FISH. CC in combination with molecular cytogenetic techniques M-FISH and WCP can unravel complex chromosomal aberrations more precisely.

Trisomy 22 as the Sole Abnormality Is an Important Marker for Inversion 16 in Acute Myeloid Leukemia.

Inv(16) has been reported in 10%~12% of acute myeloid leukemia (AML), mostly being associated with the M4Eo subtype, and is associated with a relatively favorable outcome. However, it is a cryptic rearrangement and often difficult to recognize in conventional cytogenetics (CC). Trisomy 22 is an uncommon karyotypic aberration in AML and is often associated with inv(16)(p13q22). In order to explore the value of trisomy 22 in the diagnosis of AML with inv(16), dual-color interphase fluorescence in situ hybridization (FISH) was performed in 19 AML cases with trisomy 22 abnormality. The probe was two-color break apart probe for CBFb with SpectrumRed on the centromeric side and SpectrumGreen on the telomeric side. And the results were compared with that of R-banding CC. CC did not reveal inv(16) in any of the 19 AML with trisomy 22, but FISH analysis showed inv(16) in 11 cases and del(16)(q22) in one case. Among 11 cases with inv(16), 9 were trisomy 22 as the sole abnormality, one was complicated with trisomy 8, and one was del(16)(q22). Four AML patients with trisomy 22 and inv(16) were analyzed by multiplex FISH (M-FISH) which revealed trisomy 22 only. This study further confirmed that trisomy 22 as the sole abnormality can be regarded as an important marker for the inv(16) in AML.

Application of multiplex FISH, CGH and MSSCP techniques for cytogenetic and molecular analysis of transitional cell carcinoma (TCC) cells in voided urine specimens

Multiplex FISH (UroVysion), Comparative Genomic Hybridization (CGH), and Multitemperature Single-Strand Conformation Polymorphism (MSSCP) were applied for non-invasive diagnosis and prognosis of bladder cancer. The UroVysion test was positive in 80% of patients with pT1 and in 100% of patients with either pT2 or pT3 tumours. Tumours with pT3T4 stages were characterized by high numbers of chromosomal imbalances, detected by CGH. The mutation of the p53 gene was detected in 16% of patients, but only in those with pT2 or pT3 tumours.