Characterization of 20q deletions in patients with myeloproliferative disorders or myelodysplastic syndromes

Atypical chronic myeloid leukemia with isochromosome (X)(p10): A case report

Atypical chronic myeloid leukemia (aCML) is a rare subtype of myelodysplastic/myeloproliferative neoplasm (MDS/MPN). Although recurrent chromosomal and genetic abnormalities are frequently observed in aCML, none are specific to this type of leukemia. The present study reported a case of aCML associated with i(X)(p10), a rare recurrent chromosomal abnormality of hematological malignancy. A 40-year-old female was referred to the Tokyo Medical and Dental University Hospital (Tokyo, Japan) due to slight leukocytosis and anemia. A bone marrow aspiration revealed 4% blasts and granulocytic hyperplasia with dysplasia. A G-banded cytogenetic analysis of the bone marrow cells revealed 46, X, isochromosome X(iX)(p10) in all metaphases. The percentage of the neutrophil precursors promyelocytes, myelocytes and metamyelocytes in the peripheral blood was >10% throughout the clinical course of the patient, which resulted in a diagnosis of atypical chronic myeloid leukemia. Treatment with hydroxycarbamide was not able to effectively alleviate leukocytosis, and the disease progressed with the appearance of an additional cytogenetic abnormality, t(10;17)(p13;q21). Subsequently, the patient underwent allogeneic stem cell transplantation from a sibling donor, and subsequent cytogenetic analysis revealed a normal karyotype with full donor chimerism. The isodicentric X(idicX)(q13) mutation is a similar abnormality to i(X)(p10) and may result in a loss of the X-inactive specific transcript gene located at Xq13.2, the deletion of which has been previously reported to result in the development of MDS/MPN in mice. In addition, i(X)(p10) was identified as the sole chromosomal abnormality at the diagnosis of aCML in the case of the present study, which is similar to patients from previous studies of other hematological malignancies and supports the hypothesis that i(X)(p10) may have served a primary role in the leukemogenesis of aCML.

Recurrent Cytogenetic Abnormalities in Myeloproliferative Neoplasms and Chronic Myeloid Leukemia

The commonest types of myeloproliferative neoplasm (MPN) have remarkably similar recurrent chromosome abnormalities, but with varying incidence and prognostic implications. After a clear decade of treatment of chronic myeloid leukemia (CML) with tyrosine kinase inhibitors, the differing prognostic implications of abnormalities additional to the Ph chromosome are being revealed. This chapter provides a description of the main chromosome abnormalities in MPN and CML and their clinical implications in a time of rapid changes in both the application of new diagnostic techniques and the introduction of targeted therapies.

Clinical significance of newly emerged isolated del(20q) in patients following cytotoxic therapies

Deletion 20q is a common chromosomal abnormality in myeloid neoplasms. Detection of del(20q) in patients following cytotoxic therapies raises concerns for an emerging therapy-related myeloid neoplasm. In this study, we identified 92 patients who acquired isolated del(20q) in their bone marrow following cytotoxic therapies for malignant neoplasms. Seventy-six patients showed interstitial and sixteen patients showed terminal 20q deletion. The median interval from prior cytotoxic therapies to detection of del(20q) was 58 months (range, 5-213 months). With a median follow-up of 23 months (range, 1-183 months), 21 (23%) patients developed therapy-related myeloid neoplasm and 71 (77%) patients did not. In patients who developed therapy-related myeloid neoplasm, del(20q) presented in a higher percentage of metaphases (60 vs 25%, P<0.0001); persisted for a longer period of time (24 vs 10 months, P=0.0487); and was more often a terminal deletion (33 vs 13%, P=0.0006) compared with patients who did not develop therapy-related myeloid neoplasm. Clonal evolution was only detected in patients with therapy-related myeloid neoplasm (4 patients, 19%). We conclude that del(20q) emerging after cytotoxic therapy represents an innocuous finding in more than two-thirds of patients. In patients who develop a therapy-related myeloid neoplasm, del(20q) often involves a higher percentage of metaphases, persists longer and more frequently is a terminal rather than an interstitial deletion.

Three-way translocation (X;20;16)(p11;q13;q23) in essential thrombocythemia implicates NFATC2 in dysregulation of CSF2 expression and megakaryocyte proliferation

Essential thrombocythemia (ET) is a myeloproliferative neoplasm essentially characterized by excessive production of platelets. Molecular pathogenesis of ET is linked in approximately half of the patients to intracellular cytokine signaling dysregulation as a result of thrombopoietin receptor or Janus kinase 2 (JAK2) mutations. However, genetic defects underlying cytokine transcription have not been associated with ET. Using molecular cytogenetics and whole-genome array analyses, we uncovered a submicroscopic deletion at 20q13.2 in a JAK2V617F-positive ET patient with an acquired complex chromosome translocation. The deletion encompassed the nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 (NFATC2) gene that encodes a transcription factor involved in the regulation of hematopoietic cytokines. RNA interference-mediated suppression of NFATC2 mRNA or pharmacological inhibition of NFATC2 protein with 11R-VIVIT in cultured JAK2V617F-positive SET-2 megakaryocytes increased colony stimulating factor 2 (granulocyte-macrophage) (CSF2) mRNA and promoted cell proliferation. Moreover, impairment of NFATC2-calcineurin interaction with 11R-VIVIT further reduced the transcription of the NFATC2 gene. Antibody-mediated neutralization of CSF2 cytokine in inhibitor-treated cells prevented 11R-VIVIT-induced cell proliferation, indicating that impairment of NFATC2-calcineurin interaction promotes megakaryocyte proliferation through up-regulation of CSF2 transcription. Our results suggest a model in which haplo-insufficiency of NFATC2 cooperates with activation of the JAK-STAT signaling pathway in the pathogenesis of JAK2V617F-positive ET with del(20q). These results further indicate that pathogenesis of ET may be linked to genetic defects of other transcription factor genes involved in the regulation of cytokine expression.

Microarray CGH analyses of chromosomal 20q deletions in patients with hematopoietic malignancies

The chromosomal abnormality del(20q) is mostly found in various myeloid disorders, including myelodysplastic syndromes, myeloproliferative neoplasms, and acute myeloid leukemia. Here, microarray comparative genomic hybridization (aCGH) analyses of 14 patients cytogenetically confirmed to carry the del(20q) aberration in their bone marrow demonstrated that all deletions were interstitial and both the proximal and distal breakpoints varied among individuals. The centromeric breakpoints were located in the 20q11.21-12 region, and the telomeric breakpoints, in the 20q13.13-13.33 region. The extent of the deletion ranged from 11.2 to 27.3 Mb, and the commonly deleted region (CDR) was estimated to be 7.2 Mb in size. Two commonly retained regions were present, the proximal region adjacent to the centromere (20q11.1-11.21) and a subtelomeric one (20q13.33). The CDR of our study was more distal than reported previously. Furthermore, in three patients fluorescence in situ hybridization (FISH) demonstrated that del(20q) cells were detected at a higher frequency in the karyotype analyses than by interphase FISH and aCGH analyses. As the size and breakpoints of del(20q) have been reported to vary among patients, the presence of one or more tumor suppressor genes in the CDR has been suggested. Our study will contribute to the identification of candidate tumor suppressor genes on 20q.

Improvement of pancytopenia and thrombocytopenia with decreasing mosaicism for isochromosome Xp

We report the unique association of variable constitutional mosaicism 46,X, i(X)(p10)/46,XX with recurrent thrombocytopenia in a child with failure to thrive and apnea in infancy. Her bone marrow had equal distribution of the normal and abnormal cell lines at diagnosis, at nearly 6 years of age. Improvement of her pancytopenia and thrombocytopenia was concurrent with a decreasing level of mosaicism observed in multiple studies over the next 3 years. This suggests that extra copies of genes on the p-arm are inhibitory to blood cell maturation, with long-term selection against the i(Xp)-containing cells.

Isochromosome (X)(p10) in hematologic disorders: FISH study of 14 new cases show three types of centromere signal patterns

Though X chromosome anomalies are uncommon in hematologic malignancies, isodicentric X chromosomes, idic(X)(q13), with break and fusion points at Xq13 are well known among older females with de novo myelodysplasia. In contrast, only 17 patients with X isochromosomes involving break and fusion points at the centromere i(X)(p10) have been published, to our knowledge. We present 14 new patients with i(X)(p10) identified by G-banding and further characterized by fluorescence in situ hybridization (FISH) using probes for the X p-arm, X alpha-satellite DNA (DXZ1), and the XIST gene (Xq13). These anomalies each had an X p-arm probe signal on either side of a single centromeric FISH signal, thus they are monocentric isochromosomes. On the basis of FISH, the following three centromeric patterns were identified: (1) centromere signal same size as normal X, (2) centromere signal larger than normal X, and (3) centromere signal smaller than normal X. These centromere patterns may be related to the mechanism of i(X)(p10) formation. In 9 (64%) of 14 patients, the i(X)(p10) was the sole anomaly, attesting to its pathogenic potential. Our series, when collated with information on previously reported cases of i(X)(p10), show that this anomaly is associated with females with a median age 74 years, though patients from 3.75 to 49 years, including a 17-year-old in the present cohort, have been described. i(X)(p10) is observed in a wide range of hematologic malignancies, including myeloid and lymphoid disorders, as well as a patient with therapy-related AML in the present series. i(X)(p10) has been reported in occasional males, indicating that this anomaly can arise from active X chromosomes. It is not known whether i(X)(p10) arises randomly from the active or inactive X chromosome in female patients.

Cytogenetic and molecular aspects of Philadelphia negative chronic myeloproliferative disorders: clinical implications

Chronic myeloproliferative disorders (CMPD) are clonal disorders of the hematopoietic stem cell. The myeloid lineage shows increased proliferation with effective maturation, while peripheral leukocytosis, thrombocytosis or elevated red blood cell mass are found. In Philadelphia negative CMPD recurrent cytogenetic abnormalities occur, but no specific abnormality has been defined to date. The spectrum of cytogenetic aberrations is heterogeneous ranging from numerical gains and losses to structural changes including unbalanced translocations. The most common chromosomal abnormalities are 20q-, 13q-, 12p-, +8, +9, partial duplication of 1q, balanced translocations involving 8p11 and gains in 9p. Cytogenetic analysis of CMPD by conventional or molecular techniques has an important role in establishing the diagnosis of a malignant disease, adding also more information for disease outcome. Molecular studies may detect the possible role of candidate genes implicated in the neoplastic process, addressing new molecular target therapies. FIP1L1/PDGFRalpha rearrangements, as well as alterations of PDGFRbeta or FGFR1 gene have been found to be associated with specific types of CMPD. Recently, a novel somatic mutation, JAK2V617F, has been reported in most of the polycthemia vera (PV) patients, as well as in a lower percentage in essential thrombocythemia (ET) or idiopathic myelofibrosis (IMF) patients. This finding represents the most important advance in understanding of the molecular mechanisms underlined the pathogenesis of CMPD, contributing to the classification and management of patients.

Cytogénétique et génétique moléculaire dans la myélofibrose avec métaplasie myéloïde et dans la polyglobulie de Vaquez

Myelofibrosis with myeloid metaplasia (MMM) is a rare myeloproliferative disorder (MPD) characterized by clonal proliferation of hematopoietic progenitors. 40-50% of karyotypes on blood (or more rarely on bone marrow) revealed at least one abnormality: 30% at diagnosis and 90% in blastic transformation phase. A minority of patients with newly diagnosed polycythemia vera (PV) presented chromosomal abnormalities in their myeloid cells. The most frequent visible alteration in MMM and PV is a 20q deletion, also characterized in other MPDs and myeloid malignancies. Among other chromosomal changes, deletion 13q is more common in MMM than in other MPDs, trisomy 9 and 9p alterations appear more frequent in PV. Cytogenetic studies have disclosed cryptic anomalies and pointed out the high frequency of 9p alterations. JAK2 (V617F) mutation was found in almost all PV patients and near half of MMM patients. This molecular abnormality takes an increased importance in the knowledge of the physiopathology of MPDs, particularly in PV and also in prognosis of MMM patients.

Prognostic significance of del(20q) in patients with hematological malignancies

Deletions of the long arm of chromosome 20 represent a common chromosomal abnormality associated with myeloid malignancies, in particular with myeloproliferative disorders (MPD), myelodysplastic syndromes (MDS), and acute myeloid leukemia (AML). Using G-banding cytogenetic techniques, we found clones with del(20q) in 36 patients with hematological malignancies examined in our laboratory during the years 2001-2003: in 23 patients as a sole cytogenetic aberration and in 13 patients together with other chromosomal changes. Fluorescence in situ hybridization (FISH) with a probe specific for the 20q12 region was used in all cases to confirm the presence of the clone with deletion. For patients with additional or complex chromosomal rearrangements, multicolor FISH (M-FISH) analysis was performed. Statistical evaluation of the prognostic impact of sex, age, diagnosis, and karyotype was performed. The survival time correlated with the type of chromosomal aberration; no significant differences in survival were found for sex, age, and diagnosis.

Reverse painting highlights the origin of chromosome aberrations

Reverse chromosome painting, as the opposite of forward chromosome painting, means that an abnormal chromosome of interest is recovered by flow sorting or by chromosome microdissection, amplified and labelled by DOP-PCR and hybridized onto normal metaphases of optimal quality. This provides rapid and unequivocal information about the chromosomal origin on the aberrant chromosome in one hybridization. Not only will the specific chromosome(s) involved be identified, but also the subchromosomal origin, including the breakpoints. The method has been used for over 10 years and has proven to be very useful for resolving complex chromosome rearrangements in a variety of different applications, both as a research tool and for clinical purposes in pre- and postnatal diagnosis.

Characterization of psu dic(6;5)(p21.3;q13) with reverse chromosome painting in a patient with secondary myelodysplastic syndrome following treatment for multiple myeloma

We report a case of a psu dic(6;5)(p21.3;q13) in a patient with secondary myelodysplastic syndrome (sMDS) following treatment for multiple myeloma. The abnormal chromosome was isolated by flow karyotyping and initially identified by reverse chromosome painting. The findings were then confirmed by forward painting. The value of flow karyotyping as a diagnostic technique in hematologic malignancies is discussed.

Double Philadelphia masquerading as chromosome 20q deletion - a new recurrent abnormality in chronic myeloid leukaemia blast crisis

The most common abnormality of chromosome 20 in haematological malignancy is deletion of the long arm [del(20q)]. These interstitial deletions are variable in size and are seen in both premalignant haematological conditions and acute myeloid neoplasia. A commonly deleted region (CDR), mapped within the 20q11.2/q13.1 segment with an estimated size of 1.7 Mbp, is considered to present a primary genetic lesion marking a gene(s), the loss of which is responsible for the pathogenesis of these haematological disorders. While a small number of recurrent translocations involving chromosome 20 have also been reported, no recurrent aberration of this chromosome has been associated with myeloid disease progression. We present nine cases of Philadelphia (Ph)-positive chronic myeloid leukaemia (CML) in which deletions of chromosome 20 were also detected by conventional karyotyping. In six cases, fluorescent in situ hybridization (FISH) mapping confirmed a del(20q) which corresponded to the myeloid CDR. In the remaining three cases however, the presumed del(20q) marker was shown to be the result of an unbalanced translocation between band 20p11 and a second copy of the Ph chromosome. This new abnormality, termed dic(20;Ph) for short, was identical to a del(20)q by G-banding, and combined duplication of the breakpoint cluster region and Abelson murine leukaemia viral oncogene homologue (BCR-ABL) fusion with loss of the 20p11-pter segment. In all three cases, the dic(20;Ph) was associated with disease progression and therefore represents a new recurrent abnormality in CML blast crisis.

Myeloproliferative disorders

The myeloproliferative disorders (MPDs) are a group of pre-leukaemic disorders characterized by proliferation of one or more lineages of the myelo-erythroid series. Unlike the Philadelphia chromosome in chronic myeloid leukaemia, there is no pathognomonic chromosomal abnormality associated with the MPDs. Chromosomal abnormalities are seen in 30-40% of patients with polycythaemia vera (PV) and idiopathic myelofibrosis (IMF) and seem to indicate a poor prognosis. On the other hand, chromosomal abnormalities are rare in essential thrombocythaemia. Consistent acquired changes seen at diagnosis include deletion of the long arm of chromosome 20, del(13q), trisomy 8 and 9 and duplication of parts of 1q. Furthermore del(20q), trisomy 8 and dupl(lq) all arise in multipotent progenitor cells. Molecular mapping of 20q deletions and, to some extent, 13q deletions has identified a number of candidate target genes, although no mutations have yet been found. Finally, translocations associated with the rare 8p11 myeloproliferative syndrome and other atypical myeloproliferative disorders have permitted the identification of a number of novel fusion proteins involving fibroblast growth factor receptor-1.

Identification of candidate genes on chromosome band 20q12 by physical mapping of translocation breakpoints found in myeloid leukemia cell lines

Deletions of the long arm of chromosome 20 have been reported in a wide range of myeloid disorders and may reflect loss of critical tumor suppressor gene(s). To identify such candidate genes, 65 human myeloid cell line DNAs were screened by polymerase chain reaction (PCR) for evidence of allelic loss at 39 highly polymorphic loci on the long arm of chromosome 20. A mono-allelic pattern was present in eight cell lines at multiple adjacent loci spanning the common deleted regions (CDRs) previously defined in primary hematological samples, suggesting loss of heterozygosity (LOH) at 20q. Fluorescence in situ hybridization (FISH) was then performed using a series of yeast artificial chromosomes (YACs) ordered in the CDR, and in five of eight cell lines, the deletions resulted from cytogenetically detectable whole chromosomal loss or large interstitial deletion, whereas in another cell line deletion was associated with an unbalanced translocation. LOH in the CMK megakaryocytic cell line, which has a hypotetraploid karyotype, was associated with a der(20)t(1;20)(q32;q12)x2 leading to complete deletion of the CDR. Three additional unbalanced translocations were found within the CDR and all three breakpoints mapped to a single YAC. We then used a series of P1 artificial chromosomes (PACs) spanning this YAC clone, and two PACs produced 'split' signals suggesting that they each span one of these breakpoints. Exon trapping using PACs that overlap the breakpoint regions yielded portions of six genes and evaluation of these genes as candidate tumor suppressor genes is underway. The limited information available about these genes suggests that the h-l(3)mbt gene is the most attractive candidate.

Identification of novel regions of allelic loss in ependymomas by high-resolution allelotyping with 384 microsatellite markers

OBJECT

Ependymomas are rare glial neoplasms; little is known about the molecular pathogenesis of this tumor entity. In a previous study the authors found multiple genomic imbalances in ependymomas resected in 20 adults and eight children, including loss of chromosomes 1p, 6, 16, 17, 19q, 20q, and 22q, as well as gain of chromosomes 4q, 5q, 7q, 9q, and 12q on comparative genomic hybridization. The aim of this study was to map in more detail the commonly affected regions in ependymomas.

METHODS

A comprehensive allelotype analysis of 16 ependymomas was conducted using 384 microsatellite markers that span the 22 autosomes. Based on this high-resolution loss of heterozygosity analysis, multiple overlapping deletion regions were identified as follows: 6q25.2-27, 16p12-13.1, 16q22.3-24.1, 17q22-24, 19q12-13.2, 20q13.2-13.3, and 22q13.1-13.3.

CONCLUSIONS

These data confirmed previous reports that loss of chromosomes 17 and 22 were common in ependymomas. Moreover, the authors were able to identify loss of chromosomes 13, 16, 19, and 20 as novel findings in ependymomas. It is believed that potential tumor suppressor genes that reside in these commonly deleted regions may contribute to the molecular tumorigenesis of ependymomas.

Acquired, nonrandom chromosomal abnormalities associated with the development of acute promyelocytic leukemia in transgenic mice

We previously generated a transgenic mouse model for acute promyelocytic leukemia (APL) by expressing the promyelocytic leukemia (PML)-retinoic acid receptor (RARalpha) cDNA in early myeloid cells. This fusion protein causes a myeloproliferative disease in 100% of animals, but only 15-20% of the animals develop acute leukemia after a long latency period (6-13 months). PML-RARalpha is therefore necessary, but not sufficient, for APL development. The coexpression of a reciprocal form of the fusion, RARalpha-PML, increased the likelihood of APL development (55-60%), but did not shorten latency. Together, these results suggested that additional genetic events are required for the development of APL. We therefore evaluated the splenic tumor cells from 18 transgenic mice with APL for evidence of secondary genetic events, by using spectral karyotyping analysis. Interstitial or terminal deletions of the distal region of one copy of chromosome 2 [del(2)] were found in 1/5 tumors expressing PML-RARalpha, but in 11/13 tumors expressing both PML-RARalpha and RARalpha-PML (P < 0.05). Leukemic cells that contained a deletion on chromosome 2 often contained additional chromosomal gains (especially of 15), chromosomal losses (especially of 11 or X/Y), or were tetraploid (P </= 0.001). These changes did not commonly occur in nontransgenic littermates, nor in aged transgenic mice that did not develop APL. These results suggest that expression of RARalpha-PML increases the likelihood of chromosome 2 deletions in APL cells. Deletion 2 appears to predispose APL cells to further chromosomal instability, which may lead to the acquisition of additional changes that provide an advantage to the transformed cells.

Chromosome 20 deletions in myeloid malignancies: reduction of the common deleted region, generation of a PAC/BAC contig and identification of candidate genes. UK Cancer Cytogenetics Group (UKCCG)

Deletion of the long arm of chromosome 20 represents the most common chromosomal abnormality associated with the myeloproliferative disorders (MPDs) and is also found in other myeloid malignancies including myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML). Previous studies have identified a common deleted region (CDR) spanning approximately 8 Mb. We have now used G-banding, FISH or microsatellite PCR to analyse 113 patients with a 20q deletion associated with a myeloid malignancy. Our results define a new MPD CDR of 2.7 Mb, an MDS/AML CDR of 2.6 Mb and a combined 'myeloid' CDR of 1.7 Mb. We have also constructed the most detailed physical map of this region to date--a bacterial clone map spanning 5 Mb of the chromosome which contains 456 bacterial clones and 202 DNA markers. Fifty-one expressed sequences were localized within this contig of which 37 lie within the MPD CDR and 20 within the MDS/AML CDR. Of the 16 expressed sequences (six genes and 10 unique ESTs) within the 'myeloid' CDR, five were expressed in both normal bone marrow and purified CD34 positive cells. These data identify a set of genes which are both positional and expression candidates for the target gene(s) on 20q.

Refinement of the smallest commonly deleted segment of chromosome 20 in malignant myeloid diseases and development of a PAC-based physical and transcription map

A deletion of the long arm of chromosome 20, del(20q), is a recurring abnormality in malignant myeloid diseases. In previous studies, we delineated a commonly deleted segment (CDS) of 5 Mb within band 20q12 flanked by D20S206 (proximal) and D20S481 (distal). We have generated a detailed physical map of P1 artificial chromosome (PAC) clones of this interval as well as a transcriptional map. The contig consists of 81 clones to which 152 markers (27 genes, 45 unique expressed sequence tags (ESTs) or UniGenes, 24 polymorphisms, and 56 sequence-tagged sites) have been mapped. Using PAC clones for fluorescence in situ hybridization analysis of myeloid leukemia cells with reciprocal translocations of 20q, or unbalanced rearrangements leading to loss of 20q, we have narrowed the CDS to an approximately 250-kb interval encompassing two overlapping PACs, P201E16 and P29M7 (between EST AA368224 and D20S481). This interval is gene-rich and contains 5 characterized genes, 4 UniGenes, and 9 single ESTs. The development of a transcriptional map and the identification of the smallest CDS will facilitate the molecular cloning of a myeloid leukemia suppressor gene on 20q.

Chromosomal instability in acute myelocytic leukemia and myelodysplastic syndrome patients among atomic bomb survivors

To clarify the mechanism of leukemogenesis in atomic bomb survivors, leukemic cells were investigated using fluorescence in situ hybridization (FISH) analysis on the basis of conventional G-banding in patients with a history of radiation exposure and also in de novo patients. Conventional G-banding showed higher incidences (p < 0.005) of structural and numerical abnormalities without any specific types of chromosome aberrations in the group exposed to a dose of more than one Gy, compared to the non-exposed group. FISH analysis revealed significantly higher incidences (P < 0.05) of subclones with monosomy 7 and deletion of the 20q13.2 region, which were not found in conventional cytogenetic analysis in the exposed group (more than one Gy) compared to the non-exposed controls. Furthermore, segmental jumping translocation (SJT) of the c-MYC gene region was observed only in the exposed group. These chromosomal instability suggested that the leukemic cells from the heavily exposed patients contained persistent cellular genetic instability which may strongly influence the development of leukemia in people exposed to radiation.

The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors

DNA methylation in mammals is required for embryonic development, X chromosome inactivation and imprinting. Previous studies have shown that methylation patterns become abnormal in malignant cells and may contribute to tumorigenesis by improper de novo methylation and silencing of the promoters for growth-regulatory genes. RNA and protein levels of the DNA methyltransferase DNMT1 have been shown to be elevated in tumors, however murine stem cells lacking Dnmt1 are still able to de novo methylate viral DNA. The recent cloning of a new family of DNA methyltransferases (Dnmt3a and Dnmt3b) in mouse which methylate hemimethylated and unmethylated templates with equal efficiencies make them candidates for the long sought de novo methyltransferases. We have investigated the expression of human DNMT1, 3a and 3b and found widespread, coordinate expression of all three transcripts in most normal tissues. Chromosomal mapping placed DNMT3a on chromosome 2p23 and DNMT3b on chromosome 20q11.2. Significant overexpression of DNMT3b was seen in tumors while DNMT1 and DNMT3a were only modestly over-expressed and with lower frequency. Lastly, several novel alternatively spliced forms of DNMT3b, which may have altered enzymatic activity, were found to be expressed in a tissue-specific manner.

Identification of multiple copies of a 20q-chromosome in a case of myelodysplastic syndrome: a FISH study

In myelodysplastic syndromes (MDS) karyotypic aberrations identify subgroups of patients with distinct clinical-morphological features and can be relevant in risk assessment of developing leukemia. Often conventional cytogenetic analysis is not sufficiently informative due to the presence of partially or completely unrecognizable chromosome markers. By chromosome microdissection (MD) and fluorescence in situ hybridization (FISH) we investigated the nature of a karyotypic marker occurring in multiple copies in one case of MDS arisen in a patient previously treated for breast cancer. Results showed dicentrics derived from telomeric fusion between interstitially deleted 20q-chromosomes. The abnormal karyotype resulted into polysomy for a deleted chromosome 20q.

Molecular genetics and cytogenetics of myeloproliferative disorders

The myeloproliferative disorders are believed to represent clonal malignancies resulting from transformation of a pluripotent stem cell. X-inactivation patterns of peripheral blood cells have been proposed as a useful diagnostic tool but this method is limited by the finding of a clonal X-inactivation pattern in a significant proportion of normal elderly women. There is no pathognomonic chromosomal abnormality associated with the myeloproliferative disorders. However, consistent acquired cytogenetic changes include del(20q), del(13q), trisomy 8 and 9 and duplication of segments of 1q, all of which have been observed at diagnosis or before cytoreductive therapy and therefore represent early lesions which contribute to the pathogenesis of these disorders. Although, the acquired molecular defects underlying most myeloproliferative disorders have not yet been elucidated, translocations associated with the rare 8p11 syndrome have permitted identification of a novel fusion protein. The role of a number of candidate genes in the other myeloproliferative disorders has also been studied, but no mutations have been identified so far. It is likely that a number of genes will be involved, given the varied phenotypes of the diseases. Identification of causal genes will be of considerable interest to both clinicians, who currently lack a specific and sensitive diagnostic test, and scientists interested in fundamental issues of stem cell behaviour.

Comparative genomic hybridization: a comparison with molecular and cytogenetic analysis

Comparative genomic hybridization (CGH) is a powerful technique for detecting copy number changes throughout the genome. We describe the development of a versatile image analysis program for CGH studies. Several methods for the production of metaphases which give optimum hybridization signals have also been assessed. CGH analysis was performed on DNA samples from several different and clinically relevant specimens: amniotic fluid cells trisomic for a single chromosome, lymphoblastoid cell lines with abnormalities involving single chromosome bands, malignant cell lines and biopsy material from primary ovarian carcinomas. The results were compared with those derived from G-banding, chromosome painting, and molecular genetic techniques. Our data demonstrate that CGH was able to detect a wide range of quantitative genetic alterations including duplication or deletion of single chromosome bands. CGH analysis also indicated the presence of genetic abnormalities that were not detected by other cytogenetic or molecular approaches. Moreover, our CGH methodology allowed the ready comparison of CGH results from different tumors, a process which greatly facilitated identification of shared genetic changes.

Improved Sensitivity of BCR-ABL Detection: A Triple-Probe Three-Color Fluorescence In Situ Hybridization System

Chronic myeloid leukemia is a clonal stem cell disorder associated with the Philadelphia (Ph) translocation [t(9; 22) (q34; q11)]. As a result of the Ph translocation, parts of the ABL and BCR genes become fused. Cytogenetic quantification of Ph+ metaphases can be used to monitor patient response to treatment but is of limited sensitivity and applies only to cycling cells. Fluorescence in situ hybridization (FISH) with probes from the BCR and ABL regions can also identify the Ph translocation in interphase cells. Established systems for the detection of fusion genes by FISH rely on colocalization of two different probes but are associated with a high rate of false-positive results. We have introduced a third probe labeled with a different fluorochrome to create a triple-probe/three-color system that permits identification of both the Ph chromosome and the derivative 9 chromosome in Ph+ cells. This system was used to determine the frequency of interphase cells carrying the BCR-ABL fusion gene in bone marrow and peripheral blood granulocytes from patients showing variable cytogenetic responses to interferon. Our data show that the triple-probe/three-color approach allows highly sensitive detection of residual disease. Moreover, this method is readily applicable to the analysis of other chromosome translocations.

Improved Sensitivity of BCR-ABL Detection: A Triple-Probe Three-Color Fluorescence In Situ Hybridization System

Chronic myeloid leukemia is a clonal stem cell disorder associated with the Philadelphia (Ph) translocation [t(9; 22) (q34; q11)]. As a result of the Ph translocation, parts of the ABL and BCR genes become fused. Cytogenetic quantification of Ph+ metaphases can be used to monitor patient response to treatment but is of limited sensitivity and applies only to cycling cells. Fluorescence in situ hybridization (FISH) with probes from the BCR and ABL regions can also identify the Ph translocation in interphase cells. Established systems for the detection of fusion genes by FISH rely on colocalization of two different probes but are associated with a high rate of false-positive results. We have introduced a third probe labeled with a different fluorochrome to create a triple-probe/three-color system that permits identification of both the Ph chromosome and the derivative 9 chromosome in Ph+ cells. This system was used to determine the frequency of interphase cells carrying the BCR-ABL fusion gene in bone marrow and peripheral blood granulocytes from patients showing variable cytogenetic responses to interferon. Our data show that the triple-probe/three-color approach allows highly sensitive detection of residual disease. Moreover, this method is readily applicable to the analysis of other chromosome translocations.

The application of FISH techniques for physical mapping in the dog (Canis familiaris)

The abundance of CA/GT repeats in the DNA of the dog (Canis familiaris) has established the importance of polymorphic microsatellites in the development of a low density map of the canine genome. The assignment of linkage groups of markers to chromosomes by physical mapping requires reliable cytogenetic techniques for routine production of metaphase cells. The dog has 78 chromosomes, many of which are smaller and more contracted than those of other mammals. Although the molecular study of inherited disease in dogs has important implications for both improved welfare in dogs and the provision of animal models for human diseases, the small size and large number of chromosomes in the canine genome has discouraged the inclusion of cytogenetic analysis in the planning of relevant research protocols. In this report, Fluorescence In Situ Hybridization (FISH) techniques have been optimized for the physical mapping of probes in C. familiaris. A method to obtain a good yield of early and midmetaphases from short-term peripheral blood cultures and the optimal conditions for hybridization and detection of probes is described. Thirteen microsatellite-containing cosmid probes from a canine genomic library in pWE15, a highly repetitive probe (human ribosomal DNA pHr14E3), and a human X Chromosome (Chr) paint have been mapped. Six microsatellites, two ribosomal sites, and the human paint have been assigned to specific chromosomes.