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David R Betts

Publications and source records attributed to David R Betts.

18 recordsLinked to original sources
PubMed2007

Array comparative genomic hybridization reveals unbalanced gain of the MYCN region in Wilms tumors.

Wilms tumor (WT) is one of the most common solid tumors in childhood. It is characterized by a nonrandom pattern of chromosomal aberrations whose clinical significance is still uncertain. To gain further insight into different genetic events and their corresponding biological role, conventional cytogenetics and array comparative genomic hybridization (array CGH) were performed on 13 tumor samples. In two of these, array CGH revealed, together with other aberrations, a low-level amplification and an unbalanced gain in the region of chromosome bands 2p23 approximately p24 that encompass the MYCN gene. Both events were confirmed with a MYCN-specific fluorescence in situ hybridization probe, which showed a signal pattern consistent with a small homogenous staining region in one case. In addition, mRNA expression levels for MYCN were determined by quantitative reverse-transcriptase polymerase chain reaction and revealed that gain of chromosomal material was reflected in enhanced levels of MYCN mRNA in both tumors, whereby also additional tumors showed increased MYCN expression. Therefore, our findings suggest that WT is an additional childhood tumor where MYCN gain might play an important role in tumor development.

Child↗
PubMed2007

Prediction of chromosomal aneuploidy from gene expression data.

Chromosomal aneuploidy is commonly observed in neoplastic diseases and is an important prognostic marker. Here we examine how gene expression profiles reflect aneuploidy and whether these profiles can be used to detect changes in chromosome copy number. We developed two methods for detecting such changes in the gene expression profile of a single sample. The first method, fold-change analysis, relies on the availability of gene expression data from a large cohort of patients with the same disease. The expression profile of the sample is compared with that of the dataset. The second method, chromosomal relative expression analysis, is more general and requires the expression data from the tested sample only. We found that the relative expression values are stable among different chromosomes and exhibit little variation between different normal tissues. We exploited this novel finding to establish the set of reference values needed to detect changes in the copy number of chromosomes in a single sample on the basis of gene expression levels. We measured the accuracy of the performance of each method by applying them to two independent leukemia datasets. The second method was also applied to two solid tumor datasets. We conclude that chromosomal aneuploidy can be detected and predicted by analysis of gene expression profiles. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.

Aneuploidy↗
PubMed2006

SKY analysis of childhood neural tumors and cell lines demonstrates a susceptibility of aberrant chromosomes to further rearrangements.

Malignant solid tumors are commonly characterized by a large number of complex structural and numerical chromosomal alterations, which often reflect the level of genomic instability and can be associated with disease progression. The aim of this study was to evaluate whether chromosomes that harbor primary aberrations have a higher susceptibility to accumulate further alterations. We used spectral karyotyping (SKY), to compare the individual chromosomal instability of two chromosome types: chromosomes that have a primary aberration and chromosomes without an aberration, in 13 primary childhood neural tumors and seven cell lines. We found that chromosomes that contain a primary aberration are significantly (p-value<0.001) more likely to gain further structural rearrangements or to undergo numerical changes (22.6%, 36 of 159 chromosomes) than chromosomes with no initial aberration (4.9%, 54 of 1099 chromosomes). These results are highly suggestive that aberrant chromosomes in solid tumors have a higher susceptibility to accumulate further rearrangements than "normal" chromosomes.

Aneuploidy↗
PubMed2006

Cytogenetics of pineoblastoma: four new cases and a literature review.

Pineoblastoma represents a class of primitive neuroectodermal tumors (PNET) with poorly differentiated neuroepithelial cells that are histologically indistinguishable from medulloblastomas. It is a rare tumor, typically arising in childhood, and to date only a few cytogenetic cases have been published. We report four new cases in which conventional cytogenetics demonstrated the presence of an abnormal clone. The tumors showed a variety of ploidy levels, from hypodiploid to hypertetraploid. Both structural and numerical aberrations were frequent, and in three out of the four cases a large degree of cell-to-cell variation was observed. The most frequently involved chromosome in structural rearrangements was chromosome 1, observed in three of the four cases. The short arm was involved in two of the three cases; in the third case, the anomaly was in the long arm. Two cases showed unbalanced gain of chromosome 17q, one of them showing i(17)(q10). Together, the four cases illustrate the complex karyotypic nature of this tumor type and represent a step toward determining whether a nonrandom cytogenetic picture exists and how this may be related to other associated tumor types.

Adolescent↗
PubMed2006

ATM alterations in childhood non-Hodgkin lymphoma.

ATM gene alterations and impaired ATM protein expression have been described in various adult lymphoproliferative malignancies, suggesting that ATM contributes to lymphomagenesis. The present study investigated the prevalence of ATM gene and ATM protein expression alterations in sporadic childhood non-Hodgkin lymphoma (NHL). Twenty-seven cases of NHL were screened for ATM mutations by denaturing high-performance liquid chromatography (DHPLC). Direct and indirect criteria, including in silico tools, were used to classify the gene alterations. The methylation status of the ATM promoter CpG island was determined in 25 samples; ATM protein expression was assessed by Western blot in 9 lymphomas. ATM alterations were detected in 12 NHLs (44%). Ten different heterozygous base substitutions were identified in 10 NHLs (37%). Five samples (19%) were found to harbor a gene alteration considered to be a mutation or a rare variant potentially pathogenic. In one case, an ATM mutation was found in the germline. Four NHLs (44%) showed reduced or absent ATM protein expression. Except for one sample, no definite genetic or epigenetic alteration was identified to account for impaired ATM protein expression. These observations document a high prevalence of ATM gene and protein expression alterations, suggesting that ATM is involved in childhood NHL.

Adolescent↗
PubMed2006

A t(12;17)(p13;q12) identifies a distinct TEL rearrangement-negative subtype of precursor-B acute lymphoblastic leukemia.

Structural rearrangements involving the short arm of chromosome 12 are common in acute lymphoblastic leukemia (ALL) and often involve the TEL locus at 12p13. The balanced t(12;17)(p13;q12) is a rare but recurrent aberration in ALL. Whereas the TEL gene has been postulated as a likely candidate for involvement in the t(12;17), the precise molecular consequences of this translocation have not yet been elucidated. We identified a t(12;17) in 2 of 398 childhood ALL patients karyotyped at presentation in our institute. Both cases had a precursor-B immunophenotype and were CD10 negative and CD33 positive. Fluorescence in situ hybridization excluded involvement of the TEL locus in the t(12;17) and provided no evidence for concomitant cryptic deletion of the 12p commonly deleted region. Comparison of these and previously published cases demonstrates that the translocation predominately occurs in children and young adults with precursor B-ALL and is typically characterized by low CD10 expression and high CD33 expression. Our data support the involvement of a new locus telomeric to TEL in the pathogenesis of t(12;17)-positive ALL.

Adolescent↗
PubMed2006

Favorable outcome of triploid neuroblastomas: a contribution to the special oncogenesis of neuroblastoma.

There is a well-known association between patient outcome and tumor ploidy in neuroblastoma. To date, however, most clinical trials have not used this parameter for therapy stratification. Using conventional cytogenetics and fluorescence in situ hybridization (FISH), we investigated 36 tumors in terms of ploidy and chromosome 1 copy number (polysomy). In addition, interphase FISH for polysomy was performed on a second cohort of 440 neuroblastomas, together with the status of 1p, MYCN, and 11q. The main goals were as follows: (1) to assess the reliability of FISH to determine ploidy; (2) to illustrate associations between somy 1 and clinical/biologic factors; and (3) to investigate the role of somy 1 for predicting outcome. The comparison between karyotyping and FISH in the smaller cohort revealed 86% consistency between ploidy and polysomy (31/36). According to FISH, trisomic tumors in the second cohort showed structural chromosomal aberrations less frequently compared to di-/tetrasomic tumors (15 vs. 60%, P < 0.001). The portion of trisomic neuroblastomas was higher in stages 1, 2, and 4S versus stages 3 and 4 (55 vs. 24%, P < 0.001) and in children 18 months or younger versus those older than 18 months (55 vs. 19%, P < 0.001). Prognosis was significantly better for trisomic tumors versus di-/tetrasomic in the whole cohort [event-free (EFS) and overall survival (OS), P < 0.001]. In the subgroup without abnormalities of other molecular markers, EFS of trisomic neuroblastomas was better (P = 0.048), but was most likely due to an unequal stage distribution. In further subgroups, in terms of age and stage, significance between the somy groups was not reached, neither for EFS nor OS. The multivariate analyses including age, stage, chromosomal markers, and somy 1 confirmed the lack of independent prognostic power for the copy number of chromosome 1. This study demonstrates the following: (1) FISH is a practical alternative to other more labor-intensive techniques for determining ploidy; (2) trisomic tumors correlate with younger age at diagnosis, localized stage, and the lack of structural alterations; and (3) polysomy is not an independent prognostic marker. The sharp decline of trisomic tumors after the age of 18 months supports the idea of different genetic tumor entities.

Age of Onset↗
PubMed2005

ATM promoter analysis in childhood lymphoid malignancies: a brief communication.

ATM promoter hypermethylation has been recently reported in adult carcinomas, but no information is available concerning the methylation status of ATM gene promoter in childhood B-precursor acute lymphoblastic leukaemia (ALL). Furthermore, involvement of somatic ATM promoter mutations in cancer is not known. We report a complete ATM gene promoter analysis in 74 childhood lymphoid malignancies.

Adult↗
PubMed2005

A new and a reclassified ICF patient without mutations in DNMT3B and its interacting proteins SUMO-1 and UBC9.

The ICF syndrome (immunodeficiency, centromeric instability, facial anomalies) (OMIM#242860) is a rare autosomal, recessively inherited disorder. Another rare condition, ischiadic hypoplasia, renal dysgenesis, immunodeficiency, and polydactyly (IHRDIP, OMIM#243340), displays features that resemble those of the ICF syndrome. Due to the overlapping symptoms in both syndromes, we asked whether a shared underlying molecular defect exists. Two patients, each with the clinical characteristics of one of these syndromes, were subjected to conventional cytogenetic analysis and the determination of the methylation state of satellite II DNA. We found that both displayed the two hallmark features of the ICF syndrome, namely hypomethylation and centromeric instability of chromosomes 1 and 16. Therefore, we reclassified the patient previously diagnosed with the IHRDIP syndrome as an ICF patient. Since the majority of ICF patients are carriers of mutations in the methytransferase gene DNMT3B, we determined the sequence of its coding, splice site, and putative promoter region and analyzed its transcripts in both patients, without detecting any alterations. Similarly, the coding region of two DNMT3B-interacting proteins, SUMO-1 and UBC9, did not reveal mutations. With this study, the published number of patients that lack mutations in DNMT3B coding region increases to almost 40% of all ICF patients reported. It is, therefore, implied that a significant subset of ICF patients will have a yet unknown, alternative alteration, which may include the involvement of DNMT3B-interacting factors or aberrations of an independent pathway.

Abnormalities, Multiple↗
PubMed2005

CBFB-SMMHC is correlated with increased calreticulin expression and suppresses the granulocytic differentiation factor CEBPA in AML with inv(16).

The pericentric inversion of chromosome 16, inv(16)(p13q22), is associated with acute myeloid leukemia (AML) subtype M4Eo that is characterized by the presence of myelomonocytic blasts and atypical eosinophils. This rearrangement fuses the CBFB and MYH11 genes, with the latter encoding the smooth muscle myosin heavy chain (SMMHC). The myeloid transcription factor CCAAT/enhancer-binding protein alpha (CEBPA) is crucial for normal granulopoiesis. Alterations of structure and expression of CEBPA have been implicated in particular subtypes of AML. Here, we found that conditional expression of core-binding factor beta (CBFB)-SMMHC in U937 cells suppresses CEBPA protein expression and binding activity. However, CEBPA mRNA levels remained unchanged. No differences were detected in CEBPA mRNA levels in patients with inv(16) AML-M4Eo (n = 12) compared to patients with AML with a normal karyotype and M4 subtype (n = 6), whereas CEBPA protein and binding activity were significantly reduced in patients with CBFB-SMMHC. Furthermore, calreticulin, an inhibitor of CEBPA translation, was induced on mRNA and protein level in CBFB-SMMHC patients with AML and after expression of CBFB-SMMHC in the U937-cell system. Inhibition of calreticulin by siRNA restored CEBPA levels. Our results suggest that modulation of CEBPA by calreticulin represents a novel mechanism involved in the differentiation block in CBFB-SMMHC AML.

Acute Disease↗
PubMed2005

Characterization of karyotypic events and evolution in neuroblastoma.

BACKGROUND: Neuroblastoma (NB) is cytogenetically characterized by a number of non-random events. However, knowledge is limited concerning the timing of occurrence and inter-action of many of these events. METHODS: Karyotypic patterns were obtained from a study group of 49 NB tumors that had been analyzed by conventional cytogenetics combined with FISH and in some instances SKY. RESULTS: All chromosomes were involved in a numerical and structural aberration in at least one tumor. There was a positive correlation between the occurrence of MYCN and del(1p) and between del(1p) and 17q. Aberrations involving chromosomes X, 3, 19, and del(1p) could be considered early events, whereas those involving chromosomes 9, 13, 15, 18, 20, and 21 were often late events. CONCLUSIONS: This study suggests that the karyotypic patterns characterizing NB are complex. There are aberrations that can be grouped into early or late karyotypic events, but others, such as gain of 17q, are variable.

Adolescent↗
PubMed2005

Cytogenetic characterization of Ewing tumors with high-ploidy.

The formation of a high-ploidy is rare in Ewing tumor (ET) and is in contrast to some other childhood tumors such as neuroblastoma. In a series of 37 Ewing tumors analyzed by conventional cytogenetics, 4 of the 34 tumors with an abnormal clone (11.8%) demonstrated the presence of a high-ploidy clone, with a chromosome number that ranged from hypotriploid to pentaploid. All 4 contained a t(11;22)(q24;q12) and the karyotypes had further aberrations of the type that would be generally expected in ET. Numerical aberrations represented the majority of the karyotypic events identified and gain of chromosome 8 and loss of chromosomes 3, 10, 16, 19, and 22 occurred in at least 3 tumors. However, no single mechanism could be implicated to explain the karyotypic picture of the 4 cases. It is proposed that high-ploidy subgroups exist in ET and it would be potentially erroneous to group these and other cases together when determining their clinical implications.

Adolescent↗
PubMed2004

The PAX5 oncogene is expressed in N-type neuroblastoma cells and increases tumorigenicity of a S-type cell line.

Neuroblastoma is a neural crest-derived neoplasm of infancy with poor outcome in patients with advanced disease. The oncogenic transcription factor PAX5 is an important developmental regulator and is implicated in the pathogenesis of several malignancies. Screening of neuroblastoma cell lines revealed PAX5 expression in a malignant subset of neuroblastoma cells, so-called 'N-type' cells, but not in the more benign 'S-type' neuroblastoma cells. PAX5 expression was also detected in small cell lung cancer, an aggressive tumor of neural crest origin. Based on this observation we hypothesized that there could be a relationship between PAX5 expression and the more malignant phenotype of N-type cells. Stable PAX5 expression was established in several clones of the S-type cell line CA-2E. A noticeable difference in morphology of these transfectants was observed and there was also a significant increase in the proliferation rate. Moreover, PAX5 expressing clones gained the ability to form colonies in a soft agar assay, a marker of tumorigenicity. Down-regulation of PAX5 in several N-type cell lines and one small cell lung cancer cell line utilizing small interfering RNA resulted in a significant decrease in growth rate. Taken together we propose PAX5 as an important factor for the maintenance of the proliferative and tumorigenic phenotype of neuroblastoma. Our data, together with a recent study on the role of PAX genes in cancer suggest that PAX5 and other PAX transcription factors might be valuable targets for cancer therapy.

Animals↗
PubMed2004

Aberrations involving 13q12 approximately q14 are frequent secondary events in childhood acute lymphoblastic leukemia.

Chromosome 13 aberrations, particularly in the region 13q12 approximately q14, are common events in hematological neoplasms that have a clinical significance in many cases. However, although chromosome 13 aberrations are a nonrandom event in childhood acute lymphoblastic leukemia (ALL), their biological and clinical associations are limited. We have studied a consecutive series of 277 cases of childhood ALL, including 33 initially at relapse, by conventional cytogenetic analysis. In 20 cases, a chromosome 13 aberration that involved the region 13q12 approximately q14 was detected at some point during the disease. An aberration was identified in 15 of 244 (6.1%) presentation cases and 7 of 54 (13%) relapsed cases, of which in 11 cases it was shown that the abnormality arose as a secondary karyotypic event. To further characterize the cases, fluorescence in situ hybridization (FISH) using the commercially available probes LSI 13 (RB1) and D13S25 (both 13q14) was undertaken. These analyses provided additional evidence for the secondary nature of many events and suggested that 13q14 deletions may confer a growth advantage in culture because the percentage of cells containing 13q14 deletions detected by FISH was often lower than that detected by G-banding. Since 13q12 approximately q14 aberrations in childhood ALL frequently occur as secondary events, these results imply that the abnormality has implications for disease progression.

Adolescent↗
PubMed2004

Karyotypic evolution pathways in medulloblastoma/primitive neuroectodermal tumor determined with a combination of spectral karyotyping, G-banding, and fluorescence in situ hybridization.

Medulloblastomas (MBs) or primitive neuroectodermal tumors (PNETs) represent 15%-30% of pediatric brain tumors and are the most common brain tumors in children; they are rare in adults. Classification of these tumors is based on tissue morphology and is often controversial and problematic. Karyotypic analysis of these tumors using conventional cytogenetic methods is often a difficult process that may be hindered by a limited number of metaphase cells and poor chromosome morphology, often leading to only partial characterization of the chromosomal abnormalities. We investigated three primary human tumors and four cell lines (CHO-707, DAOY, D-341, and PFSK) utilizing a combination of conventional G-banding, spectral karyotyping (SKY), and fluorescence in situ hybridization (FISH) techniques. A high level of intratumoral heterogeneity was seen, with multiple numerical and structural chromosomal aberrations. The chromosomes most frequently involved in structural aberrations were chromosomes 1 (14 rearrangements), 7 (9 rearrangements), and 21 (9 rearrangements). The chromosomes most frequently involved in numerical aberrations were chromosomes 1, 12, and 13 (four cases) and chromosomes 14, 17, 19, 21, 22, and X (three cases). Numerous aberrant chromosomes were characterized only with the SKY analysis, and based on these findings multiple clones were identified, facilitating analysis of karyotypic evolution. The most frequent evolution mechanism was via polyploidization, followed by acquisition of additional numerical or structural aberrations (or both); however, the results showed that the karyotypic evolution process in these tumors is typically divergent and complex.

Adult↗
PubMed2003

Clonal expansion and not cell interconversion is the basis for the neuroblast and nonneuronal types of the SK-N-SH neuroblastoma cell line.

The ability of neuroblastoma (NB) cells to interconvert bidirectionally, in vitro, from a neuroblast (N) to a nonneuronal (S) form is a well-studied biologic phenomenon of great clinical importance. Differences in the morphologic/ biochemical characteristics and gene expression patterns of the two cell populations have been investigated extensively in an effort to unravel the transdifferentiation process. Subcloning of the SK-N-SH NB cell line has led to two morphologically distinct cell types: SH-SY5Y (N-type) and SH-EP (S-type). Karyotypic analysis combined with G-banding and SKY showed a difference between these two cell types in the copy number of the 2p15 approximately pter segment, including the MYC-N gene. FISH analysis showed an extra copy of MYC-N present in all three lines: in SK-N-SH and SH-SY5Y the majority of cells had three copies of MYC-N, whereas in SH-EP the majority had two copies and only a small cell population with three copies was present. We suggest that the simultaneous coexistence of both cell types and the subsequent clonal expansion of one over the other is a possible explanation for the phenomenon observed and not the accepted interconversion model. According to the clonal expansion model, both N and S cells are simultaneously present in both cell lines. Under certain conditions, the less-aggressive S cells can dominate over the highly aggressive N cells, which eventually lead to the formation of the SH-EP and vice-versa.

Cell Differentiation↗
PubMed2002

Interphase fluorescence in situ hybridization detection of chromosome 17 and 17q region gains in neuroblastoma: are they secondary events?

Gains of chromosome 17 and 17q region are the most frequent chromosomal abnormalities in neuroblastoma and have been associated with established prognostic indicators. Interphase fluorescence in situ hybridization (FISH) was used to define the status of chromosome 17 in near-triploid (3n) and near-diploid/tetraploid (2n/4n) primary tumors. Gains of chromosome 17 and 17q were detected in 22 and 26 tumors, respectively, in which the ploidy status was determined mainly by the copy number of chromosome 1. Four different types of gains were detected: gain of whole chromosome 17 (+17) and three partial gains (17q11.2 approximately qter, 17q21.1 approximately qter, and 17q21.3 approximately qter). The 17q11.2 approximately qter gains were found in both the 2n/4n and the 3n tumors. Gains of 17q21.1 approximately qter and 17q21.3 approximately qter were found only in the 2n/4n group, and the latter was involved always as a der(22)t(17;22)(q21;q13). A high association was found between chromosome 17 gains and 3n ploidy: +17 was detected in 93% of the 3n group and was not observed in the 2n/4n group. The +17 clone or clones were always present in combination with a clone with normal copies of chromosome 17 and, in the majority, with a +17q11.2 approximately qter clone. We conclude that interphase FISH is a sensitive method for detecting whole and partial chromosome 17 gains in neuroblastoma and can demonstrate the simultaneous presence of several clones with different status of chromosome 17 in 3n neuroblastomas. We suggest that chromosome 17 and 17q gains are not a primary event in the development of neuroblastoma.

Chromosome Aberrations↗