[Show abstract][Hide abstract] ABSTRACT: Hepatosplenic T-cell lymphoma (HSTL) is an aggressive lymphoma cytogenetically characterized by isochromosome 7q [i(7)(q10)], of which the molecular consequences remain unknown. We report here results of an integrative genomic and transcriptomic (expression microarray and RNA-sequencing) study of six i(7)(q10)-positive HSTL cases, including HSTL-derived cell line (DERL-2), and three cases with ring 7 [r(7)], the recently identified rare variant aberration. Using high resolution array CGH, we profiled all cases and mapped the common deleted region (CDR) at 7p22.1p14.1 (34.88 Mb; 3506316-38406226 bp) and the common gained region (CGR) at 7q22.11q31.1 (38.77 Mb; 86259620-124892276 bp). Interestingly, CDR spans a smaller region of 13 Mb (86259620-99271246 bp) constantly amplified in cases with r(7). In addition, we found that TCRG (7p14.1) and TCRB (7q32) are involved in formation of r(7), which seems to be a byproduct of illegitimate somatic rearrangement of both loci. Further transcriptomic analysis has not identified any CDR-related candidate tumor suppressor gene. Instead, loss of 7p22.1p14.1 correlated with an enhanced expression of CHN2 (7p14.1) and the encoded β2-chimerin. Gain and amplification of 7q22.11q31.1 are associated with an increased expression of several genes postulated to be implicated in cancer, including RUNDC3B, PPP1R9A and ABCB1, a known multidrug resistance gene. RNA-sequencing did not identify any disease-defining mutation or gene fusion. Thus, chromosome 7 imbalances remain the only driver events detected in this tumor. We hypothesize that the Δ7p22.1p14.1-associated enhanced expression of CHN2/β2-chimerin leads to downmodulation of the NFAT pathway and a proliferative response, while upregulation of the CGR-related genes provides growth advantage for neoplastic δγT-cells and underlies their intrinsic chemoresistance. Finally, our study confirms the previously described gene expression profile of HSTL and identifies a set of 24 genes, including three located on chromosome 7 (CHN2, ABCB1 and PPP1R9A), distinguishing HSTL from other malignancies.
PLoS ONE 07/2014; 9(7):e102977. DOI:10.1371/journal.pone.0102977 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: AIMS: Chronic lymphocytic leukemia (CLL) is the most common adult leukemia with a very heterogeneous course. Progress in molecular genetic characterization of CLL has confirmed the prognostic role of unbalanced chromosomal abnormalities currently defined by molecular cytogenetic methods: conventional karyotyping and FISH. However, a significant percentage of genomic abnormalities escapes routine investigation due to the limitations of these methods. It is presently clear that some of these aberrations have impact on prognosis and disease progression. METHODS: We examined copy number changes in the tumor genomes of 50 CLL patients using bacterial artificial chromosome (BAC) and/or oligonucleotide array platforms. We compared the results of arrayCGH with those obtained by FISH and conventional cytogenetics and evaluated their clinical importance. RESULTS: A total of 111 copy number changes were detected in 43 patients (86%) with clonal abnormalities present in at least 23% of the cells. Moreover, 14 patients (28%) were found to have 39 genomic changes that had not been detected by standard cytogenetic and/or FISH analyses. These included possibly prognostically important recurrent 2p and 8q24 gains. The most frequent unbalanced changes involved chromosomes 18, 7, 3, 9 and 17. We also determined the minimal deleted region on chromosome 6q in 7 cases by chromosome 6/7 specific array. CONCLUSIONS: The results showed that a subset of potentially significant genomic aberrations in CLL is being missed by the current routine techniques. Further, we clearly demonstrated the robustness, high sensitivity and specificity of the arrayCGH analysis as well as its potential for use in routine screening of CLL.
Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czechoslovakia 06/2012; 158(1). DOI:10.5507/bp.2012.031 · 1.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Abstract Genetic background of mature B cell neoplasms with villous lymphocytes is poorly understood. We identified a novel breakpoint region at 14q32.13 that was rearranged together with IGH/14q32.33 in 4 BRAF/V600E-negative leukemia/lymphoma cases with villous lymphocytes carrying either t(14;14)(q32.13;q32.33) (3 patients) or del(14)(q32.13q32.33) (1 patient). The 14q32.13 breakpoints were mapped by FISH in the region harboring the TCL1A/TCL1B/TCL6 genes, known to be affected by TCRA/D-mediated t(14;14)(q11;q32)/inv(14)(q11q32) occurring in T-cell leukemia/lymphoma. To identify the target of t(14;14)(q32.13;q32.33) and del(14)(q32.13q32.33), qRT-PCR analysis of 25 candidate genes located centromerically and telomerically to the 14q3213 breakpoint was performed. Any of the analyzed genes was commonly overexpressed in the presented cases. Of note, upregulated transcription of TCL1A was observed in 2 cases. In summary, we provide evidence that IGH-mediated chromosomal aberrations affecting the 14q32.13/TCL1A-TCL6 region are recurrent in mature B-cell neoplasms with villous lymphocytes. Despite extensive qRT-PCR studies, molecular consequences of these novel aberrations remain elusive.
[Show abstract][Hide abstract] ABSTRACT: Genetic events underlying pathogenesis of nodal and extranodal marginal zone lymphoma are not completely understood. We report here a novel t(X;14)(p11.4;q32.33) identified in 4 lymphoma cases: 2 with a mucosa-associated lymphoid tissue lymphoma, one with a nodal marginal zone lymphoma and one with gastric diffuse large B-cell lymphoma. In all cases, lymphoma evolved from a previous auto-immune disorder. Fluorescence in situ hybridization and molecular studies showed that t(X;14), which is mediated by immunoglobulin heavy chain locus, targets the GPR34 gene at Xp11.4. Upregulation of GPR34 mRNA and aberrant expression of GPR34 protein has been demonstrated in 3 presented cases by quantitative real-time polymerase chain reaction and immunohistochemistry, respectively. GPR34 belongs to the largest family of cell surface molecules involved in signal transmission that play important roles in many physiological and pathological processes, including tumorigenesis. Although functional consequences of t(X;14) have not been identified, our studies suggest that up-regulated GPR34 activate neither nuclear factor-κB nor ELK-related tyrosine kinase.
[Show abstract][Hide abstract] ABSTRACT: Array-based comparative genomic hybridization (arrayCGH) studies in chronic lymphocytic leukemia (CLL) have revealed novel recurrent chromosomal imbalances, such as a gain of chromosome 2p. However, a detailed cytogenetic analysis of the 2p gain region has not been elucidated. Here, we present cytogenetic and molecular cytogenetic analysis of 16 such cases selected from a group of 200 patients with CLL based on CGH and/or arrayCGH data. We revealed significant heterogeneity of the region of gain on 2p in CLL, including a new recurrent aberration: the dicentric chromosome, dic(2;18). In our cases, the region of gain involved three genes (MYCN, REL, and ALK) and was associated with an unmutated IgVH status in 14 out of 16 cases. We consider this aberration clinically important in CLL and suggest that an examination of the gene(s) located in region of gain should be included in the routine fluorescence in situ hybridization screening method used for patients with CLL.
[Show abstract][Hide abstract] ABSTRACT: Leukemias/lymphomas with IGH-involving del(14q)(1) commonly lose the DLK1-GTL2 imprinted domain that comprises several paternally and maternally expressed genes, including a cluster of microRNAs. Given that deletion of this region could lead to inactivation of a monoallelically expressed tumor suppressor gene, our study aimed at determination of the parental origin of del(14q/IGH). The designed allele-specific methylation study of the DLK1/GTL2 intergenic differentially methylated region allowed us to determine the parental origin of del(14q/IGH) in 9/20 analyzed cases. In six cases del(14q/IGH) was of the paternal origin and in three cases of the maternal origin. These findings argue against the concept that a TSG/anti-oncomir located in the imprinted region is systematically inactivated by a targeted deletion of its functional allele.
Epigenetics: official journal of the DNA Methylation Society 10/2009; 4(7):469-75. DOI:10.4161/epi.4.7.9924 · 5.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Hepatoblastoma is the most common primary hepatic tumor in children, and only a limited number of detailed karyotypic analyses have been reported to date. In the present study, cytogenetic abnormalities were identified in nine cases of hepatoblastoma from a single institution. Among characteristic chromosomal changes detected were simple numerical aberrations, structural alterations of chromosomes 1, 2, and 8, and the recurrent unbalanced rearrangements der(4)t(1;4)(q25.2;q35.1) and der(6)t(1;6)(q21;q26). Array comparative genomic hybridization was applied in four of the cases. The combined cytogenetic, molecular cytogenetic, and histopathologic analyses are presented here, together with clinical data. The results substantially confirm previous findings of aberrations involving chromosomal loci on 1q, 2 or 2q, 4q, 6q, 8 or 8q, and 20 as significant in the development and clinical course of this disease.
Cancer genetics and cytogenetics 10/2009; 194(2):82-7. DOI:10.1016/j.cancergencyto.2009.06.001 · 1.93 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Abnormalities of chromosome 1 are among the most frequent chromosomal aberrations in patients with multiple myeloma (MM) and are considered a poor-risk genetic feature. To define the frequency and minimal region of 1q gain, we performed immunophenotyping and fluorescence in situ hybridization, comparative genomic hybridization (CGH), and array-CGH in 30 patients in relapse and progression of MM. Gain of 1q21 was found in 15 patients (50%), and in 14 of them whole-arm gain was found. One of these 14 patients had trisomy of chromosome 1 together with whole arm 1q gain, and two others had segmental duplication together with whole arm 1q gain. Segmental duplication of 1q21.1 approximately q23.1 alone was found in one patient. These results confirmed a high frequency of 1q aberrations and revealed that the vast majority of patients with 1q aberration in relapse and progression of MM display whole arm 1q gain. Finally, we observed that 1q gain is highly associated with number of additional changes.
Cancer genetics and cytogenetics 08/2009; 192(2):68-72. DOI:10.1016/j.cancergencyto.2009.02.020 · 1.93 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Reported here are 72 previously treated Philadelphia chromosome-positive (Ph+) CML patients on imatinib (IM) therapy, with a focus on patients with additional chromosomal aberrations (CAs). At the start of IM treatment, 49 patients exhibited only the Ph chromosome (68%) and 23 patients (32%) had one or more additional CAs. The most frequent additional changes were deletions on the der(9q) (8 of 23), trisomy 8 (3 of 23), and an extra copy of the Ph chromosome (2 of 23). Five patients had a complex karyotype. At the latest follow-up, 49 of the 72 patients (68%) were alive, including 15 of the 23 patients with additional CAs (65%). Median follow-up was 6.6 years; median duration of IM treatment was 4.4 years. In all, 35 of the 49 patients with Ph only (71%) and 10 of the 23 patients with additional CAs (43%) achieved complete cytogenetic response. All patients with deletion on der(9q) achieved complete cytogenetic response. There was no statistically significant difference in the overall survival of patients with additional CAs and patients with Ph as the sole abnormality. Patients in accelerated phase had significantly worse overall survival on IM, regardless of additional CAs. The present results confirm that the majority of previously treated Ph+ CML patients benefit from starting IM therapy, including patients with defined additional changes. In contrast, patients with complex karyotypes have poor prognosis, even with IM.
Cancer genetics and cytogenetics 06/2009; 191(1):1-9. DOI:10.1016/j.cancergencyto.2008.12.013 · 1.93 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We present the results of a cytogenetic and molecular cytogenetic analysis of a series of patients with bone and soft tissue tumors. PATIENTS ANDMETHODS: We analyzed a cohort of 26 patients with Ewing sarcoma/PNET, 15 patients with rhabdomyosarcoma, 5 with synovial sarcoma and one patient with an undifferentiated sarcoma using the cytogenetic and molecular cytogenetic techniques M-FISH and arrayCGH.
We found nonrandom chromosomal structural and numerical changes with diagnostic and prognostic relevance in most patients. Eight patients with ES/PNET had only a t(11;22)(q24;q12), eight patients had secondary aberrations as well and six had only secondary aberrations. In the RMS patients we detected the t(1;13)(p36;q14) once and the t(2;13)(q35;q14) four times, both of them characteristic for the alveolar subtype with poor prognosis and numerical aberrations, characteristic for the embryonal subtype, in five patients. Four patients with synovial sarcoma had the diagnostic t(X;18)(p11.2;q11.2), one of them had a complex karyotype with a complex t(X;18;21) (p11.2;q11.2;q11.2) together with t(2;5)(q24-32;p13-14) and t(12;20)(p11;q13). We correlated the karyotype of cancer cells with histopathologic morphologic analysis, clinical outcome and foreign published results.
Cytogenetic and molecular cytogenetic analysis is a valuable diagnostic tool in bone and soft tissue tumors, especially in less differentiated subtypes, and as such it should be an integral part of curative care.
Klinická onkologie: casopis Ceské a Slovenské onkologické spolecnosti 02/2009; 22(2):58-66.