51
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Peiró AM, Tang CM, Murray F, Zhang L, Brown LM, Chou D, Rassenti L, Kipps TJ, Kipps TA, Insel PA. Genetic variation in phosphodiesterase (PDE) 7B in chronic lymphocytic leukemia: overview of genetic variants of cyclic nucleotide PDEs in human disease. J Hum Genet 2011; 56:676-81. [PMID: 21796143 DOI: 10.1038/jhg.2011.80] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Expression of cyclic adenosine monophosphate-specific phosphodiesterase 7B (PDE7B) mRNA is increased in patients with chronic lymphocytic leukemia (CLL), thus suggesting that variation may occur in the PDE7B gene in CLL. As genetic variation in other PDE family members has been shown to associate with numerous clinical disorders (reviewed in this manuscript), we sought to identify single-nucleotide polymorphisms (SNPs) in the PDE7B gene promoter and coding region of 93 control subjects and 154 CLL patients. We found that the PDE7B gene has a 5' non-coding region SNP -347C>T that occurs with similar frequency in CLL patients (1.9%) and controls (2.7%). Tested in vitro, -347C>T has less promoter activity than a wild-type construct. The low frequency of this 5' untranslated region variant indicates that it does not explain the higher PDE7B expression in patients with CLL but it has the potential to influence other settings that involve a role for PDE7B.
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Affiliation(s)
- Ana M Peiró
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0636, USA
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52
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Abstract
Genomic aberrations are of predominant importance to the biology and clinical outcome of patients with chronic lymphocytic leukemia (CLL), and FISH-based genomic risk classifications are routinely used in clinical decision making in CLL. One of the known limitations of CLL FISH is the inability to comprehensively interrogate the CLL genome for genomic changes. In an effort at overcoming the existing limitations in CLL genome analysis, we have analyzed high-purity DNA isolated from FACS-sorted CD19(+) cells and paired CD3(+) or buccal cells from 255 patients with CLL for acquired genomic copy number aberrations (aCNAs) with the use of ultra-high-density Affymetrix SNP 6.0 arrays. Overall, ≥ 2 subchromosomal aCNAs were found in 39% (100 of 255) of all cases analyzed, whereas ≥ 3 subchromosomal aCNAs were detected in 20% (50 of 255) of cases. Subsequently, we have correlated genomic lesion loads (genomic complexity) with the clinical outcome measures time to first therapy and overall survival. With the use of multivariate analyses incorporating the most important prognostic factors in CLL together with SNP 6.0 array-based genomic lesion loads at various thresholds, we identify elevated CLL genomic complexity as an independent and powerful marker for the identification of patients with aggressive CLL and short survival.
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53
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Wan J, Gao Y, Zhao X, Wu Q, Fu X, Shao Y, Yang H, Guan M, Yu B, Zhang W. The association between the copy-number variations of ZMAT4 and hematological malignancy. ACTA ACUST UNITED AC 2011; 16:20-3. [PMID: 21269563 DOI: 10.1179/102453311x12902908411751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Copy-number variations (CNVs) have been found in association with various types of diseases, including hematological malignancies. A recent array-based study implicated the presence of CNVs of ZMAT4 in the genome of acute myelogenous leukemia. In our study, we collected 617 bone marrow samples from multitypes of hematological malignancies as well as healthy controls. We found significant association between the CNVs of ZMAT4 and these hematological malignancies, including acute lymphoblastic leukemia, acute myelogenous leukemia, chronic lymphocytic leukemia, chronic myelogenous leukemia, multiple myeloma, and myelodysplastic syndrome. We also examined the expression of ZMAT4 mRNA in the samples with 1 or 2 copies of DNA, and observed a weak yet positive correlation between the relative expression level and gene dosage. In conclusion, the CNVs of ZMAT4 have the potential to serve as a diagnostic indicator, alone or in combination with other markers, for hematological malignancies.
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Affiliation(s)
- Jun Wan
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, China
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54
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Fabbri G, Rasi S, Rossi D, Trifonov V, Khiabanian H, Ma J, Grunn A, Fangazio M, Capello D, Monti S, Cresta S, Gargiulo E, Forconi F, Guarini A, Arcaini L, Paulli M, Laurenti L, Larocca LM, Marasca R, Gattei V, Oscier D, Bertoni F, Mullighan CG, Foá R, Pasqualucci L, Rabadan R, Dalla-Favera R, Gaidano G. Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation. ACTA ACUST UNITED AC 2011; 208:1389-401. [PMID: 21670202 PMCID: PMC3135373 DOI: 10.1084/jem.20110921] [Citation(s) in RCA: 476] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Next generation sequencing and copy number analysis provide insights into the complexity of the CLL coding genome, and reveal an association between NOTCH1 mutational activation and poor prognosis. The pathogenesis of chronic lymphocytic leukemia (CLL), the most common leukemia in adults, is still largely unknown. The full spectrum of genetic lesions that are present in the CLL genome, and therefore the number and identity of dysregulated cellular pathways, have not been identified. By combining next-generation sequencing and copy number analysis, we show here that the typical CLL coding genome contains <20 clonally represented gene alterations/case, including predominantly nonsilent mutations, and fewer copy number aberrations. These analyses led to the discovery of several genes not previously known to be altered in CLL. Although most of these genes were affected at low frequency in an expanded CLL screening cohort, mutational activation of NOTCH1, observed in 8.3% of CLL at diagnosis, was detected at significantly higher frequency during disease progression toward Richter transformation (31.0%), as well as in chemorefractory CLL (20.8%). Consistent with the association of NOTCH1 mutations with clinically aggressive forms of the disease, NOTCH1 activation at CLL diagnosis emerged as an independent predictor of poor survival. These results provide initial data on the complexity of the CLL coding genome and identify a dysregulated pathway of diagnostic and therapeutic relevance.
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Affiliation(s)
- Giulia Fabbri
- Institute for Cancer Genetics and the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
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55
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Fabris S, Scarciolla O, Morabito F, Cifarelli RA, Dininno C, Cutrona G, Matis S, Recchia AG, Gentile M, Ciceri G, Ferrarini M, Ciancio A, Mannarella C, Neri A, Fragasso A. Multiplex ligation-dependent probe amplification and fluorescence in situ hybridization to detect chromosomal abnormalities in chronic lymphocytic leukemia: a comparative study. Genes Chromosomes Cancer 2011; 50:726-34. [PMID: 21638517 DOI: 10.1002/gcc.20894] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 04/29/2011] [Indexed: 12/25/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease characterized by recurrent chromosomal aberrations of prognostic significance. We aimed to evaluate the potential of the multiplex ligation-dependent probe amplification (MLPA) assay to detect genomic alterations in CLL. Highly purified (>90%) peripheral mononuclear CD19+ cell populations from 100 untreated CLL patients (pts) in early stage disease (Binet stage A) were included in this study. All samples were investigated by fluorescence in situ hybridization (FISH) for the presence of trisomy 12 and 17p13.1, 11q22.3, and 13q14.3 deletions. For MPLA analysis, DNA was amplified by means of two commercially available probes sets allowing the simultaneous screening of 56 genomic sequences. Overall, a high degree of concordance (95%) between MPLA and FISH results was found, if the abnormal clone was present in more than 30% of the leukemic cell population. The use of multiple MPLA probes allowed the fine-mapping of the 13q14 deletion and the identification of intragenic or small alterations undetected by FISH. Moreover, additional alterations in 2p24 (MYCN) (3 pts), 8q24 (MYC) (1 pt), 9p21 (CDKN2A2B) (1 pt), 1q21 (LMNA) (1 pt), and 6q25-26 (1 pt) regions not covered by a standard FISH assay were detected and all confirmed by FISH. Our data extend previously limited evidence that MLPA may represent a useful technique for the characterization of well-known lesions as well as the investigation of additional genomic changes in CLL.
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Affiliation(s)
- Sonia Fabris
- Ematologia 1-CTMO, Fondazione Cà Granda IRCCS Policlinico and Dipartimento di Scienze Mediche, Università di Milano, Via F. Sforza 35, Milan, Italy
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56
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Abstract
Advances in whole genome amplification and next-generation sequencing methods have enabled genomic analyses of single cells, and these techniques are now beginning to be used to detect genomic lesions in individual cancer cells. Previous approaches have been unable to resolve genomic differences in complex mixtures of cells, such as heterogeneous tumors, despite the importance of characterizing such tumors for cancer treatment. Sequencing of single cells is likely to improve several aspects of medicine, including the early detection of rare tumor cells, monitoring of circulating tumor cells (CTCs), measuring intratumor heterogeneity, and guiding chemotherapy. In this review we discuss the challenges and technical aspects of single-cell sequencing, with a strong focus on genomic copy number, and discuss how this information can be used to diagnose and treat cancer patients.
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Gunnarsson R, Mansouri L, Isaksson A, Göransson H, Cahill N, Jansson M, Rasmussen M, Lundin J, Norin S, Buhl AM, Smedby KE, Hjalgrim H, Karlsson K, Jurlander J, Geisler C, Juliusson G, Rosenquist R. Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia. Haematologica 2011; 96:1161-9. [PMID: 21546498 DOI: 10.3324/haematol.2010.039768] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND High-resolution genomic microarrays enable simultaneous detection of copy-number aberrations such as the known recurrent aberrations in chronic lymphocytic leukemia [del(11q), del(13q), del(17p) and trisomy 12], and copy-number neutral loss of heterozygosity. Moreover, comparison of genomic profiles from sequential patients' samples allows detection of clonal evolution. DESIGN AND METHODS We screened samples from 369 patients with newly diagnosed chronic lymphocytic leukemia from a population-based cohort using 250K single nucleotide polymorphism-arrays. Clonal evolution was evaluated in 59 follow-up samples obtained after 5-9 years. RESULTS At diagnosis, copy-number aberrations were identified in 90% of patients; 70% carried known recurrent alterations, including del(13q) (55%), trisomy 12 (10.5%), del(11q) (10%), and del(17p) (4%). Additional recurrent aberrations were detected on chromosomes 2 (1.9%), 4 (1.4%), 8 (1.6%) and 14 (1.6%). Thirteen patients (3.5%) displayed recurrent copy-number neutral loss of heterozygosity on 13q, of whom 11 had concurrent homozygous del(13q). Genomic complexity and large 13q deletions correlated with inferior outcome, while the former was linked to poor-prognostic aberrations. In the follow-up study, clonal evolution developed in 8/24 (33%) patients with unmutated IGHV, and in 4/25 (16%) IGHV-mutated and treated patients. In contrast, untreated patients with mutated IGHV (n=10) did not acquire additional aberrations. The most common secondary event, del(13q), was detected in 6/12 (50%) of all patients with acquired alterations. Interestingly, aberrations on, for example, chromosome 6q, 8p, 9p and 10q developed exclusively in patients with unmutated IGHV. CONCLUSIONS Whole-genome screening revealed a high frequency of genomic aberrations in newly diagnosed chronic lymphocytic leukemia. Clonal evolution was associated with other markers of aggressive disease and commonly included the known recurrent aberrations.
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Affiliation(s)
- Rebeqa Gunnarsson
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
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58
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Chu F, Feng Q, Qian Y, Zhang C, Fang Z, Shen G. ERBB2 gene amplification in oral squamous cell malignancies: a correlation with tumor progression and gene expression. ACTA ACUST UNITED AC 2011; 112:90-5. [PMID: 21531597 DOI: 10.1016/j.tripleo.2011.01.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 01/24/2011] [Accepted: 01/24/2011] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Chromosomal instability is hallmark of carcinoma. Amplification of chromosome 17q11-q12 is present in some oral squamous cell cancer (OSCC) cases. In this study, we investigated the copy number variations of ERBB2 gene, which is located at this locus in collected OSCC samples and their correlation with tumor progression and gene expression. STUDY DESIGN Quantitative real-time polymerase chain reaction was performed to detect the copy number of ERBB2 gene and the mRNA expression in 92 OSCC samples with matched adjacent normal tissues (ANTs). Proportional odds regression and 2-way repeated measurement analysis of variance were used to analyze the association between copy number variations and mRNA expression of the targeted gene. RESULTS Copy number gains of ERBB2 were detected in some of the OSCCs (19.6%, 18/92) and correlated with tumor stage (P < .001). Copy number gains of ERBB2 also showed a positive correlation with mRNA overexpression in OSCCs (P < .001). However, enhanced ERBB2 mRNA expression was also detected in a group of OSCC samples with unaltered copy number of ERBB2 gene (P < .05). CONCLUSIONS Copy number increase of ERBB2 is observed in OSCCs and correlates with gene overexpression in these tumors. In addition, overexpression of ERBB2 is also observed in some OSCCs that lack copy number changes, indicating involvement of another mechanism.
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Affiliation(s)
- Fengting Chu
- Department of Orthodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, China
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59
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Cavazzini F, Ciccone M, Negrini M, Rigolin GM, Cuneo A. Clinicobiologic importance of cytogenetic lesions in chronic lymphocytic leukemia. Expert Rev Hematol 2011; 2:305-14. [PMID: 21082972 DOI: 10.1586/ehm.09.22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Molecular cytogenetic lesions play a major role in the pathogenesis of chronic lymphocytic leukemia (CLL) and represent important prognostic markers. Besides FISH, conventional banding analysis using effective mitogens is important for an accurate assessment of the cytogenetic profile of CLL. The most frequent aberrations are represented by 13q-, 11q-, +12, 6q- and 14q32/IGH translocations and 17p-. Chromosome translocations and complex karyotype may occur in up to 30 and 16% of the cases, respectively. The frequency of 17p- and 11q- is higher in patients requiring treatment and in relapsed/refractory patients, reflecting the association of these rearrangements with unfavorable prognosis. Mutations of the TP53 gene may also confer an inferior outcome, as is the case with 14q32 translocations and unbalanced translocations. Evidence was provided that distinct treatment approaches may be effective in specific cytogenetic entities of CLL, making molecular cytogenetic investigations a necessary tool for a modern diagnostic work-up in CLL.
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Affiliation(s)
- Francesco Cavazzini
- Section of Hematology, Department of Biomedical Sciences and Advanced Therapies, University of Ferrara, Via Savonarola 9, Ferrara, Italy
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60
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Bertilaccio MTS, Scielzo C, Muzio M, Caligaris-Cappio F. An overview of chronic lymphocytic leukaemia biology. Best Pract Res Clin Haematol 2011; 23:21-32. [PMID: 20620968 DOI: 10.1016/j.beha.2009.12.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chronic lymphocytic leukaemia (CLL) is characterised by accumulation of CD5(+) monoclonal B cells in primary and secondary lymphoid tissues. Genetic defects and stimuli originating from the microenvironment concur to the selection and expansion of the malignant clone. Several lines of evidence, including molecular and functional analysis of the monoclonal immunoglobulin, support the hypothesis that stimulation through the B-cell receptor affects life and death of leukaemic cells. The microenvironment also has a critical role in the survival and accumulation of leukaemic cells within lymphoid organs where signals delivered from the surrounding cells are likely crucial in inducing proliferation. Nevertheless, several major biological issues still remain to be solved including regulation of the balance between proliferation and survival of leukaemic cells and the links between emerging gene abnormalities and microenvironment. In this context, mouse models are helpful tools in understanding disease mechanisms and in evaluating the efficacy of novel therapeutic agents.
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Affiliation(s)
- M T S Bertilaccio
- Laboratory of Lymphoid Malignancies, Division of Molecular Oncology, Istituto Scientifico San Raffaele, Milan, Italy.
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61
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Zhao X, Wu Q, Fu X, Yu B, Shao Y, Yang H, Guan M, Huang X, Zhang W, Wan J. Examination of copy number variations of CHST9 in multiple types of hematologic malignancies. ACTA ACUST UNITED AC 2011; 203:176-9. [PMID: 21156230 DOI: 10.1016/j.cancergencyto.2010.07.132] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 07/13/2010] [Accepted: 07/25/2010] [Indexed: 11/24/2022]
Abstract
Carbohydrate N-acetylgalactosamine 4-0 sulfotransferase 9 (CHST9) belongs to the N-acetylgalactosamine 4-sulfotransferase (GalNAc4ST) family. A recent array-based study implicated the presence of copy-number variations (CNV) of the region encompassing CHST9 in the genomes of acute myelogenous leukemia. Most of the current studies, however, focused on the genome-wide screening of CNV, and the functional impact of such regions needs to be extensively investigated in large amounts of clinical samples. In our study, we collected 617 bone marrow samples from multi-types of hematologic malignancies, as well as healthy controls, and detected the CNV of CHST9 by real-time polymerase chain reaction (PCR). We found significant association between the CNV of CHST9 and these hematologic malignancies including acute lymphoblastic leukemia, acute myelogenous leukemia, chronic lymphocytic leukemia, chronic myelogenous leukemia, multiple myeloma, and myelodysplastic syndrome. We also examined CHST9 mRNA expression in the samples with one or two copies of DNA, and observed a weak yet positive correlation between the relative expression level and gene dosage. In general, the CNV of CHST9 have been shown to associate with hematologic malignancies. The functional consequences of CNV, however, need to be investigated extensively in the future.
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Affiliation(s)
- Xiaosu Zhao
- Department of Hematology, Peking University People's Hospital, Peking University Institute of Hematology, #11, South Street of Xi-Zhi-Men, 100044 Beijing, China
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62
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Gene dosage effects in chronic lymphocytic leukemia. ACTA ACUST UNITED AC 2011; 203:149-60. [PMID: 21156227 DOI: 10.1016/j.cancergencyto.2010.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 08/25/2010] [Accepted: 09/01/2010] [Indexed: 11/21/2022]
Abstract
To understand the influence of chromosomal alterations on gene expression in a genome-wide view, chromosomal imbalances detected by single nucleotide polymorphism (SNP) chips were compared with global gene expression in 16 cases of chronic lymphocytic leukemia (CLL). A strong concordance between chromosomal gain or loss and increased or reduced expression of genes in the affected regions was found, respectively. Regions of uniparental disomy (UPD) were rare and had usually no consistent influence on gene expression, but in one instance, a large UPD was associated with a downregulation of most genes in the affected chromosome. The frequently deleted miRNAs, MIRN15A and MIRN16-1, did not show a reduced expression in cases with monoallelic deletions. The BCL2 protein, considered to be downregulated by these miRNAs, was upregulated not only in CLL with biallelic deletion of MIRN15A and MIRN16-1, but also in cases with monoallelic deletion. This suggests a complex regulation of BCL2 levels in CLL cells. Taken together, in CLL, a global gene dosage effect exists for chromosomal gains and deletions and in some instances for UPDs. We did not confirm a consistent correlation between MIRN15A and MIRN16-1 expression levels and BCL2 protein levels, indicating a complex regulation of BCL2 expression.
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63
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Zhang C, Fang Z, Xiong Y, Li J, Liu L, Li M, Zhang W, Wan J. Copy number increase of aurora kinase A in colorectal cancers: a correlation with tumor progression. Acta Biochim Biophys Sin (Shanghai) 2010; 42:834-8. [PMID: 20929925 DOI: 10.1093/abbs/gmq088] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The centrosome-associated kinase aurora A (AURKA) is involved in genetic instability and is over-expressed in several human carcinomas including colorectal cancer (CRC). The choromosome locus of AURKA, 20q13, is frequently amplified in CRC, and the functional impact of such regions needs to be extensively investigated in large amount of clinical samples. Case-matched tissues of colorectal adenocarcinomas and adjacent normal epithelium (n= 134) were included in this study. Quantitative PCR was carried out to examine the copy number and mRNA level of AURKA in CRC. Our results showed that copy number gains of AUKRA were detected in a relative high percentage of CRC samples (32.4%, 43 of 134). There was a positive correlation between copy number increase of AURKA and tumor progression. And copy number gains of AURKA also showed a positive correlation with mRNA over-expression in CRC. However, the expression level of AURKA mRNA was also enhanced in the group of CRC samples with unaltered copy numbers. These findings indicated that sporadic colorectal cancers exhibit different mechanisms of aurora A regulation and this may impact the efficacy of aurora-targeted therapies.
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Affiliation(s)
- Chao Zhang
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, China
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64
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Investigation of copy-number variations of C8orf4 in hematological malignancies. Med Oncol 2010; 28 Suppl 1:S647-52. [PMID: 20878554 DOI: 10.1007/s12032-010-9698-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 09/17/2010] [Indexed: 10/19/2022]
Abstract
C8orf4, thyroid cancer-1 (TC1), was first identified in papillary thyroid carcinoma and encodes a nucleus-localized protein. A recent array-based study implicated the presence of copy-number variations (CNVs) of C8orf4 in the genomes of acute myelogenous leukemia. However, the functional impact of such regions needs to be extensively investigated in large amount of clinical samples. The purpose of this study is to confirm the relationship between C8orf4 CNVs and hematological malignancies. In our study, we collected bone marrow samples from 515 hematological malignancies and 102 healthy controls. And the CNVs of C8orf4 were detected by real-time PCR. We found significant association between the copy-number deletions of C8orf4 and the risk of these hematological malignancies including acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), multiple myeloma (MM), and myelodysplastic syndrome (MDS). We also found that the expression of C8orf4 mRNA was relatively lower in the samples with 1 copy of DNA than those with 2 copies of DNA. The CNVs of C8orf4 were associated with the risk of hematological malignancies.
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65
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Fang Z, Xiong Y, Zhang C, Li J, Liu L, Li M, Zhang W, Wan J. Coexistence of copy number increases of ZNF217 and CYP24A1 in colorectal cancers in a Chinese population. Oncol Lett 2010; 1:925-930. [PMID: 22966406 DOI: 10.3892/ol_00000163] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 07/19/2010] [Indexed: 01/03/2023] Open
Abstract
Evidence suggests that the amplification of chromosome 20q13 is common in colorectal cancers (CRCs). Certain candidate oncogenes located in this region are reported to be associated with tumorigenesis of the gastrointestinal tract. The functional impact of such regions should be extensively investigated in a large number of clinical samples. In this study, 145 CRC samples with matched adjacent normal tissues were collected from a Chinese population for copy number variation (CNV) analysis. Our results showed that both the copy numbers of 25-hydroxy vitamin D3 24-hydroxylase (CYP24A1) and zinc-finger protein 217 (ZNF217) were amplified in a relatively high percentage of CRC samples (51.1 and 60%, respectively). The mRNA expression levels of both CYP24A1 and ZNF217 were found to have increased in the collected CRC samples as compared to the matched adjacent normal tissues. ZNF217, but not CYP24A1, showed a positive correlation between copy number increases and mRNA overexpression. These findings suggest the potential role of CNVs of certain oncogenes in CRCs.
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Affiliation(s)
- Zhengyu Fang
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center and Shenzhen Hospital, Peking University, Guangdong, P.R. China
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66
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Setlur SR, Ihm C, Tchinda J, Shams S, Werner L, Cho EK, Thompson C, Phillips K, Rassenti LZ, Kipps TJ, Neuberg D, Freedman AS, Lee C, Brown JR. Comparison of familial and sporadic chronic lymphocytic leukaemia using high resolution array comparative genomic hybridization. Br J Haematol 2010; 151:336-45. [PMID: 20812997 DOI: 10.1111/j.1365-2141.2010.08341.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Approximately 10% of patients with chronic lymphocytic leukaemia (CLL) have a family history of the disease or a related lymphoproliferative disorder, yet the relationship of familial CLL to genomic abnormalities has not been characterized in detail. We therefore studied 75 CLL patients, half familial and half sporadic, using high-resolution array comparative genomic hybridization (CGH), in order to better define the relationship of genomic abnormalities to familial disease and other biological prognostic factors. Our results showed that the most common high-risk deletion in CLL, deletion 11q, was significantly associated with sporadic disease. Comparison of familial to sporadic disease additionally identified a copy number variant region near the centromere on 14q, proximal to IGH@, in which gains were associated both with familial CLL, and with mutated IGHV and homozygous deletion of 13q. Homozygous deletion of 13q was also found to be associated with mutated IGHV and low expression of ZAP-70, and a significantly longer time to first treatment compared to heterozygous deletion or lack of alteration. This study is the first high resolution effort to investigate and report somatic genetic differences between familial and sporadic CLL.
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Affiliation(s)
- Sunita R Setlur
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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67
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Lange C, Mittermayr L, Dohm JC, Holtgräwe D, Weisshaar B, Himmelbauer H. High-throughput identification of genetic markers using representational oligonucleotide microarray analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:549-565. [PMID: 20379697 DOI: 10.1007/s00122-010-1329-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 03/22/2010] [Indexed: 05/29/2023]
Abstract
We describe a novel approach for high-throughput development of genetic markers using representational oligonucleotide microarray analysis. We test the performance of the method in sugar beet (Beta vulgaris L.) as a model for crop plants with little sequence information available. Genomic representations of both parents of a mapping population were hybridized on microarrays containing in total 146,554 custom made oligonucleotides based on sugar beet bacterial artificial chromosome (BAC) end sequences and expressed sequence tags (ESTs). Oligonucleotides showing a signal with one parental line only, were selected as potential marker candidates and placed onto an array, designed for genotyping of 184 F(2) individuals from the mapping population. Utilizing known co-dominant anchor markers we obtained 511 new dominant markers (392 derived from BAC end sequences, and 119 from ESTs) distributed over all nine sugar beet linkage groups and calculated genetic maps. Further improvements for large-scale application of the approach are discussed and its feasibility for the cost-effective and flexible generation of genetic markers is presented.
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Affiliation(s)
- Cornelia Lange
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany
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Fang Z, Xiong Y, Li J, Liu L, Li M, Zhang C, Zhang W, Wan J. Copy-number increase of AURKA in gastric cancers in a Chinese population: a correlation with tumor progression. Med Oncol 2010; 28:1017-22. [PMID: 20585902 DOI: 10.1007/s12032-010-9602-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 06/12/2010] [Indexed: 12/25/2022]
Abstract
The centrosome-associated kinase aurora A (AURKA) has been shown to be involved in genetic instability and to be over-expressed in several human carcinomas including gastric cancers (GCs). The chromosome locus of AURKA, 20q13, is frequently amplified in GCs, and the functional impact of such regions needs to be extensively investigated in large amount of clinical samples. Case-matched tissues of gastric carcinomas and adjacent normal epithelium (n=141) were included in this study. Quantitative PCR was carried out to examine the copy number and mRNA expression of AURKA in GCs. Our results showed copy-number gains of AUKRA were detected in a relative high percentage of GC samples (30.5%, 43 out of 141). There was a positive correlation between copy-number increase of AURKA and tumor progression. And copy-number gains of AURKA also showed a positive correlation with mRNA over-expression in GCs. However, expression level of AURKA mRNA was also enhanced in the group of GC samples with unaltered copy numbers. These findings indicated that sporadic gastric cancers exhibit different mechanisms of AURKA regulation and that this may impact the efficacy of aurora-targeted therapies.
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Affiliation(s)
- Zhengyu Fang
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Shenzhen, Guangdong Province, People's Republic of China.
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69
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Yang H, Zhang C, Zhao X, Wu Q, Fu X, Yu B, Shao Y, Guan M, Zhang W, Wan J, Huang X. Analysis of copy number variations of BS69 in multiple types of hematological malignancies. Ann Hematol 2010; 89:959-64. [DOI: 10.1007/s00277-010-0966-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 04/12/2010] [Indexed: 10/19/2022]
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70
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Watkins AJ, Huang Y, Ye H, Chanudet E, Johnson N, Hamoudi R, Liu H, Dong G, Attygalle A, McPhail ED, Law ME, Isaacson PG, de Leval L, Wotherspoon A, Du MQ. Splenic marginal zone lymphoma: characterization of 7q deletion and its value in diagnosis. J Pathol 2010; 220:461-74. [PMID: 20077527 DOI: 10.1002/path.2665] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The diagnosis of splenic marginal zone lymphoma (SMZL) is frequently a challenge, due to its lack of specific histological features and immunophenotypic markers, and the existence of other poorly characterized splenic lymphomas defying classification. Moreover, the clinical outcome of SMZL is variable, with 30% of cases pursuing an aggressive clinical course, the prediction of which remains problematic. Thus, there is a real need for biomarkers in the diagnosis and prognostication of SMZL. To search for genetic markers, we comprehensively investigated the genomic profile, TP53 abnormalities, and immunoglobulin heavy gene (IGH) mutation in a large cohort of SMZLs. 1 Mb resolution array comparative genomic hybridization (aCGH) on 25 SMZLs identified 7q32 deletion (44%) as the most frequent copy number change, followed by gains of 3q (32%), 8q (20%), 9q34 (20%), 12q23-24 (8%), and chromosome 18 (12%), and losses of 6q (16%), 8p (12%), and 17p (8%). High-resolution chromosome 7 tile-path aCGH on 17 SMZLs with 7q32 deletion identified by 1 Mb aCGH or interphase FISH screening mapped the minimal common deletion to a 3 Mb region at 7q32.1-32.2. Although it is not yet possible to identify the genes targeted by the deletion, interphase FISH screening showed that the deletion was seen in SMZL (19/56 = 34%) and splenic B-cell lymphoma/leukaemia unclassifiable (3/9 = 33%), but not in 39 cases of other splenic lymphomas including chronic lymphocytic leukaemia (n = 14), hairy cell leukaemia (4), mantle cell lymphoma (12), follicular lymphoma (6), and others. In SMZL, 7q32 deletion was inversely correlated with trisomy 18, but not associated with other copy number changes, TP53 abnormalities, or IGH mutation status. None of the genetic parameters examined showed significant and independent association with overall or event-free survival. In conclusion, 7q32 deletion is a characteristic feature of SMZL, albeit seen in isolated cases of splenic B-cell lymphoma/leukaemia unclassifiable, and its detection may help the differential diagnosis of splenic B-cell lymphomas.
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Affiliation(s)
- A James Watkins
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, UK
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71
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Crowther-Swanepoel D, Broderick P, Di Bernardo MC, Dobbins SE, Torres M, Mansouri M, Ruiz-Ponte C, Enjuanes A, Rosenquist R, Carracedo A, Jurlander J, Campo E, Juliusson G, Montserrat E, Smedby KE, Dyer MJS, Matutes E, Dearden C, Sunter NJ, Hall AG, Mainou-Fowler T, Jackson GH, Summerfield G, Harris RJ, Pettitt AR, Allsup DJ, Bailey JR, Pratt G, Pepper C, Fegan C, Parker A, Oscier D, Allan JM, Catovsky D, Houlston RS. Common variants at 2q37.3, 8q24.21, 15q21.3 and 16q24.1 influence chronic lymphocytic leukemia risk. Nat Genet 2010; 42:132-6. [PMID: 20062064 PMCID: PMC5321238 DOI: 10.1038/ng.510] [Citation(s) in RCA: 185] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 11/20/2009] [Indexed: 12/20/2022]
Abstract
To identify new risk variants for chronic lymphocytic leukemia (CLL), we conducted a genome-wide association study of 299,983 tagging SNPs, with validation in four additional series totaling 2,503 cases and 5,789 controls. We identified four new risk loci for CLL at 2q37.3 (rs757978, FARP2; odds ratio (OR) = 1.39; P = 2.11 x 10(-9)), 8q24.21 (rs2456449; OR = 1.26; P = 7.84 x 10(-10)), 15q21.3 (rs7169431; OR = 1.36; P = 4.74 x 10(-7)) and 16q24.1 (rs305061; OR = 1.22; P = 3.60 x 10(-7)). We also found evidence for risk loci at 15q25.2 (rs783540, CPEB1; OR = 1.18; P = 3.67 x 10(-6)) and 18q21.1 (rs1036935; OR = 1.22; P = 2.28 x 10(-6)). These data provide further evidence for genetic susceptibility to this B-cell hematological malignancy.
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Affiliation(s)
| | - Peter Broderick
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey. UK
| | | | - Sara E Dobbins
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey. UK
| | - María Torres
- Genomic Medicine Group, University of Santiago de Compostela and Galician Foundation of Genomic Medicine, CIBERER, Santiago de Compostela, Spain
| | - Mahmoud Mansouri
- Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Clara Ruiz-Ponte
- Genomic Medicine Group, University of Santiago de Compostela and Galician Foundation of Genomic Medicine, CIBERER, Santiago de Compostela, Spain
| | - Anna Enjuanes
- Hematopathology Unit, Center for Biomedical Diagnosis Hospital Clinic, University of Barcelona, Spain
| | - Richard Rosenquist
- Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Angel Carracedo
- Genomic Medicine Group, University of Santiago de Compostela and Galician Foundation of Genomic Medicine, CIBERER, Santiago de Compostela, Spain
| | - Jesper Jurlander
- Department of Hematology, Leukemia Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Elias Campo
- Hematopathology Unit, Center for Biomedical Diagnosis Hospital Clinic, University of Barcelona, Spain
| | - Gunnar Juliusson
- Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Hematology and Transplantation, Lund University, Lund, Sweden
| | - Emilio Montserrat
- Department of Hematology, Institut d’Investigacions Biomediques August Pi i Sunyer, Hospital Clinic, University of Barcelona, Spain
| | - Karin E Smedby
- Unit of Clinical Epidemiology, Dept of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Martin JS Dyer
- MRC Toxicology Unit, Leicester University, Leicester. UK
| | - Estella Matutes
- Section of Haemato-oncology, Institute of Cancer Research, Sutton, Surrey. UK
| | - Claire Dearden
- Section of Haemato-oncology, Institute of Cancer Research, Sutton, Surrey. UK
| | - Nicola J Sunter
- Northern Institute for Cancer Research, Paul O’Gorman Building, Newcastle University, Newcastle-upon-Tyne. UK
| | - Andrew G Hall
- Northern Institute for Cancer Research, Paul O’Gorman Building, Newcastle University, Newcastle-upon-Tyne. UK
| | - Tryfonia Mainou-Fowler
- Haematological sciences, Leech Building, The Medical School, Newcastle University, Newcastle-upon-Tyne. UK
| | - Graham H Jackson
- Department of Haematology, Royal Victoria Infirmary, Newcastle-upon-Tyne. UK
| | - Geoffrey Summerfield
- Department of Haematology, Queen Elizabeth Hospital, Gateshead, Newcastle-upon-Tyne. UK
| | - Robert J Harris
- Division of Haematology, University of Liverpool School of Cancer Studies, Liverpool, UK
| | - Andrew R Pettitt
- Division of Haematology, University of Liverpool School of Cancer Studies, Liverpool, UK
| | - David J Allsup
- Department of Haematology, Hull Royal Infirmary, Hull. UK
| | - James R Bailey
- Hull York Medical School and University of Hull, Hull. UK
| | - Guy Pratt
- Department of Haematology, Birmingham Heartlands Hospital, Birmingham. UK
| | - Chris Pepper
- Department of Haematology, School of Medicine, Cardiff University. Cardiff. UK
| | - Chris Fegan
- Cardiff and Vale NHS Trust, Heath Park, Cardiff. UK
| | | | | | - James M Allan
- Northern Institute for Cancer Research, Paul O’Gorman Building, Newcastle University, Newcastle-upon-Tyne. UK
| | - Daniel Catovsky
- Section of Haemato-oncology, Institute of Cancer Research, Sutton, Surrey. UK
| | - Richard S Houlston
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey. UK
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Zent CS, Van Dyke DL. Detection of recurrent chromosomal defects in chronic lymphocytic leukemia/small lymphocytic lymphoma: innovations and applications. Leuk Lymphoma 2010; 51:186-7. [PMID: 20109070 DOI: 10.3109/10428190903580436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Clive S Zent
- Division of Hematology, Mayo Clinic, Rochester, MN 55905, USA.
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73
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Stevens-Kroef M, Simons A, Gorissen H, Feuth T, Weghuis DO, Buijs A, Raymakers R, Geurts van Kessel A. Identification of chromosomal abnormalities relevant to prognosis in chronic lymphocytic leukemia using multiplex ligation-dependent probe amplification. ACTA ACUST UNITED AC 2009; 195:97-104. [PMID: 19963108 DOI: 10.1016/j.cancergencyto.2009.06.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 06/17/2009] [Accepted: 06/20/2009] [Indexed: 01/10/2023]
Abstract
B-cell chronic lymphocytic leukemia (CLL) is characterized by a highly variable clinical course. Characteristic genomic abnormalities provide clinically important prognostic information. Because karyotyping and fluorescence in situ hybridization (FISH) are laborious techniques, we investigated the diagnostic efficacy of the more recently developed multiplex ligation-dependent probe amplification (MLPA) technique. MLPA and interphase FISH data of 88 CLL patients were compared for loci encompassing the 13q14 region, chromosome 12, and the ATM (11q22) and TP53 (17p13) genes. We found a perfect correlation, provided that the abnormal clone was present in at least 10-20% of the cells. Because multiple loci and multiple probes per locus were included in the MLPA assay, additional abnormalities not covered by the FISH probes were detected. Furthermore, in 13 cases deletions partly covering the 13q14.3 locus were observed, including three deletions that remained undetected by FISH. All the deletions included the noncoding RNA locus DLEU1 (previously BCMS), which is considered to be the most likely CLL-associated candidate tumor suppressor gene within the 13q14 region. We conclude that MLPA serves as a comprehensive and reliable technique for the simultaneous identification of different clinically relevant and region-specific genomic aberrations in CLL.
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Affiliation(s)
- Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Nijmegen Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
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74
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Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S, Zetterberg A, Hicks J, Wigler M. Inferring tumor progression from genomic heterogeneity. Genome Res 2009; 20:68-80. [PMID: 19903760 DOI: 10.1101/gr.099622.109] [Citation(s) in RCA: 369] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form of the phylogenetic relationships. We have developed a method we call Sector-Ploidy-Profiling (SPP) to study the clonal composition of breast tumors. SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization (CGH). Breast carcinomas display two classes of genomic structural variation: (1) monogenomic and (2) polygenomic. Monogenomic tumors appear to contain a single major clonal subpopulation with a highly stable chromosome structure. Polygenomic tumors contain multiple clonal tumor subpopulations, which may occupy the same sectors, or separate anatomic locations. In polygenomic tumors, we show that heterogeneity can be ascribed to a few clonal subpopulations, rather than a series of gradual intermediates. By comparing multiple subpopulations from different anatomic locations, we have inferred pathways of cancer progression and the organization of tumor growth.
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Affiliation(s)
- Nicholas Navin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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75
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McCarthy S, Makarov V, Kirov G, Addington A, McClellan J, Yoon S, Perkins D, Dickel DE, Kusenda M, Krastoshevsky O, Krause V, Kumar RA, Grozeva D, Malhotra D, Walsh T, Zackai EH, Kaplan P, Ganesh J, Krantz ID, Spinner NB, Roccanova P, Bhandari A, Pavon K, Lakshmi B, Leotta A, Kendall J, Lee YH, Vacic V, Gary S, Iakoucheva L, Crow TJ, Christian SL, Lieberman J, Stroup S, Lehtimäki T, Puura K, Haldeman-Englert C, Pearl J, Goodell M, Willour VL, DeRosse P, Steele J, Kassem L, Wolff J, Chitkara N, McMahon FJ, Malhotra AK, Potash JB, Schulze TG, Nöthen MM, Cichon S, Rietschel M, Leibenluft E, Kustanovich V, Lajonchere CM, Sutcliffe JS, Skuse D, Gill M, Gallagher L, Mendell NR, Craddock N, Owen MJ, O’Donovan MC, Shaikh TH, Susser E, DeLisi LE, Sullivan PF, Deutsch CK, Rapoport J, Levy DL, King MC, Sebat J. Microduplications of 16p11.2 are associated with schizophrenia. Nat Genet 2009; 41:1223-7. [PMID: 19855392 PMCID: PMC2951180 DOI: 10.1038/ng.474] [Citation(s) in RCA: 517] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 09/23/2009] [Indexed: 12/21/2022]
Abstract
Recurrent microdeletions and microduplications of a 600-kb genomic region of chromosome 16p11.2 have been implicated in childhood-onset developmental disorders. We report the association of 16p11.2 microduplications with schizophrenia in two large cohorts. The microduplication was detected in 12/1,906 (0.63%) cases and 1/3,971 (0.03%) controls (P = 1.2 x 10(-5), OR = 25.8) from the initial cohort, and in 9/2,645 (0.34%) cases and 1/2,420 (0.04%) controls (P = 0.022, OR = 8.3) of the replication cohort. The 16p11.2 microduplication was associated with a 14.5-fold increased risk of schizophrenia (95% CI (3.3, 62)) in the combined sample. A meta-analysis of datasets for multiple psychiatric disorders showed a significant association of the microduplication with schizophrenia (P = 4.8 x 10(-7)), bipolar disorder (P = 0.017) and autism (P = 1.9 x 10(-7)). In contrast, the reciprocal microdeletion was associated only with autism and developmental disorders (P = 2.3 x 10(-13)). Head circumference was larger in patients with the microdeletion than in patients with the microduplication (P = 0.0007).
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Affiliation(s)
- Shane McCarthy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Vladimir Makarov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - George Kirov
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - Anjene Addington
- Child Psychiatry Branch, National Institute for Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Jon McClellan
- Department of Psychiatry, University of Washington, Seattle, Washington, USA
| | - Seungtai Yoon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Dianna Perkins
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina USA
| | - Diane E. Dickel
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Mary Kusenda
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Graduate Program in Genetics State University of New York, Stony Brook, New York, USA
| | - Olga Krastoshevsky
- Psychology Research Laboratory, McLean Hospital, Belmont, Massachusetts, USA
| | - Verena Krause
- Psychology Research Laboratory, McLean Hospital, Belmont, Massachusetts, USA
| | - Ravinesh A. Kumar
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Detelina Grozeva
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - Dheeraj Malhotra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Tom Walsh
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Elaine H. Zackai
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Paige Kaplan
- Section of Biochemical Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jaya Ganesh
- Section of Biochemical Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ian D. Krantz
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nancy B. Spinner
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | - Kevin Pavon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - B. Lakshmi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Anthony Leotta
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Yoon-ha Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Vladimir Vacic
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sydney Gary
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Lilia Iakoucheva
- Laboratory of Statistical Genetics, The Rockefeller University, New York, USA
| | - Timothy J. Crow
- The Prince of Wales International Center for SANE Research, Warneford Hospital, Oxford, UK
| | - Susan L. Christian
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Jeffrey Lieberman
- College of Physicians and Surgeons of Columbia University, Columbia University, New York, USA
| | - Scott Stroup
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, University of Tampere, Tampere, Finland
| | - Kaija Puura
- Department of Child Psychiatry, Tampere University and University Hospital, Tampere, Finland
| | - Chad Haldeman-Englert
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Justin Pearl
- Genetic Basis of Mood and Anxiety Disorders Unit, National Institute for Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Meredith Goodell
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Virginia L. Willour
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Pamela DeRosse
- Department of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, New York, USA
| | - Jo Steele
- Genetic Basis of Mood and Anxiety Disorders Unit, National Institute for Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Layla Kassem
- Genetic Basis of Mood and Anxiety Disorders Unit, National Institute for Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Jessica Wolff
- Genetic Basis of Mood and Anxiety Disorders Unit, National Institute for Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Nisha Chitkara
- Department of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, New York, USA
| | - Francis J. McMahon
- Genetic Basis of Mood and Anxiety Disorders Unit, National Institute for Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Anil K. Malhotra
- Department of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, New York, USA
| | - James B. Potash
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Thomas G. Schulze
- Genetic Basis of Mood and Anxiety Disorders Unit, National Institute for Mental Health, National Institutes of Health, Bethesda, Maryland, USA
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, University of Heidelburg, Germany
| | - Markus M. Nöthen
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Sven Cichon
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, University of Heidelburg, Germany
- Department of Psychiatry and Psychotherapy, University of Bonn, Germany
| | - Ellen Leibenluft
- Mood and Anxiety Disorders Program, National Institute for Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Vlad Kustanovich
- Autism Genetic Resource Exchange, Autism Speaks, Los Angeles, California, USA
| | - Clara M. Lajonchere
- Autism Genetic Resource Exchange, Autism Speaks, Los Angeles, California, USA
| | - James S. Sutcliffe
- Center for Molecular Neuroscience, Vanderbilt University, Nashville, Tennessee, USA
| | - David Skuse
- Behavioral Sciences Unit, Institute of Child Health University College London, London, UK
| | - Michael Gill
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Louise Gallagher
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Nancy R. Mendell
- Department of Applied Mathematics and Statistics, State University of New York, Stony Brook, New York. USA
| | | | - Nick Craddock
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael J. Owen
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael C. O’Donovan
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - Tamim H. Shaikh
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ezra Susser
- College of Physicians and Surgeons of Columbia University, Columbia University, New York, USA
| | - Lynn E. DeLisi
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
- Brockton VA Boston Health Care Services, Brockton, Massachusetts, USA
| | - Patrick F. Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Curtis K. Deutsch
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
- Eunice Kennedy Shriver Center, University of Massachusetts Medical School, Waltham, Massachusetts, USA
| | - Judith Rapoport
- Child Psychiatry Branch, National Institute for Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Deborah L. Levy
- Psychology Research Laboratory, McLean Hospital, Belmont, Massachusetts, USA
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jonathan Sebat
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
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77
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In vivo intraclonal and interclonal kinetic heterogeneity in B-cell chronic lymphocytic leukemia. Blood 2009; 114:4832-42. [PMID: 19789386 DOI: 10.1182/blood-2009-05-219634] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Clonal evolution and outgrowth of cellular variants with additional chromosomal abnormalities are major causes of disease progression in chronic lymphocytic leukemia (CLL). Because new DNA lesions occur during S phase, proliferating cells are at the core of this problem. In this study, we used in vivo deuterium ((2)H) labeling of CLL cells to better understand the phenotype of proliferating cells in 13 leukemic clones. In each case, there was heterogeneity in cellular proliferation, with a higher fraction of newly produced CD38+ cells compared with CD38- counterparts. On average, there were 2-fold higher percentages of newly born cells in the CD38+ fraction than in CD38- cells; when analyzed on an individual patient basis, CD38+ (2)H-labeled cells ranged from 6.6% to 73%. Based on distinct kinetic patterns, interclonal heterogeneity was also observed. Specifically, 4 patients exhibited a delayed appearance of newly produced CD38+ cells in the blood, higher leukemic cell CXC chemokine receptor 4 (CXCR4) levels, and increased risk for lymphoid organ infiltration and poor outcome. Our data refine the proliferative compartment in CLL based on CD38 expression and suggest a relationship between in vivo kinetics, expression of a protein involved in CLL cell retention and trafficking to solid tissues, and clinical outcome.
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78
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Gunnarsson R, Isaksson A, Mansouri M, Göransson H, Jansson M, Cahill N, Rasmussen M, Staaf J, Lundin J, Norin S, Buhl AM, Smedby KE, Hjalgrim H, Karlsson K, Jurlander J, Juliusson G, Rosenquist R. Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: a high-resolution genomic screening of newly diagnosed patients. Leukemia 2009; 24:211-5. [DOI: 10.1038/leu.2009.187] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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79
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Codony C, Crespo M, Abrisqueta P, Montserrat E, Bosch F. Gene expression profiling in chronic lymphocytic leukaemia. Best Pract Res Clin Haematol 2009; 22:211-22. [DOI: 10.1016/j.beha.2009.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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80
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