Anayisis of Chromosomal Alterations by Array-Based Comparative Genomic Hybridization in 25 Patients with Sézary Syndrome.

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2714-2714
Author(s):  
Giorgia Saporiti ◽  
Laura Corti ◽  
Francesco Onida ◽  
Daniele Fanoni ◽  
Luigia Venegoni ◽  
...  

Abstract Abstract 2714 Sézary Syndrome (SS) is an aggressive type of cutaneous CD4+ T-cell lymphoma characterized by erythroderma, generalized lymphadenopathy and presence of malignant T cells in peripheral blood. Patients with SS have a generally poor median survival (2–4 years), with allogeneic stem cell transplantation as the only curative treatment option. Genome-wide analysis of chromosomal alterations represents a current powerful tool to investigate pathophysiology in hematological malignancies, possibly leading to development of new therapeutic agents. A recent important study reported gain of 17q22–25 and 8q22–24, as well as loss of 17p13 and 10q25 as characteristic genomic aberrations in SS. In this study, by array-based comparative genomic hybridization (a-CGH), we aimed to further explore genomic alterations in 25 patients with Sézary Syndrome (SS) referred to our Institution. The patient series included 11 males and 14 females, with a median age of 65 years (range 29 to 85). At diagnosis, 3 patients were in stage IIIB, 18 in stage IVA1 and 4 in stage IVA2. Flow cytometry analysis unveiled typical CD4+/CD7±/CD26- lymphocytic immunophenotype, while molecular analysis showed clonal rearrangement of T-cell receptor beta and/or gamma chains in all patients. At the time of blood samples collection, 21% of patients were untreated. Among treated ones, photopheresis alone was used in 37% whereas all the others received also chemotherapy-based therapies. Lymphocyte count was higher than 3000/mcL in 75% of patients, higher than 6000/mcL in 46% and higher than 9000/mcL in 25%. Elevated LDH levels were observed in 29%. Genomic DNA was isolated from peripheral blood mononuclear cells of 10 patients and from CD4+/CD14− cells of 15 patients, selected by an immunomagnetic method. Quantity and quality of all gDNA samples were assessed using UV- VIS spectrophotometry and agarose gel electrophoresis. Genome-wide array-based comparative genomic hybridization (aCGH) was performed using the Agilent Human Genome CGH Microarray Kit 4×44K. Copy number profiles from CGH arrays were compared using Integrative Genome Viewer. Most frequently observed recurrent copy number alterations involved gains in chromosomes 7, 8 and 17 and losses in chromosome 10, 17 and 19. In particular, chromosomal gains involved 7q11.21-7q11.23 in 32% of patients, 7q21.3-7q22.1 in 36%, 8q24.2-8q24.3 in 44% (with amplification of the MYC oncogene in 36%), while chromosomal losses involved 10p11.22 in 44% of patients, 10q11.22–21.1 in 48%, 10q23.3 (harbouring the PTEN tumor suppressor gene) in 40%, 10q24 (involving NFkB2 gene) in 56%, 10q25.1-q26.3 in 56%, and 19p13.3 (involving the cell growth/apoptosis regulating GADD45B gene) in 32%. With regard to chromosome 17, we observed loss of region 17p13.1 (containing the TP53 gene) in 60% of cases, whereas a gain in 17q21 (harbouring genes coding for STAT3, STAT5A e STAT5B) was documented in 64% of patients. Worth mentioning, 52% of cases showed both losses in the p arm and gains in the q arm within chromosome 17. In summary, our results partially confirmed those previously reported with regard to alterations in chromosomes 7, 8, 10 and 17, resulting in amplification of oncogenes and deletion of tumor suppressor genes. We also observed genome alterations associated with activation of the signal transduction JAK/STAT pathway, possibly involved in SS malignant phenotype. Further genome alterations emerged in this study, such as those in chromosome 7 and 19, are also worth investigating for their possible pathophysiological meanings. Disclosures: No relevant conflicts of interest to declare.

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 995-995
Author(s):  
Esteban Braggio ◽  
Brian Patrick O'Neill ◽  
William Macon ◽  
Maria Beatriz Lopes ◽  
David Schiff ◽  
...  

Abstract Abstract 995 PCNSL is an aggressive primary brain tumor characterized by a perivascular accumulation of malignant lymphoid cells. Most PCNSLs (90%) are diffuse large B-cell lymphoma (DLBCL); the remaining 10% are poorly characterized low-grade, Burkitt, and T-cell lymphomas. Since most patients are biopsed, genomic analyses are challenging. To determine the pattern of genetic alterations in PCNSL, frozen samples and formalin fixed embedded paraffin sections from 17 EBV and HIV negative and immunocompetent patients were studied by array-based comparative genomic hybridization (aCGH) using Sureprint G3 (1 million probes) array (Agilent). B-cell differentiation status was characterized by immunostains for CD10, MUM-1, and BCL-6. All cases were characterized by complex genomic aberrations with a median of 21 copy-number abnormalities (CNA) per patient (range 10–49). Overall, 22 minimal deleted regions (MDR) and 14 minimal amplified regions (MAR) were found in more than 20% of patients. Focal deletion affecting CDKN2A (9p21) was the most common CNA, found in 14 of 17 cases (82%); biallelic in six cases. Losses of 6q were observed in 71% of cases. Deletions of 6q23.3 (TNFAIP3) and 6q21 (PRDM1) were found in 59% (10/17) and 47% (8/17) of cases, respectively. Other common CNA were deletions of 6p21 (9/17; 53%), 3p21.1 (5/17; 29%), 3q26.32 (5/17; 29%), 8q12.1 (5/17; 29%), 10p14-p15.3 (5/17; 29%), 12q24.31 (5/17; 29%) and gains of 12q21-q24 (9/17; 53%), 7q21-q31 (6/17; 35%), 19q13 (6/17; 35%), 3q27.3 (5/17; 29%) and 11q24.1-q25 (5/17; 29%). Interestingly, several CNA were unique to PCNSL and were not identified in related entities as the typical DLBCL. Besides in CDKN2A, homozygous deletions were recurrently found in TMEM30A and TOX, the latter a regulator of T-cell development. Another 64 genes, including B2M, CD58, ETV6, LAPTM, MHC class II genes, PRDM1, TNFRSF10A and TNFRSF10B were also homozygously deleted. CD58, which encodes for a member of the immunoglobulin family and regulates the adhesion and activation of T lymphocytes, was also recurrently affected by focal monoallelic losses from 15 nucleotides to 1–2 exons, affecting the Ig-like C2-type domain as was confirmed by DNA resequencing. Focal heterozygous deletions affect TBL1XR1, a negative regulator of the NF-kB and Wnt pathways, and the putative tumor suppressor BCL7A in 29% of cases each. Pathway analysis done including the most commonly affected genes (Ingenuity Pathway Analysis) highlights the importance of networks associated with apoptosis and lymphocyte differentiation and proliferation, especially of T lymphocytes. In summary, this study showed evidence for a highly complex genome and identified target genes of potential relevance in the pathogenesis of PCNSL. The genomic profile described here is unique to PCNSL, thus helping to genetically differentiate this entity from the typical DLBCL and other related lymphomas. Disclosures: Fonseca: Genzyme: Consultancy; Medtronic: Consultancy; BMS: Consultancy; AMGEN: Consultancy; Otsuka: Consultancy; Celgene: Consultancy, Research Funding; Intellikine: Consultancy; Cylene: Research Funding; Onyx: Research Funding; FISH probes prognostication in myeloma: Patents & Royalties.


Blood ◽  
2009 ◽  
Vol 113 (1) ◽  
pp. 137-148 ◽  
Author(s):  
K.-John J. Cheung ◽  
Sohrab P. Shah ◽  
Christian Steidl ◽  
Nathalie Johnson ◽  
Thomas Relander ◽  
...  

Abstract The secondary genetic events associated with follicular lymphoma (FL) progression are not well defined. We applied genome-wide BAC array comparative genomic hybridization to 106 diagnostic biopsies of FL to characterize regional genomic imbalances. Using an analytical approach that defined regions of copy number change as intersections between visual annotations and a Hidden Markov model–based algorithm, we identified 71 regional alterations that were recurrent in at least 10% of cases. These ranged in size from approximately 200 kb to 44 Mb, affecting chromosomes 1, 5, 6, 7, 8, 10, 12, 17, 18, 19, and 22. We also demonstrated by cluster analysis that 46.2% of the 106 cases could be sub-grouped based on the presence of +1q, +6p/6q−, +7, or +18. Survival analysis showed that 21 of the 71 regions correlated significantly with inferior overall survival (OS). Of these 21 regions, 16 were independent predictors of OS using a multivariate Cox model that included the international prognostic index (IPI) score. Two of these 16 regions (1p36.22-p36.33 and 6q21-q24.3) were also predictors of transformation risk and independent of IPI. These prognostic features may be useful to identify high-risk patients as candidates for risk-adapted therapies.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 759-759
Author(s):  
Frank G. Rucker ◽  
Lars Bullinger ◽  
Hans A. Kestler ◽  
Peter Lichter ◽  
Konstanze Dohner ◽  
...  

Abstract Clonal chromosome abnormalities represent one of the most important prognostic factors in adult acute myeloid leukemia (AML), and cytogenetic data are used for risk-adapted treatment strategies. By conventional cytogenetic analysis, approximately 50% of patients lack clonal chromosome aberrations, and normal cytogenetics are associated with an intermediate clinical outcome. This clinically heterogeneous group seems to be in part characterized by molecular markers, such as MLL, FLT3, CEBPA, and NPM1 mutations. In order to identify novel candidate regions of genomic imbalances, we applied comparative genomic hybridization to microarrays (matrix-CGH). Using this high-resolution genome-wide screening approach we analyzed 49 normal karyotype AML cases characterized for the most common clinically relevant molecular markers (MLL-PTD n=13, FLT3-ITD n=7, FLT3-ITD/NPM1+ n=4, MLL-PTD/FLT3-ITD n=3, CEBPA+ n=12, CEBPA+/FLT3-ITD n=1; CEBPA+/NPM1+ n=1; no molecular markers n=8) with a microarray platform consisting of 2799 different BAC or PAC clones. A set of 1500 of these clones covers the whole human genome with a physical distance of approximately 2 Mb. The remaining 1299 clones either contiguously span genomic regions known to be frequently involved in hematologic malignancies (e.g., 1p, 2p, 3q, 7q, 9p, 11q, 12q, 13q, 17p, 18q) (n=600) or contain oncogenes or tumor suppressor genes (n=699). In addition to known copy number polymorphisms in 5q11, 7q22, 7q35, 14q32, and 15q11, the CLuster Along Chromosomes method (CLAC; http://www-stat.stanford.edu/~wp57/CGH-Miner) disclosed copy number alterations (CNAs) in terms of gains in 1p, 11q, 12q, and 17p. CNAs in terms of losses were identified in 9p, 11q, 12p, 12q, and 13q. Two-class supervised analyses using the significance analysis of microarrays (SAM) method identified for the MLL-PTD cases a gain of a single clone harboring the MLL gene. While the significance of these findings, which are currently validated using fluorescence in-situ hybridization (FISH), still remains to be determined, our preliminary results already demonstrate the power and reliablity of this microarray-based technique allowing genome-wide screens of genomic imbalances as the MLL aberration was detected in all cases known to have a MLL-PTD. Furthermore, ongoing correlation of high-resolution genomic profiling with global gene expression studies will help to disclose pathways underlying normal karyotype AML, thereby leading to new insights of leukemogenesis.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2054-2054
Author(s):  
Masao Nakagawa ◽  
Aya Oshiro ◽  
Hiroyuki Tagawa ◽  
Sivasundaram Karnan ◽  
Shinobu Tsuzuki ◽  
...  

Abstract Peripheral T-cell lymphoma, unspecified (PTCL-U) is the most common group among Peripheral T-cell lymphomas (PTCLs). This category consists of the cases which do not belong to any of the recognizable subtypes of PTCLs in WHO classification. PTCL-U comprises heterogeneous groups in morphology and phenotype. Molecular basis of clinical heterogeneity is needed to identify distinct subgroups with clnical relevance. Several reports of conventional cytogenetic studies including comparative genomic hybridization (CGH) showed some recurrent aberrations, but failed to identify the genetic hallmarks to categorize distinct subgroups. So far, no array-based comparative genomic hybridization (array CGH) study for PTCL-U has been reported. Here we analyzed 29 cases of PTCL-U by means of array CGH consisting of 2265 artificial chromosome clones that cover the whole genome at a 1.3 mega base resolution. The analysis clearly divided these cases into two distinct subgroups on the basis of frequency of genomic alterations. One group consists of 17 cases which showed significant lower copy number changes (average copy number gains: 0.5 regions, average copy number losses: 0.1 regions). The other group had average copy number gains of 15.7 regions and losses of 15.0 regions in 12 cases. We designate the former as “simple type” and the latter as “complex type”. In the complex type, regions of recurrent (>20%) gain are detected on chromosome 1q23.3-24.2, 3q25.31-tel, 4p15.1-16.1, 4q28.3-31.23, 5q34, 6p24.1-25.1, 7p21.3-tel, 7p21.1, 7q, 8q24.23, 11q13.4-tel, 12p11.21-11.22, 16p12.3-13.3, 17q11.2-22. Regions of recurrent (>20%) losses are detected on chromosome 1p13.1-13.3, 2q37.3, 4q21.21-21.23, 4q34.3-35.1, 5q21.2-23.1, 6p12.1-q14.3, 6q23.2-24.1, 6q25.1-26, 7p14.3-22.1, 9p21.3, 10p14-qtel, 12p13.1-13.2, 13, 14q12, 16q, 17p, 18p, 20q13-2, 22q11.21-12.2. Median age is 62 years in the simple type and 73 years in the complex type, respectively. Median survival is 27 months in the simple type and 11 months in the complex type. Log-rank test for overall survival between the simple type and the complex type showed inferior survival for the complex type but significance was marginal (p=0.21). Our findings showed that PTCL-U comprised two genetically distinct subgroups, implying that distinct mechanisms underlay in molecular pathogenesis of PTCL-U. Furthermore cilinicopathological features of each group are also being studied.


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