Array CGH and gene-expression profiling reveals distinct genomic instability patterns associated with DNA repair and cell-cycle checkpoint pathways in Ewing's ... View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2007-10-22

AUTHORS

B I Ferreira, J Alonso, J Carrillo, F Acquadro, C Largo, J Suela, M R Teixeira, N Cerveira, A Molares, G Goméz-López, Á Pestaña, A Sastre, P Garcia-Miguel, J C Cigudosa

ABSTRACT

Ewing's sarcoma (ES) is characterized by specific chromosome translocations, the most common being t(11;22)(q24;q12). Additionally, other type of genetic abnormalities may occur and be relevant for explaining the variable tumour biology and clinical outcome. We have carried out a high-resolution array CGH and expression profiling on 25 ES tumour samples to characterize the DNA copy number aberrations (CNA) occurring in these tumours and determine their association with gene-expression profiles and clinical outcome. CNA were observed in 84% of the cases. We observed a median number of three aberrations per case. Besides numerical chromosome changes, smaller aberrations were found and defined at chromosomes 5p, 7q and 9p. All CNA were compiled to define the smallest overlapping regions of imbalance (SORI). A total of 35 SORI were delimited. Bioinformatics analyses were conducted to identify subgroups according to the pattern of genomic instability. Unsupervised and supervised clustering analysis (using SORI as variables) segregated the tumours in two distinct groups: one genomically stable (⩽3 CNA) and other genomically unstable (>3 CNA). The genomic unstable group showed a statistically significant shorter overall survival and was more refractory to chemotherapy. Expression profile analysis revealed significant differences between both groups. Genes related with chromosome segregation, DNA repair pathways and cell-cycle control were upregulated in the genomically unstable group. This report elucidates, for the first time, data about genomic instability in ES, based on CNA and expression profiling, and shows that a genomically unstable group of Ewing's tumours is correlated with a significant poor prognosis. More... »

PAGES

2084-2090

Journal

TITLE

Oncogene

ISSUE

14

VOLUME

27

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/sj.onc.1210845

DOI

http://dx.doi.org/10.1038/sj.onc.1210845

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1025623018

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/17952124


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20 schema:description Ewing's sarcoma (ES) is characterized by specific chromosome translocations, the most common being t(11;22)(q24;q12). Additionally, other type of genetic abnormalities may occur and be relevant for explaining the variable tumour biology and clinical outcome. We have carried out a high-resolution array CGH and expression profiling on 25 ES tumour samples to characterize the DNA copy number aberrations (CNA) occurring in these tumours and determine their association with gene-expression profiles and clinical outcome. CNA were observed in 84% of the cases. We observed a median number of three aberrations per case. Besides numerical chromosome changes, smaller aberrations were found and defined at chromosomes 5p, 7q and 9p. All CNA were compiled to define the smallest overlapping regions of imbalance (SORI). A total of 35 SORI were delimited. Bioinformatics analyses were conducted to identify subgroups according to the pattern of genomic instability. Unsupervised and supervised clustering analysis (using SORI as variables) segregated the tumours in two distinct groups: one genomically stable (⩽3 CNA) and other genomically unstable (>3 CNA). The genomic unstable group showed a statistically significant shorter overall survival and was more refractory to chemotherapy. Expression profile analysis revealed significant differences between both groups. Genes related with chromosome segregation, DNA repair pathways and cell-cycle control were upregulated in the genomically unstable group. This report elucidates, for the first time, data about genomic instability in ES, based on CNA and expression profiling, and shows that a genomically unstable group of Ewing's tumours is correlated with a significant poor prognosis.
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28 DNA copy number aberrations
29 DNA repair
30 DNA repair pathways
31 ES tumour samples
32 Ewing tumors
33 Ewing's sarcoma
34 SORI
35 aberrations
36 abnormalities
37 analysis
38 array CGH
39 association
40 bioinformatics analysis
41 biology
42 cases
43 cell cycle checkpoint pathways
44 cell cycle control
45 changes
46 checkpoint pathway
47 chemotherapy
48 chromosome 5p
49 chromosome changes
50 chromosome segregation
51 chromosome translocation
52 clinical outcomes
53 control
54 copy number aberrations
55 data
56 differences
57 distinct genomic instability patterns
58 distinct groups
59 expression
60 expression profile analysis
61 expression profiling
62 first time
63 gene expression profiles
64 gene expression profiling
65 genes
66 genetic abnormalities
67 genomic instability
68 genomic instability patterns
69 genomic unstable group
70 group
71 high-resolution array CGH
72 imbalance
73 instability
74 instability patterns
75 median number
76 number
77 number aberrations
78 numerical chromosome changes
79 outcomes
80 overall survival
81 pathway
82 patterns
83 poor prognosis
84 profile
85 profile analysis
86 profiling
87 prognosis
88 region
89 regions of imbalance
90 repair
91 repair pathways
92 report
93 samples
94 sarcoma
95 segregation
96 shorter overall survival
97 significant differences
98 significant poorer prognosis
99 significant shorter overall survival
100 small aberrations
101 specific chromosome translocations
102 subgroups
103 survival
104 time
105 total
106 translocation
107 tumor biology
108 tumor samples
109 tumors
110 types
111 unstable group
112 variable tumor biology
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