Comparative expressed sequence hybridization to chromosomes for tumor classification and identification of genomic regions of differential gene expression

Lu, Yong‐Jie; Williamson, Daniel; Clark, Jeremy; Wang, Rubin; Tiffin, Nicki; Skelton, Lorraine; Gordon, Tony; Williams, Richard; Allan, B; Jackman, Ann L.; Cooper, Colin S.; Pritchard‐Jones, Kathy; Shipley, Janet

doi:10.1073/pnas.161272798

Cited by 50 publications

(68 citation statements)

References 27 publications

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“…CESH analysis was carried out as described previously (Lu et al, 2001) using the same capture system and software as for CGH analysis. Five good quality metaphases with 320 -450 band resolution were analysed for each case using the Quips CGH analysis software (Vysis) to produce an average profile of the fluorescence intensity ratios.…”

Section: Comparative Expressed Sequence Hybridisationmentioning

confidence: 99%

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Genomic copy number and expression patterns in testicular germ cell tumours

McIntyre

Summersgill

et al. 2007

Br J Cancer

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Testicular germ cell tumours of adults and adolescents (TGCT) include seminomas (SE) and nonseminomas (NS), with spermatocytic seminomas (SSE) representing a distinct entity in older men. SE and NS have gain of 12p material in all cases, whereas SSE are associated with overrepresentation of chromosome 9. Here, we compare at the chromosomal level, copy number imbalances with global expression changes, identified by comparative expressed sequence hybridisation analyses, in seven SE, one combined tumour, seven NS and seven cell lines. Positive correlations were found consistent with copy number as a main driver of expression change, despite reported differences in methylation status in SE and NS. Analysis of chromosomal copy number and expression data could not distinguish between SE and NS, in-keeping with a similar genetic pathogenesis. However, increased expression from 4q22, 5q23.2 and 9p21 distinguished SSE from SE and NS and decreased copy number and expression from 2q36 -q37 and 6q24 was a specific feature of NS-derived cell lines. Our analysis also highlights 19 regions with both copy number and expression imbalances in greater than 40% of cases. Mining available expression array data identified genes from these regions as candidates for involvement in TGCT development. Supplementary data is available at

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Section: Comparative Expressed Sequence Hybridisationmentioning

confidence: 99%

“…Here, we investigate a series of SSE, SE, NS and cell lines using the approach of comparative expressed sequence hybridisation (CESH) (Lu et al, 2001) to determine a global chromosomal level view of the expression patterns in these tumours. This and CGH data are analysed to determine the relationship between expression patterns and copy number imbalances.…”

mentioning

confidence: 99%

Genomic copy number and expression patterns in testicular germ cell tumours

McIntyre

Summersgill

et al. 2007

Br J Cancer

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“…Comparative expressed sequence hybridization followed a previously described protocol. 23 Labeled cDNA probes were prepared for hybridization using the CGH hybridization kit (Abbott). To reduce background noise, we pretreated metaphase target slides (Abbott) with Rnase (0.1 ml/ml) at 371C for 30 min.…”

Section: Comparative Expressed Sequence Hybridizationmentioning

confidence: 99%

“…22 To investigate the molecular mechanisms underlying the pathogenetic role of t(11;18)(q21;q21) in MALT lymphomas, we applied a recently developed molecular cytogenetic technique termed comparative expressed sequence hybridization (CESH). 23 This technique gives a genome-wide view of relative expression patterns within tissues according to chromosomal location in a way similar to that of comparative genomic hybridization (CGH). This is achieved by converting RNA extracted from the test sample into cDNA, amplifying it by PCR and competitively hybridizing this to normal metaphase chromosomes in the presence of cDNA obtained from a reference tissue.…”

mentioning

confidence: 99%

“…24,25 Other groups successfully used CESH in the study of solid tumors and childhood acute lymphoblastic leukemia. 23,26,27 In this study, we aimed to get more insight into the pathogenesis of gastric MALT lymphomas in general and to study the impact of the API2-MALT1 fusion protein. To this end, we compared t(11;18)(q21;q21)-positive and -negative gastric MALT lymphomas with each other and with normal spleen by CESH expression profiling.…”

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Comparative expressed sequence hybridization studies of t(11;18)(q21;q21)-positive and -negative gastric MALT lymphomas reveal both unique and overlapping gene programs

et al. 2010

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Among the genetic abnormalities reported to occur in MALT lymphomas, the translocation t(11;18)(q21;q21) is of particular interest because it is exclusively documented in MALT lymphomas, mainly with gastrointestinal location. It results in the creation of a fusion protein API2-MALT1 that activates the transcription factor NF-jB through enhanced IKKc polyubiquitination. Here, we apply the recently developed molecular technique termed comparative expressed sequence hybridization to identify differentially expressed chromosomal regions related to the pathogenesis of gastric MALT lymphomas. By comparing t(11;18)(q21;q21)-positive gastric MALT lymphomas to their t(11;18)(q21;q21)-negative counterparts, we found that the location of the MALT1 break point determines a difference in expression pattern within the t(11;18)(q21;q21)-positive group. Moreover, we could define a gastric MALT lymphoma signature, which most likely comprises the regions and genes with significance in the development of MALT lymphomas, by comparing both t(11;18)(q21;q21)-positive and -negative MALT lymphomas to normal lymphoid tissue. Finally, a significant imprint of the marginal zone signature, established by comparing microdissected, splenic B follicles with and without marginal zone, was evident in the expression profile of MALT lymphoma, further supporting a marginal zone origin for this type of B-cell non-Hodgkin's lymphoma.

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Comparative Expressed Sequence Hybridization ( CESH )

2004

Encyclopedic Dictionary of Genetics, Genomics and Proteomics

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Comparative expressed sequence hybridization to chromosomes for tumor classification and identification of genomic regions of differential gene expression

Cited by 50 publications

References 27 publications

Genomic copy number and expression patterns in testicular germ cell tumours

Genomic copy number and expression patterns in testicular germ cell tumours

Comparative expressed sequence hybridization studies of t(11;18)(q21;q21)-positive and -negative gastric MALT lymphomas reveal both unique and overlapping gene programs

Comparative Expressed Sequence Hybridization ( CESH )

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