Comparative expressed sequence hybridization reveals differential gene expression in morphological breast cancer subtypes

Bempt, Isabelle Vanden; Vanhentenrijk, Vera; Drijkoningen, Maria; Wolf-Peeters, Christiane De

doi:10.1002/path.1911

Cited by 10 publications

(3 citation statements)

References 45 publications

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“…Any review of the analysis of chromosomal copy numbers in breast cancer by array-CGH would be incomplete without mention of some related technologies (e.g. genome-wide LOH analysis, SNP [haplotype] analysis, CESH [ 94 , 99 ] [also called expressive genomic hybridization [ 100 ]], large-scale PCR [ 101 ] and expression array studies) that often have similar or overlapping goals, including classification, clinical prognostication, defining treatment subgroups, finding novel genes, and so on.…”

Section: Some Related Array-based Methodsmentioning

confidence: 99%

“…There are several effective ways to avoid some of the risks involved in searching complexly rearranged genomes for candidate genes. One is to map global gene expression onto genomic positions using comparative expressed sequence hybridization (CESH) [ 94 ]. Another is to focus on known candidate regions and simultaneously monitor gene expression as a filtering step to exclude genes.…”

Section: Cgh and Cancermentioning

confidence: 99%

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Array-CGH and breast cancer

Beers

Nederlof

2006

Breast Cancer Res

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The introduction of comparative genomic hybridization (CGH) in 1992 opened new avenues in genomic investigation; in particular, it advanced analysis of solid tumours, including breast cancer, because it obviated the need to culture cells before their chromosomes could be analyzed. The current generation of CGH analysis uses ordered arrays of genomic DNA sequences and is therefore referred to as array-CGH or matrix-CGH. It was introduced in 1998, and further increased the potential of CGH to provide insight into the fundamental processes of chromosomal instability and cancer. This review provides a critical evaluation of the data published on array-CGH and breast cancer, and discusses some of its expected future value and developments. IntroductionThe precise aetiology of the majority of breast cancers is elusive, which contrasts with the estimated 5-10% that are caused by inherited mutations. It is clear that breast cancer presents as a collection of distinct disease types that differ in disease progression, treatment response and disease-free survival. In addition to conventional pathology, emerging technologies, including micro-arrays, have proven to be excellent tools in enhancing our understanding of individual breast cancers and providing assistance in treatment decision making in clinically relevant subgroups [1]. Initial observations, indeed most of our current understanding of chromosome abnormalities came from conventional cytogenetics. The importance of DNA copy number alterations has been demonstrated in many tumours [2]. More recently, the results of array comparative genomic hybridization (array-CGH) analysis of tumour tissues have been described from several perspectives, including identification of subgroups (class discovery); identification of genes that are involved in tumour progression, metastasis and treatment response; identification of candidate oncogenes (in genetic amplifications) or tumour suppressors (in homozygous deletions); and classification of hereditary cancers. A few studies have also described CGH-based distinctions between sporadic and familial cases of breast cancer. Among familial cases, further classification into BRCA1, BRCA2, or 'other genetic risk factor(s)' is useful in these families in general but also for potential additional gene discovery.Array-CGH technology is a fairly recent and important upgrade to the groundbreaking (conventional, metaphase chromosome) CGH technology [3,4], and it is applied to detect chromosomal DNA copy number alterations (CNA) in cells or tissues that occur as a result of genomic instability. CGH technology caused a paradigm shift in (clinical) cytogenetics because it avoids the need to culture (tumour) cells. This is perhaps the main reason why there was considerable over-representation of information on nonsolid tumours in cytogenetic databases. Array-CGH can measure genomewide copy numbers in an unprecedented and objective manner. More importantly, complex karyotypes -a hallmark of many tumours -could be analyzed, including those ...

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Section: Some Related Array-based Methodsmentioning

confidence: 99%

Section: Cgh and Cancermentioning

confidence: 99%

Array-CGH and breast cancer

Beers

Nederlof

2006

Breast Cancer Res

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“…This recently developed technique identifies chromosomal regions of differential expression in a way similar to that of comparative genomic hybridization (CGH) 22. Previously, we successfully adapted this technique for use in the molecular investigation of lymphomas and of breast cancer 23, 24.…”

Section: Introductionmentioning

confidence: 99%

Relationship between classic Hodgkin lymphoma and overlapping large cell lymphoma investigated by comparative expressed sequence hybridization expression profiling

Vanhentenrijk

Bempt

Dierickx

et al. 2006

The Journal of Pathology

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There is a diagnostic grey zone between classic Hodgkin lymphoma (cHL) and some non-Hodgkin lymphoma (NHL), including primary mediastinal B cell lymphoma, diffuse large B cell lymphoma, and anaplastic large cell lymphoma. They all have some morphological and/or phenotypic features in common. To investigate this, we undertook an expression profiling study of these lymphomas using comparative expressed sequence hybridization. This technique detects chromosomal regions that are differentially expressed between a test and a reference tissue in a manner similar to comparative genomic hybridization, and is particularly suitable when the number of informative biopsies is limited. Using this approach, we identified a unique expression profile for all lymphoma types investigated. Unsupervised hierarchical cluster analysis of the acquired data showed that cHL separates from all investigated NHLs, including ALCL-like HL. Moreover, anaplastic lymphoma kinase (ALK)-negative ALCL clustered in a separate branch together with ALCL-like HL. Thus, analysing the neoplastic cells concurrently with their microenvironment, ALK-negative ALCL and ALCL-like HL seem to be related to each other, while cHL constitutes a separate lymphoma entity.

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Nascent pre-rRNA overexpression correlates with an adverse prognosis in alveolar rhabdomyosarcoma

Williamson

Fang

et al. 2006

Genes Chromosom. Cancer

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Comparative expressed sequence hybridization (CESH) is an expression profiling technique which identifies chromosomal regions corresponding to differential gene expression. Here, we observe that various tumor samples including rhabdomyosarcoma show very prominent staining on the short arms of the acrocentric chromosomes suggesting an increase in expression of ribosomal RNA synthesized from the repetitive rDNA of the nucleolar organizer regions located on these chromosomes. Survival analysis showed a correlation with overexpression from this region and a poor prognosis in rhabdomyosarcoma. This phenomenon was studied in an extended set of rhabdomyosarcoma tumor samples using quantitative real-time reverse transcriptase-PCR to quantify levels of pre-rRNA (precursor ribosomal RNA). It was demonstrated first that the strong CESH signals did correspond to a marked increase in pre-rRNA expression and second that high pre-rRNA expression correlated with an adverse prognosis in alveolar subtype rhabdomyosarcoma. In addition, we demonstrate that pre-rRNA expression is significantly correlated with tumor stage. We conclude that measuring expression of pre-rRNA by real-time PCR is a useful prognostic marker in alveolar rhabdomyosarcoma. Furthermore, given that we have observed similar rDNA staining in all cancer types that we have studied by CESH, we propose that pre-rRNA overexpression is a general phenomenon in cancer and that our real-time PCR assay may be applicable as a prognostic marker in other tumor types.

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Comparative expressed sequence hybridization reveals differential gene expression in morphological breast cancer subtypes

Cited by 10 publications

References 45 publications

Array-CGH and breast cancer

Array-CGH and breast cancer

Relationship between classic Hodgkin lymphoma and overlapping large cell lymphoma investigated by comparative expressed sequence hybridization expression profiling

Nascent pre-rRNA overexpression correlates with an adverse prognosis in alveolar rhabdomyosarcoma

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