Expression profiling of formalin-fixed paraffin embedded primary human uveal melanomas using DASL matrices

Cesare, Sebastian Di; Nantel, André; Marshall, Jean‐Claude; Fernandes, Bruno F.; Antecka, E.; Orellana, María Eugenia; Abourbih, Daniel; Saornil, Antonia M.; Burnier, Miguel N.

doi:10.1007/s00432-009-0692-3

Cited by 7 publications

(5 citation statements)

References 28 publications

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“…We can conclude that HER3, as the only member of the EGFR family of tyrosine kinase receptors, is commonly expressed in UM and predicts overall survival if it is localized in the cell nuclei. In contrast to the study of Di Cesare et al,24 we could not show any significant association between nuclear HER3 and spindle cell type in our material, suggesting that these properties are not strictly dependent of each other. In contrast to the subcellular distribution, the expression level of HER3 had no prognostic impact.…”

Section: Discussioncontrasting

confidence: 99%

“…, epitheloid cell type). In contrast, none of the other HER family receptors (EGFR, HER2 and HER4) appeared in the lists of prognostic factors 24…”

mentioning

confidence: 89%

“…In a recent study, Di Cesare et al investigated gene profiling of 41 cases of paraffin‐embedded primary UMs, and clinicopathological parameters were imputed in the analysis 24. They identified two genes, whose expression was highly associated with clinical parameters; Ligase IV expression was correlated with metastasis and HER3 with spindle cell morphology of UM 24. Spindle cell type is associated with good prognosis compared to other morphological variants ( e.g.…”

mentioning

confidence: 99%

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Nuclear HER3 is associated with favorable overall survival in uveal melanoma

Trocmé

Mougiakakos

Johansson

et al. 2011

Intl Journal of Cancer

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HER3 is a member of the epidermal growth factor receptor (EGFR) family and is expressed in several types of cancer. Both the cytoplasmic and nuclear appearances of the receptor have been reported. Here, we investigate the expression and subcellular distribution of HER3 in uveal melanoma (UM) cells and tissues and its potential impact on clinical outcome of patients. Paraffin-embedded samples from 128 consecutive UM patients, enucleated without alternative treatment on UM diagnosis, were evaluated for HER3 using immunohistochemistry. Immunoreactivity was scored for frequency, intensity of positive cells, and subcellular distribution. The results were correlated with the established clinicopathological parameters using univariate and multivariate statistical analyses. HER3 expression was shown in 70% of the cases (89/128). This contrasts with the other EGFR family receptors (EGFR, HER2 and HER4) that are infrequently expressed in UM. Surprisingly, HER3 was found to be localized solely in the cell nuclei in 56 cases. The remaining 33 HER3 positive cases showed diffuse distribution (cytoplasmic 6 nuclear). Nuclear HER3 was independently correlated with a more favorable overall survival (p 5 0.043 and hazard ratio 5 0.618) compared to cases with diffuse and/or no HER3. Nuclear localization of HER3 was also confirmed in fresh UM material and in UM cell lines. In conclusion, HER3 is frequently localized solely in the cell nuclei in UM and as such it predicts a more favorable overall survival.Uveal melanoma (UM) is the most common intraocular malignancy in adults. Roughly seven individuals per million are affected in Caucasian populations. 1 Its relatively low incidence is offset by a high mortality rate as $50% of the affected patients ultimately succumb to fatal metastases. 2,3 Patient survival has remained poor, presumably due to silent hematogenous systemic micrometastases occurring before the diagnosis of clinically evident ocular disease. The metastases have a characteristic hepatic tropism, and once the metastases have established themselves and are of detectable size, death occurs nearly uniformly 6-12 months later. 3,4 Several growth factor receptors are expressed in this malignancy, for example, c-Met, c-Kit and the insulin-like growth factor receptor (IGF-1R) and may promote a metastatic phenotype. [5][6][7][8][9] Recently, the role of the receptor tyrosine kinase HER3 has become a topic of interest. HER3, also known as ErbB3, belongs to the epidermal growth factor receptor (EGFR) family, which also includes EGFR (HER1), HER2 and HER4. 10,11 Unlike its family members, HER3 does not possess an active kinase domain and is therefore unable, in a homodimeric state, to convey signals into the cell via protein phosphorylation. 10 Instead, it relies on heterodimerization with other members of the EGFR family, which can thereby emit signaling responsible for cell proliferation and differentiation.Nuclear localization of the receptors in the EGFR family has been shown in several cancers to mark an especially aggressiv...

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Section: Discussioncontrasting

confidence: 99%

“…, epitheloid cell type). In contrast, none of the other HER family receptors (EGFR, HER2 and HER4) appeared in the lists of prognostic factors 24…”

mentioning

confidence: 89%

mentioning

confidence: 99%

See 1 more Smart Citation

Nuclear HER3 is associated with favorable overall survival in uveal melanoma

Trocmé

Mougiakakos

Johansson

et al. 2011

Intl Journal of Cancer

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“…Recent articles have shown concordance between fresh-frozen and FFPE profiles, using a variety of array technologies (Farragher et al , 2008; Linton et al , 2009; Di Cesare et al , 2010; Saleh et al , 2010; Williams et al , 2010). While signatures derived from fresh-frozen material have been subsequently tested in FFPE tissue (Roberts et al , 2009; Rodriguez et al , 2010), this is, to the best of our knowledge, the first time a genome-wide signature has been generated de novo from FFPE material and has been shown to successfully stratify an independent clinical data set.…”

Section: Discussionmentioning

confidence: 99%

Exon-array profiling unlocks clinically and biologically relevant gene signatures from formalin-fixed paraffin-embedded tumour samples

et al. 2011

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Background:Degradation and chemical modification of RNA in formalin-fixed paraffin-embedded (FFPE) samples hamper their use in expression profiling studies. This study aimed to show that useful information can be obtained by Exon-array profiling archival FFPE tumour samples.Methods:Nineteen cervical squamous cell carcinoma (SCC) and 9 adenocarcinoma (AC) FFPE samples (10–16-year-old) were profiled using Affymetrix Exon arrays. The gene signature derived was tested on a fresh-frozen non-small cell lung cancer (NSCLC) series. Exploration of biological networks involved gene set enrichment analysis (GSEA). Differential gene expression was confirmed using Quantigene, a multiplex bead-based alternative to qRT–PCR.Results:In all, 1062 genes were higher in SCC vs AC, and 155 genes higher in AC. The 1217-gene signature correctly separated 58 NSCLC into SCC and AC. A gene network centered on hepatic nuclear factor and GATA6 was identified in AC, suggesting a role in glandular cell differentiation of the cervix. Quantigene analysis of the top 26 differentially expressed genes correctly partitioned cervix samples as SCC or AC.Conclusion:FFPE samples can be profiled using Exon arrays to derive gene expression signatures that are sufficiently robust to be applied to independent data sets, identify novel biology and design assays for independent platform validation.

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“…The concentration and average size of the RNA product have been used to predict DASL performance 5. Alternatively, performance in the DASL assays can be predicted with a real‐time PCR assay to evaluate the expression of RPL13A , because an inverse correlation between RPL13A cycle threshold (Ct) values from real‐time PCR and DASL performance has been reported 1, 5–10.…”

Section: Introductionmentioning

confidence: 99%

Gene expression profiling of formalin‐fixed, paraffin‐embedded familial breast tumours using the whole genome‐DASL assay

Waddell

Cocciardi

Johnson

et al. 2010

The Journal of Pathology

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Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin-fixed, paraffin-embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumour banks. Once samples are fixed in formalin, the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study, we have evaluated the ability of the whole genome DASL (cDNA-mediated Annealing, Selection, extension, and Ligation) assay from Illumina to perform transcriptomic analysis of archived breast tumour tissue in formalin-fixed, paraffin-embedded (FFPE) blocks. We profiled 76 familial breast tumours from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non-BRCA1/2 families. We found that replicate samples correlated well with each other (r(2) = 0.9-0.98). In 12/15 cases, the matched formalin-fixed and frozen samples predicted the same tumour molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterization of many diseases.

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Expression profiling of formalin-fixed paraffin embedded primary human uveal melanomas using DASL matrices

Cited by 7 publications

References 28 publications

Nuclear HER3 is associated with favorable overall survival in uveal melanoma

Nuclear HER3 is associated with favorable overall survival in uveal melanoma

Exon-array profiling unlocks clinically and biologically relevant gene signatures from formalin-fixed paraffin-embedded tumour samples

Gene expression profiling of formalin‐fixed, paraffin‐embedded familial breast tumours using the whole genome‐DASL assay

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