title: A reliable method for the selection of exploitable melanoma archival paraffin embedded tissues for transcript biomarker profiling.
abstract: The source tissue for biomarkers mRNA expression profiling of tumors has traditionally been fresh-frozen tissue. The adaptation of formalin-fixed, paraffin-embedded (FFPE) tissues for routine mRNA profiling would however be invaluable in view of their abundance and the clinical information related to them. However, their use in the clinic remains a challenge due to the poor quality of RNA extracted from such tissues. Here, we developed a method for the selection of melanoma archival paraffin-embedded tissues that can be reliably used for transcript biomarker profiling. For that, we used qRT-PCR to conduct a comparative study in matched pairs of frozen and FFPE melanoma tissues of the expression of 25 genes involved in angiogenesis/tumor invasion and 15 housekeeping genes. A classification method was developed that can select the samples with a good frozen/FFPE correlation and identify those that should be discarded on the basis of paraffin data for four reference genes only. We propose therefore a simple and inexpensive assay which improves reliability of mRNA profiling in FFPE samples by allowing the identification and analysis of "good" samples only. This assay which can be extended to other genes would however need validation at the clinical level and on independent tumor series.
authors.affiliation: Département de Dermatologie, hôpital saint Louis Paris, Paris, France.
authors.forename: Celeste
authors.initials: C
authors.lastname: Lebbe
authors.forename: Mickael
authors.initials: M
authors.lastname: Guedj
authors.forename: Nicole
authors.initials: N
authors.lastname: Basset-Seguin
authors.forename: Marie Pierre
authors.initials: MP
authors.lastname: Podgorniak
authors.forename: Suzanne
authors.initials: S
authors.lastname: Menashi
authors.forename: Anne
authors.initials: A
authors.lastname: Janin
authors.forename: Samia
authors.initials: S
authors.lastname: Mourah
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D005629:Frozen Sections; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008545:Melanoma / Q000235:genetics*; D016612:Paraffin Embedding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016707:Tissue Fixation
chemical_list: D014408:Biomarkers, Tumor; D012333:RNA, Messenger