title: MicroRNA profiling of clear cell renal cell carcinoma by whole-genome small RNA deep sequencing of paired frozen and formalin-fixed, paraffin-embedded tissue specimens.
abstract: Renal cell carcinoma (RCC) is one of the leading causes of cancer mortality. Characterization of microRNA (miRNA) expression of RCC will help disclose new pathogenic pathways in tumourigenesis and progression and may lead to the development of molecular biomarkers and target-specific therapies for diagnosis, prognostication and treatment. With limitations in test specificity and the ability to detect novel miRNA and other small non-coding RNAs (smRNAs), microarray and RT-PCR techniques are being replaced by the evolving deep-sequencing technologies, at least in the discovery phase. Until now, cancer miRNA profiling of human benign and tumour specimen sets, using smRNA deep-sequencing (smRNA-seq), has not been reported. Specifically, due to concern over possible poor RNA quality/integrity, formalin-fixed paraffin-embedded (FFPE) samples have not been used for such studies. Here, we performed whole-genome smRNA-seq analysis using a benign and RCC specimen set and have successfully profiled the miRNA expression. Studies performed on paired frozen and FFPE specimens showed very similar results. Moreover, a comparison study of microarray, deep-sequencing and RT-PCR methodologies also showed a high correlation among the three technologies. To our knowledge, this is the first study to demonstrate that FFPE specimens can be used reliably for miRNA deep-sequencing analysis, making future large-scale clinical cohort/trial-based studies possible.
authors.affiliation: Department of Pathology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA.
authors.forename: Lihong
authors.initials: L
authors.lastname: Weng
authors.forename: Xiwei
authors.initials: X
authors.lastname: Wu
authors.forename: Hanlin
authors.initials: H
authors.lastname: Gao
authors.forename: Bing
authors.initials: B
authors.lastname: Mu
authors.forename: Xuejun
authors.initials: X
authors.lastname: Li
authors.forename: Jin-Hui
authors.initials: JH
authors.lastname: Wang
authors.forename: Chao
authors.initials: C
authors.lastname: Guo
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Jin
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Chen
authors.forename: Maricela
authors.initials: M
authors.lastname: Covarrubias
authors.forename: Yate-Ching
authors.initials: YC
authors.lastname: Yuan
authors.forename: Lawrence M
authors.initials: LM
authors.lastname: Weiss
authors.forename: Huiqing
authors.initials: H
authors.lastname: Wu
mesh_terms: D002292:Carcinoma, Renal Cell / Q000235:genetics*; D016000:Cluster Analysis; D015925:Cryopreservation; D005557:Formaldehyde; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016612:Paraffin Embedding; D012334:RNA, Neoplasm / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D016707:Tissue Fixation / Q000379:methods
chemical_list: D035683:MicroRNAs; D012334:RNA, Neoplasm; D005557:Formaldehyde