title: Targeted next-generation sequencing and non-coding RNA expression analysis of clear cell papillary renal cell carcinoma suggests distinct pathological mechanisms from other renal tumour subtypes.
abstract: Clear cell tubulopapillary renal cell carcinoma (CCPRCC) is a recently described rare renal malignancy that displays characteristic gross, microscopic and immunohistochemical differences from other renal tumour types. However, CCPRCC remains a very poorly understood entity. We therefore sought to elucidate some of the molecular mechanisms involved in this neoplasm by carrying out targeted next-generation sequencing (NGS) to identify associated mutations, and in addition examined the expression of non-coding (nc) RNAs. We identified multiple somatic mutations in CCPRCC cases, including a recurrent [3/14 cases (21%)] non-synonymous T992I mutation in the MET proto-oncogene, a gene associated with epithelial-to-mesenchymal transition (EMT). Using a microarray approach, we found that the expression of mature (n = 1105) and pre-miRNAs (n = 1105), as well as snoRNA and scaRNAs (n = 2214), in CCPRCC cases differed from that of clear cell renal cell carcinoma (CCRCC) or papillary renal cell carcinoma (PRCC) tumours. Surprisingly, and unlike other renal tumour subtypes, we found that all five members of the miR-200 family were over-expressed in CCPRCC cases. As these miRNAs are intimately involved with EMT, we stained CCPRCC cases for E-cadherin, vimentin and β-catenin and found that the tumour cells of all cases were positive for all three markers, a combination rarely reported in other renal tumours that could have diagnostic implications. Taken together with the mutational analysis, these data suggest that EMT in CCPRCC tumour cells is incomplete or blocked, consistent with the indolent clinical course typical of this malignancy. In summary, as well as describing a novel pathological mechanism in renal carcinomas, this study adds to the mounting evidence that CCPRCC should be formally considered a distinct entity. Microarray data have been deposited in the GEO database [GEO accession number (GSE51554)].
authors.affiliation: Oncology Area, Biodonostia Research Institute, San Sebastian, Spain; Nuffield Department of Clinical Laboratory Sciences, University of Oxford, UK; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
authors.forename: Charles H
authors.initials: CH
authors.lastname: Lawrie
authors.forename: Erika
authors.initials: E
authors.lastname: Larrea
authors.forename: Gorka
authors.initials: G
authors.lastname: Larrinaga
authors.forename: Ibai
authors.initials: I
authors.lastname: Goicoechea
authors.forename: María
authors.initials: M
authors.lastname: Arestin
authors.forename: Marta
authors.initials: M
authors.lastname: Fernandez-Mercado
authors.forename: Ondrej
authors.initials: O
authors.lastname: Hes
authors.forename: Francisco
authors.initials: F
authors.lastname: Cáceres
authors.forename: Lorea
authors.initials: L
authors.lastname: Manterola
authors.forename: José I
authors.initials: JI
authors.lastname: López
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D002292:Carcinoma, Renal Cell / Q000235:genetics* / Q000473:pathology; D016000:Cluster Analysis; D018153:Czech Republic; D004252:DNA Mutational Analysis; D004273:DNA, Neoplasm / Q000737:chemistry / Q000235:genetics; D018572:Disease-Free Survival; D058750:Epithelial-Mesenchymal Transition; D005500:Follow-Up Studies; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics* / Q000473:pathology; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D020411:Oligonucleotide Array Sequence Analysis; D000090063:Proto-Oncogene Mas; D012334:RNA, Neoplasm / Q000235:genetics / Q000302:isolation & purification; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics*; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA
chemical_list: D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm; C000715470:MAS1 protein, human; D035683:MicroRNAs; D000090063:Proto-Oncogene Mas; D012334:RNA, Neoplasm; D022661:RNA, Untranslated
keywords: EMT; clear cell papillary renal cell carcinoma; miRNA; non-coding RNA; renal carcinoma