title: Genome-Wide Expression Screening Discloses Long Noncoding RNAs Involved in Thyroid Carcinogenesis.
abstract: BACKGROUND
  Long noncoding RNAs (lncRNAs) regulate pathological processes, yet their potential roles in papillary thyroid carcinoma (PTC) are poorly understood.
  
  
  OBJECTIVE
  To profile transcriptionally dysregulated lncRNAs in PTC and identify lncRNAs associated with clinicopathological characteristics.
  
  
  METHODS
  We performed RNA sequencing of 12 paired PTC tumors and matched noncancerous tissues and correlated the expression of lncRNAs with clinical parameters. The 2 most significantly dysregulated lncRNAs were studied in an Ohio PTC cohort (n = 109) and in PTC data (n = 497) from The Cancer Genome Atlas.
  
  
  METHODS
  A combination of laboratory-based studies and computational analysis using clinical data and samples and a publically available database.
  
  
  METHODS
  Correlation between expression values and clinical parameters.
  
  
  RESULTS
  We identified 218 lncRNAs showing differential expression in PTC (fold change ≥ 2.0, P < .01). Significant correlation was observed between the expression of 2 lncRNAs (XLOC_051122 and XLOC_006074) and 1) lymph node metastasis (N stage) and 2) BRAF(V600E) mutation. Among patients with wild-type BRAF, the expression of these 2 lncRNAs showed significantly higher levels in the patients with lymph node metastasis. In silico analysis of these lncRNAs pinpointed cell movement and cellular growth and proliferation as targeted functions.
  
  
  CONCLUSIONS
  Comprehensive expression screening identified 2 novel lncRNAs associated with risk factors of adverse prognosis in PTC patients. These lncRNAs may be novel players in PTC carcinogenesis.
authors.affiliation: Human Cancer Genetics Program and Department of Cancer Biology and Genetics (S.L., W.L., P.B., L.S., A.d.l.C., H.H.) and Departments of Internal Medicine (P.Y., P.B., L.S., M.D.R.) and Physics (R.B.), The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210.
authors.forename: Sandya
authors.initials: S
authors.lastname: Liyanarachchi
authors.affiliation: Human Cancer Genetics Program and Department of Cancer Biology and Genetics (S.L., W.L., P.B., L.S., A.d.l.C., H.H.) and Departments of Internal Medicine (P.Y., P.B., L.S., M.D.R.) and Physics (R.B.), The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Human Cancer Genetics Program and Department of Cancer Biology and Genetics (S.L., W.L., P.B., L.S., A.d.l.C., H.H.) and Departments of Internal Medicine (P.Y., P.B., L.S., M.D.R.) and Physics (R.B.), The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210.
authors.forename: Pearlly
authors.initials: P
authors.lastname: Yan
authors.affiliation: Human Cancer Genetics Program and Department of Cancer Biology and Genetics (S.L., W.L., P.B., L.S., A.d.l.C., H.H.) and Departments of Internal Medicine (P.Y., P.B., L.S., M.D.R.) and Physics (R.B.), The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210.
authors.forename: Ralf
authors.initials: R
authors.lastname: Bundschuh
authors.affiliation: Human Cancer Genetics Program and Department of Cancer Biology and Genetics (S.L., W.L., P.B., L.S., A.d.l.C., H.H.) and Departments of Internal Medicine (P.Y., P.B., L.S., M.D.R.) and Physics (R.B.), The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210.
authors.forename: Pamela
authors.initials: P
authors.lastname: Brock
authors.affiliation: Human Cancer Genetics Program and Department of Cancer Biology and Genetics (S.L., W.L., P.B., L.S., A.d.l.C., H.H.) and Departments of Internal Medicine (P.Y., P.B., L.S., M.D.R.) and Physics (R.B.), The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210.
authors.forename: Leigha
authors.initials: L
authors.lastname: Senter
authors.affiliation: Human Cancer Genetics Program and Department of Cancer Biology and Genetics (S.L., W.L., P.B., L.S., A.d.l.C., H.H.) and Departments of Internal Medicine (P.Y., P.B., L.S., M.D.R.) and Physics (R.B.), The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Ringel
authors.affiliation: Human Cancer Genetics Program and Department of Cancer Biology and Genetics (S.L., W.L., P.B., L.S., A.d.l.C., H.H.) and Departments of Internal Medicine (P.Y., P.B., L.S., M.D.R.) and Physics (R.B.), The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210.
authors.forename: Albert
authors.initials: A
authors.lastname: de la Chapelle
authors.affiliation: Human Cancer Genetics Program and Department of Cancer Biology and Genetics (S.L., W.L., P.B., L.S., A.d.l.C., H.H.) and Departments of Internal Medicine (P.Y., P.B., L.S., M.D.R.) and Physics (R.B.), The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210.
authors.forename: Huiling
authors.initials: H
authors.lastname: He
mesh_terms: D019943:Amino Acid Substitution; D014408:Biomarkers, Tumor / Q000096:biosynthesis; D002277:Carcinoma / Q000175:diagnosis / Q000378:metabolism* / Q000503:physiopathology / Q000601:surgery; D002291:Carcinoma, Papillary / Q000175:diagnosis / Q000378:metabolism* / Q000503:physiopathology / Q000601:surgery; D015331:Cohort Studies; D019295:Computational Biology; D005103:Expert Systems; D020869:Gene Expression Profiling; D055106:Genome-Wide Association Study; D006801:Humans; D008197:Lymph Node Excision / Q000009:adverse effects; D008198:Lymph Nodes / Q000473:pathology; D008207:Lymphatic Metastasis; D009154:Mutation; D009367:Neoplasm Staging; D009820:Ohio; D011379:Prognosis; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000096:biosynthesis*; D012334:RNA, Neoplasm / Q000096:biosynthesis*; D000077273:Thyroid Cancer, Papillary; D013961:Thyroid Gland / Q000378:metabolism* / Q000473:pathology / Q000503:physiopathology / Q000601:surgery; D013964:Thyroid Neoplasms / Q000175:diagnosis / Q000378:metabolism* / Q000503:physiopathology / Q000601:surgery; D013965:Thyroidectomy / Q000009:adverse effects; D015854:Up-Regulation
chemical_list: D014408:Biomarkers, Tumor; D062085:RNA, Long Noncoding; D012334:RNA, Neoplasm; C000619693:XLOC_006074 long noncoding RNA, human; C000619692:XLOC_051122 long noncoding RNA, human; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf