title: Genetic predisposition to papillary thyroid carcinoma: involvement of FOXE1, TSHR, and a novel lincRNA gene, PTCSC2.
abstract: BACKGROUND
  By genome-wide association studies, the risk allele [A] of SNP rs965513 predisposes strongly to papillary thyroid carcinoma (PTC). It is located in a gene-poor region of 9q22, some 60 kb from the FOXE1 gene. The underlying mechanisms remain to be discovered.
  
  
  OBJECTIVE
  Our objective was to identify novel transcripts in the 9q22 locus and correlate gene expression levels with the genotypes of rs965513.
  
  
  METHODS
  We performed 3' and 5' rapid amplification of cDNA ends and RT-PCR to detect novel transcripts. One novel transcript was forcibly expressed in a cell line followed by gene expression array analysis. We genotyped rs965513 from PTC patients and measured gene expression levels by real-time RT-PCR in unaffected thyroid tissue and matched tumor.
  
  
  METHODS
  This was a laboratory-based study using cells from clinical tissue samples and a cancer cell line.
  
  
  METHODS
  We detected previously uncharacterized transcripts and evaluated the gene expression levels and the correlation with the risk allele of rs965513, age, gender, chronic lymphocyte thyroiditis (CLT), and TSH levels.
  
  
  RESULTS
  We found a novel long intergenic noncoding RNA gene and named it papillary thyroid cancer susceptibility candidate 2 (PTCSC2). Transcripts of PTCSC2 are down-regulated in PTC tumors. The risk allele [A] of rs965513 was significantly associated with low expression of unspliced PTCSC2, FOXE1, and TSHR in unaffected thyroid tissue. We also observed a significant association of age and CLT with PTCSC2 unspliced transcript levels. The correlation between the rs965513 genotype and the PTCSC2 unspliced transcript levels remained significant after adjusting for age, gender, and CLT. Forced expression of PTCSC2 in the BCPAP cell line affected the expression of a subset of noncoding and coding transcripts with enrichment of genes functionally involved in cell cycle and cancer.
  
  
  CONCLUSIONS
  Our data suggest a role for PTCSC2, FOXE1, and TSHR in the predisposition to PTC.
authors.affiliation: Human Cancer Genetics Program and Department of Molecular Virology, Immunology, and Medical Genetics (H.H., W.L., S.L., J.J., M.S., R.N., A.d.l.C), and Department of Internal Medicine (R.N.), Ohio State University Comprehensive Cancer Center, the Ohio State University, Columbus, Ohio 43210; and Division of Health and Biomedical Informatics, Department of Preventive Medicine, Robert H. Lurie Comprehensive Cancer Center (R.V.D.), Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611.
authors.forename: Huiling
authors.initials: H
authors.lastname: He
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Sandya
authors.initials: S
authors.lastname: Liyanarachchi
authors.forename: Jaroslaw
authors.initials: J
authors.lastname: Jendrzejewski
authors.forename: Mukund
authors.initials: M
authors.lastname: Srinivas
authors.forename: Ramana V
authors.initials: RV
authors.lastname: Davuluri
authors.forename: Rebecca
authors.initials: R
authors.lastname: Nagy
authors.forename: Albert
authors.initials: A
authors.lastname: de la Chapelle
mesh_terms: D000483:Alleles; D002291:Carcinoma, Papillary / Q000235:genetics* / Q000473:pathology; D051858:Forkhead Transcription Factors / Q000235:genetics*; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D062085:RNA, Long Noncoding; D011989:Receptors, Thyrotropin / Q000235:genetics*; D013964:Thyroid Neoplasms / Q000235:genetics* / Q000473:pathology
chemical_list: C106894:FOXE1 protein, human; D051858:Forkhead Transcription Factors; D062085:RNA, Long Noncoding; D011989:Receptors, Thyrotropin