Long Noncoding RNAs Papillary Thyroid Carcinoma Susceptibility Candidate 3 Antisense 1 and Papillary Thyroid Carcinoma Susceptibility Candidate 3 Synergistically Regulate ZC3H12A mRNA Stability via Vimentin at 14q13.3 Thyroid Cancer Locus.

Background

The 14q13.3 has been identified as a genetic locus associated with a genetically increased risk of papillary thyroid cancer (PTC) in several cohorts, yet its underlying regulatory mechanisms remain poorly understood.

Methods

The full-length sequence of expressed sequence tag fragment AA632637 in the thyroid was obtained by rapid amplification of complementary DNA ends assay. Quantitative Reverse Transcription PCR (qRT-PCR) assays were utilized to examine the expression levels of the long noncoding RNA (lncRNA) in clinical thyroid tissues and cell lines. Functional assays, including cell proliferation, migration, invasion, and apoptosis assays, were conducted both in vitro and in vivo. Furthermore, RNA-seq analysis, actinomycin D assay, RNA pull-down, RNA immunoprecipitation, and dual-luciferase reporter assays were performed to identify the long noncoding RNA (lncRNA) binding targets and reveal the underlying regulatory mechanism.

Results

We identified a previously unannotated lncRNA gene, named papillary thyroid carcinoma susceptibility candidate 3 antisense 1 (PTCSC3-AS1), within 14q13.3. The expression of PTCSC3-AS1 was strongly downregulated in PTC tumor tissues, and restoration of PTCSC3-AS1 expression in PTC cells inhibited tumorigenesis and promoted cell apoptosis. Moreover, PTCSC3-AS1 and PTCSC3, two lncRNAs located on the opposite strands at 14q13.3, were revealed to synergistically interact with their shared binding protein vimentin. Forced overexpression of PTCSC3 and PTCSC3-AS1 revealed that ZC3H12A, a gene validated as a PTC suppressor, was the shared downstream target of the two lncRNAs. Vimentin significantly reduced the mRNA stability of ZC3H12A, while the upregulation of PTCSC3 and PTCSC3-AS1 suppressed the mRNA degradation of ZC3H12A. In addition, rs944289 and rs116909374 were identified as two potential causative variants with distinct regulatory roles in the 14q13.3 locus. Mechanistically, PTCSC3-AS1 and PTCSC3 protected ZC3H12A from vimentin-mediated mRNA degradation by targeting the ZC3H12A 3' untranslated region (3'UTR) during PTC initiation and progression.

Conclusion

Our results suggest a novel dual-lncRNA regulatory model in the 14q13.3 risk locus and provide a comprehensive annotation of the PTCSC3-AS1/PTCSC3-vimentin-ZC3H12A signaling network in PTC genetic predisposition.