Histological subtypes of follicular cell-derived thyroid carcinomas (FTC, PTC, ATC) significantly differ in their mutational landscapes and clinical characteristics. Although FTC and clPTC both are differentiated carcinomas, FTC are characterized by follicular growth pattern and tend more often to spread metastases to distant organs, while clPTC typically have papillary architecture and spread more often to lymph nodes in the neck. In FTC K/H/NRAS and PAX8/PPARG mutations are prevalent, whereas BRAF mutations and tyrosine kinase fusions prevail in clPTC . fvPTC are composed of neoplastic follicles rather than papillae, but with follicular cells showing nuclear features of PTC. The clinical characteristics of fvPTC are intermediate . The mutational profile of fvPTC is more similar to FTC: prevalence of K/H/NRAS and PAX8/PPARG mutations. In the TCGA study, fvPTC were characterized as Ras-like tumors and their classification as papillary carcinomas was questioned . Recently, reclassification of encapsulated fvPTC as “noninvasive follicular thyroid neoplasm with papillary-like nuclear features” (NIFTP) was proposed . FA are thought to be benign counterpart of FTC and understanding the common and different molecular features of these neoplasms is important for the development of diagnostic and therapeutic strategy. ATC are thought to be an advanced stage of thyroid neoplasms, it is the most aggressive thyroid cancer and it is expected that there are specific molecular features, including lncRNA, associated with its aggressive behavior.
In this study, expression of lncRNA was evaluated in the main histological subtypes of thyroid neoplasm: FA, FTC, fvPTC, clPTC and ATC. Datasets analyzed in the study (Microarray dataset of 8 independent experiments; RNA-Seq PRJEB11591 and RNA-Seq TCGA) allowed to perform robust in silico validation of the results for clPTC and fvPTC, and to include representative set of FA, FTC and ATC samples. LncRNA landscapes in FA, FTC and ATC were analyzed for the first time.
LncRNAs general for thyroid neoplasms, specific for clPTC, fvPTC, ATC and general for papillary carcinomas (associated with papillary features) were discovered. The highest number of differently expressed genes was in ATC (330 lncRNAs) followed by clPTC (137), FTC and fvPTC that reflects the more advanced stage of ATC. The lncRNAs specific for ATC and probably associated with anaplastic features were discovered for the first time. None of lncRNAs specific for FTC is differentially expressed compared to FA. The only lncRNA ENSG00000257647 is specific for fvPTC that might be explained by its intermediate morphology combining features of both papillary and follicular carcinomas and debatable classification.
Aberrant expression of some lncRNAs previously found by Liyanarachchi S. et all. (2016) was confirmed in our study. Most of these lncRNAs occurred to be general for thyroid carcinomas . Previously known promoters of cancer progression were found upregulated in thyroid carcinomas: NR2F1-AS1 and LINC00511 – in clPTC; TNRC6C-AS1 – in clPTC and fvPTC; CRNDE – in ATC. Known putative tumor suppressors were identified within downregulated lncRNAs: SLC26A4-AS1 – in clPTC and ATC; RMST – in ATC [32–38].
Putative biological process involving common and specific lncRNAs were established. LncRNAs common for all studied thyroid neoplasms might be involved in L1CAM interactions; common for follicular and classical variants of papillary carcinoma – in Tryptophan metabolism. Tryptophan degradation to kynurenine by the Indoleamine 2,3-Dioxygenase 1 (IDO1) is a well characterized immunosuppressive mechanism in cancer progression, including thyroid cancer .
Biological processes involving lncRNAs specific for FTC include processes that are associated with splicing (Processing of Capped Intron-Containing Pre-mRNA, mRNA Splicing, RNA processing). Accumulating evidence suggests that aberrant RNA splicing is a common and driving event in cancer development and progression. For instance, oncogenic Ras signaling via ERK and PI3-K/Akt pathways is described to regulate phosphorylation of splicing factors such as SRSF1, SRSF7, SPF45 and drive switching active and inactive states of tumor promoters and suppressors (MST1R, FAS, CD44, LBR, Casp-9, KLF6, and others) via alternative splicing [40, 41].
LncRNA ENSG00000257647 specific for fvPTC appeared to be involved in WNT signaling, predominantly Beta-catenin independent WNT pathway (especially, planar cell polarity that modulates cytoskeleton rearrangements through the activation of the small GTPases RhoA and Rac and their downstream effectors Rock and JNK). WNT signaling is described to play a crucial role in thyroid carcinogenesis, several mechanisms of its deregulation were described, including inhibition of β-catenin degradation complex via its phosphorylation by RET/PTC and decrease of E-cadherin expression by MAPK/ERK pathway activated by BRAF mutations. RAS mutations are described to activate both, canonical and non-canonical Wnt pathways in thyroid carcinomas [42, 43].
LncRNAs specific for clPTC are involved into extracellular matrix organization and collagen formation. Extracellular matrix (ECM) disorganization is known to play a pivotal role in cancer initiation and progression. There is emerging evidence of ECM remodeling induced by BRAF p.V600E in PTCs . Notably, it was shown that extracellular matrix of PTCs driven by BRAF p.V600E (but not mutant HRAS) is enriched with stromal-derived fibrillar collagen and it facilitates cancer progression .
For lncRNAs specific for ATC there is a strong enrichment of cell cycle and mitotic pathways which possibly reflects involvement of these lncRNAs in the loss of differentiation and high proliferation rate characteristic for ATC.