Transcriptomic landscape of TIMP3 oncosuppressor activity in thyroid carcinoma

In thyroid tumors TIMP3 methylation, and hence its downregulation, has been reported (Hoque MO et al, J Clin Endocrinol Metabolism 2005) and also found significantly associated with several aggressive features of PTC, including extrathyroidal invasion, lymph node metastasis, multifocality, advanced tumor stages and BRAF mutation (Hu S et al, Int J Cancer 2006). In a previous work, in addition to confirming TIMP3 downregulation in a consistent fraction of PTC, we evaluated the functional consequences of TIMP3 downregulation in a PTC-derived cell line model. We found that TIMP3 restoration in NIM1 cell line, in which the expression of TIMP3 is silenced by promoter hypermethylation, reduced in vitro migration, invasion and anchorage-independent growth. Using a mouse xenograft model we demonstrated that restoration of TIMP3 activity reduces tumor growth, concomitantly with reduction of angiogenesis and macrophage recruitment at tumor site (Anania et al, Oncogene 2011). Papillary thyroid cancer (PTC) is the most frequent thyroid tumor. The tissue inhibitor of metalloproteinase-3 (TIMP3) gene encodes a matrix metalloproteinases inhibitor that exerts a tumor suppressor role in several tumor types. TIMP3 is frequently downregulated in PTC by promoter methylation. We have previously functionally demonstrated that TIMP3 exerts an oncosuppressor role in PTC: TIMP3 restoration in the PTC-derived NIM1 cell line affects in vitro migration, invasion and adhesive capability, while reduces tumor growth, angiogenesis and macrophage recruitment in vivo. To have a broader view on the mediators of TIMP3 oncosuppressor activity in thyroid tumors, here we focused on the TIMP3 related transcriptome.By interrogating the TCGA data set and performing a genome-wide expression analysis of NIM1 cell line TIMP3 in vitro model, we show that different expression levels of TIMP3 lead to transcriptional changes that modulate, among other, inflammatory functions. Genome wide expression analysis of clones NIM1-T23 (expressing a high level of TIMP3 protein) and NIM1-EV (control empty vector) was performed. NIM1-T23 clone was produced by transfection of NIM1 cells with the TIMP3-myc expression plasmid carrying the TIMP3 cDNA into pcDNA3.1/mycHis(_)A vector. NIM1-EV clone was produced by transfection of NIM1 cells with the empty pcDNA3.1/mycHis(_)A vector. Both clones have been described in http://dx.doi.org/10.1038/onc.2011.18 (M.C.Anania, M.Sensi, E.Radaelli, C.Miranda, M.G.Vizioli, S.Pagliardini, E.Favini, L.Cleris, R.Supino, F.Formelli, M.G.Borrello, M.A.Pierotti, and A.Greco, TIMP3 regulates migration, invasion and in vivo tumorigenicity of thyroid tumor cells. Oncogene 30 (2011) 3011-3023).