Classification of Benign and Malignant Thyroid Nodules Using a Combined Clinical Information and Gene Expression Signatures

Gene expression profile of epithelial-mesenchymal transition mediators in papillary thyroid cancer

PURPOSE

Platelet derived growth receptor alpha (PDGFRA) promotes the epithelial-mesenchymal transition (EMT) in thyroid follicular cells and is linked to lymphatic metastases in papillary thyroid cancer (PTC). We probed the regulatory network of genes linked to PDGFRA and EMT, comparing matched patient primary tumor and metastatic specimens, as well as engineered cell lines and ex vivo primary cultures with and without PDGFRA.

METHODS

Freshly isolated thyroid tumors with or without metastases, with matching neighboring benign or normal tissue, was isolated for comparative transcriptional analysis using a TaqMan Low Density array (TLDA) assay with genes representing important markers of EMT, cellular adhesion, apoptosis, differentiation, senescence, and signal transduction pathways in thyroid cancer. Transfected primary cultures and immortalized cell lines were also analyzed with respect to PDGFRA expression and cell phenotype.

RESULTS

We reveal the consistent upregulation of serine protease DPP4 and structural protein SPP1 with the progression of PTC to metastatic disease, as well as with PDGFRA expression. Conversely, epithelial integrity gene TFF3 and transcription factor SOX10 were strongly down-regulated. This gene network also includes important mediators of EMT including DSG1, MMP3, MMP9, and BECN. We observed similar genomic changes in ex vivo normal thyroid cells transfected with PDGFRA that also exhibited a partially dedifferentiated phenotype. In particular, we observed lamellopodia with induction of PDGFRA and illustrate that DPP4 and SPP1 were upregulated in this process, with decreased TFF3 and SOX10 as seen in tissue specimens. PDGFRA did decrease nuclear protein levels of differentiation factor TTF1, but not the transcription of TTF1 and PAX8.

CONCLUSIONS

We demonstrate that PDGFRA activates EMT pathways and decreases expression of genes favoring epithelial integrity, pushing follicular cells toward a dedifferentiated phenotype. SPP1 and DPP4, previously linked with adverse outcomes in thyroid cancer, appear to be regulated by PDGFRA. PDGFRA expression promotes metastatic disease through multiple EMT levers that favor formation of an invasive phenotype and increased metalloproteinase expression.

A Novel Joint Gene Set Analysis Framework Improves Identification of Enriched Pathways in Cross Disease Transcriptomic Analysis

Motivation: Gene set enrichment analysis is a widely accepted expression analysis tool which aims at detecting coordinated expression change within a pre-defined gene sets rather than individual genes. The benefit of gene set analysis over individual differentially expressed (DE) gene analysis includes more reproducible and interpretable results and detecting small but consistent change among gene set which could not be detected by DE gene analysis. There have been many successful gene set analysis applications in human diseases. However, when the sample size of a disease study is small and no other public data sets of the same disease are available, it will lead to lack of power to detect pathways of importance to the disease. Results: We have developed a novel joint gene set analysis statistical framework which aims at improving the power of identifying enriched gene sets through integrating multiple similar disease data sets. Through comprehensive simulation studies, we demonstrated that our proposed frameworks obtained much better AUC scores than single data set analysis and another meta-analysis method in identification of enriched pathways. When applied to two real data sets, the proposed framework could retain the enriched gene sets identified by single data set analysis and exclusively obtained up to 200% more disease-related gene sets demonstrating the improved identification power through information shared between similar diseases. We expect that the proposed framework would enable researchers to better explore public data sets when the sample size of their study is limited.

Long glucocorticoid-induced leucine zipper regulates human thyroid cancer cell proliferation

Long glucocorticoid-induced leucine zipper (L-GILZ) has recently been implicated in cancer cell proliferation. Here, we investigated its role in human thyroid cancer cells. L-GILZ protein was highly expressed in well-differentiated cancer cells from thyroid cancer patients and differentiated thyroid cancer cell lines, but poorly expressed in anaplastic tumors. A fusion protein containing L-GILZ, when overexpressed in an L-GILZ-deficient 8505C cell line derived from undifferentiated human thyroid cancer tissue, inhibited cellular proliferation in vitro. In addition, when this protein was injected into nude mice, in which cells from line 8505C had been transplanted, xenograft growth was reduced. Since the mitogen-activated protein kinase (MAPK) pathway is frequently hyperactivated in thyroid cancer cells as a result of the BRAF^V600E or Ras mutation, we sought to further investigate the role of L-GILZ in the MAPK pathway. To this end, we analyzed L-GILZ expression and function in cells treated with MAPK inhibitors. We used 8505C cells, which have the BRAF^V600E mutation, or the CAL-62 cell line, which harbors a Ras mutation. The cells were treated with the BRAF-specific drug vemurafenib (PLX4032) or the MEK1/2 inhibitor, U0126, respectively. Treatment with these agents inhibited MAPK activation, reduced cell proliferation, and upregulated L-GILZ expression. L-GILZ silencing reversed the antiproliferative activity of the MAPK inhibitors, consistent with an antiproliferative role. Treatment with MAPK inhibitors led to the phosphorylation of the cAMP/response element-binding protein (CREB), and active CREB bound to the L-GILZ promoter, contributing to its transcription. We suggest that the CREB signaling pathway, frequently deregulated in thyroid tumors, is involved in L-GILZ upregulation and that L-GILZ regulates thyroid cancer cell proliferation, which may have potential in cancer treatment.