DIFFERENTIAL GENE EXPRESSION ANALYSIS OF INVASIVE AND NON-INVASIVE FOLLICULAR VARIANT OF PAPILLARY THYROID CARCINOMA

Presentation: B072
Topic: Genomics in H&N Cancer
Type: Poster
Date:
Session:
Authors: Christopher Pool, MD, David Goldenberg, MD, FACS, Erik Washburn, MD, Joshua Warrick
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Institution(s): Penn State Hershey Medical Center

BACKGROUND: It has been well described that BRAF-driven thyroid tumors include classic-type papillary thyroid cancer (PTC), and RAS-driven tumors include follicular carcinoma and follicular adenoma.  Follicular variant (FV) PTC is an interesting entity because its molecular profile shares homology with both BRAF- and RAS-driven thyroid tumors.  It has been shown that invasive FV-PTC is capable of metastasis, while noninvasive FV-PTC is not. The term “noninvasive follicular thyroid neoplasm with papillary like nuclear features” (NIFTP) has thus been proposed to reclassify noninvasive FV-PTC as a benign neoplasm. The aim of our study is to identify molecular differences between invasive and noninvasive FV-PTC..

METHODS: 65 cases of FV-PTC with available nodal data from The Cancer Genome Atlas (TCGA) database were identified.  Digital slides were methodically re-reviewed and designated as invasive, non-invasive, or cannot determine.  TCGA RNA seq data were used to determine differential expression between invasive and non-invasive tumors using t-tests with false discover rate (FDR) multiple test correction.  Hierarchical clustering was performed based on differentially expressed genes.  Mutational and RNA seq expression data from 25 patient samples were used to validate the TCGA data set, using nearest-centroid analysis.

RESULTS: Of the 65 re-reviewed TCGA cases, 18 were invasive, 29 were noninvasive, and 18 could not be determined. As expected, invasive architecture was strongly associated with lymph node metastasis (odds ratio 22, p<0.001; Fisher test). Invasive tumors were enriched in BRAF V600E mutations (p=0.024, Fisher test). Expression analysis identified 699 genes differentially expressed between invasive and noninvasive tumors (q<0.05, FDR). Hierarchical clustering based on identified genes divided tumors into two distinct clusters: one contained all RET, BRAF, and NTRK3 rearrangements, and 82% of BRAF V600E mutants; the other contained all RAS mutants. Node metastases were more common in the BRAF mutant cluster (40% cluster members vs 9% cluster members, p=0.021, Fisher).  The validation set included 3 invasive FV-PTC, 7 noninvasive FV-PTC, and 15 follicular adenomas.  Nearest centroid analysis using BRAF-like vs RAS-like gene signatures separated the validation set into invasive vs noninvasive groups with 100% sensitivity and 91% specificity, with overall accuracy of 92%.

CONCLUSION: Invasive and noninvasive FV-PTC are qualitatively different neoplasms. Invasive tumors have a BRAF-like expression signature, while noninvasive tumors have a RAS-like signature. The findings question the utility of the designation “follicular variant,” and corroborate the position that noninvasive FV-PTC should be reclassified as a benign neoplasm, separate from invasive FV-PTC.

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