Genomic dissection of Hurthle cell carcinoma reveals a unique class of thyroid malignancy

Abstract

Context: Hurthle cell cancer (HCC) is an understudied cancer with poor prognosis.

Objective: Our objective was to elucidate the genomic foundations of HCC.

Design and setting: We conducted a large-scale integrated analysis of mutations, gene expression profiles, and copy number alterations in HCC at a single tertiary-care cancer institution.

Methods: Mass spectrometry-based genotyping was used to interrogate hot spot point mutations in the most common thyroid oncogenes: BRAF, RET, NRAS, HRAS, KRAS, PIK3CA, MAP2K1, and AKT1. In addition, common oncogenic fusions of RET and NTRK1 as well as PAX8/PPARγ and AKAP9-BRAF were also assessed by RT-PCR. Global copy number changes and gene expression profiles were determined in the same tumor set as the mutational analyses.

Results: We report that the mutational, transcriptional, and copy number profiles of HCC were distinct from those of papillary thyroid cancer and follicular thyroid cancer, indicating HCC to be a unique type of thyroid malignancy. Unsupervised hierarchical clustering of gene expression showed the 3 groups of Hurthle tumors (Hurthle cell adenoma [HA], minimally invasive Hurthle cell carcinoma [HMIN], and widely invasive Hurthle cell carcinoma [HWIDE] clustered separately with a marked difference between HWIDE and HA. Global copy number analysis also indicated distinct subgroups of tumors that may arise as HWIDE and HMIN. Molecular pathways that differentiate HA from HWIDE included the PIK3CA-Akt-mTOR and Wnt/β-catenin pathways, potentially providing a rationale for new targets for this type of malignancy.

Conclusions: Our data provide evidence that HCC may be a unique thyroid cancer distinct from papillary and follicular thyroid cancer.

Figure 1.

A, Summary of mutations detected by Sequenom genotyping in HA, HMIN, and HWIDE tumors. Among the mutations known to exist in PTC and FTC, only NRAS mutations were identified in Hurthle cell tumors. Codon changes are noted. B, Example of NRAS mutation detected by Sequenom genotyping in Hurthle cell tumor HWIDE2. Peaks represent MassARRAY intensity at the site of mutation. C, Summary of genetic alterations in Hurthle cell tumors compared with other types of thyroid cancers (PTC, FTC, poorly differentiated thyroid cancer, and anaplastic thyroid cancer).

Figure 2.

Summary of chromosomal regions of gain and loss in HCC compared with PTC and FTC. Regions of gain are shown in red, and regions of loss are shown in green.

Figure 3.

Diversity of the Hurthle cell tumor copy number landscape. Clustering of copy number alterations for each tumor. Amplifications (red) and deletions (blue) are indicated across the 22 autosomes. Three main groups of Hurthle tumors are identified: tumors where large regions of amplification are predominant (subtype 3 shown on the right), tumors where deletions are predominant (subtype 1 shown on the left), and tumors with more focal chromosomal alterations (subtype 2).

Figure 4.

A, Principal component analysis of expression data derived from Hurthle cell tumors. The subclasses HA, HMIN, and HWIDE are noted in the color legend. B, Heatmap showing differential gene expression between HA, HMIN (Min Inv Ca), and HWIDE (Widely Inv Ca). HMIN shows a similar profile to HA, whereas HWIDE shows a more divergent expression profile. Histogram from clustering analysis is shown at the top. Relative expression is noted in the legend.

Figure 5.

Correlation of HWIDE signature with select gene sets in Oncomine database. The significant gene overlap is represented by −log of the P value. CTNNB1 transfection, outlined in red, has the most significant P value with a −log P value of 27.7. The complete concept datasets are shown in Supplemental Table 13.

Figure 6.

A, Principal component analysis of expression data of HWIDE tumors compared with PTC and FTC from GEO (gene expression omnibus) using Partek Genomics Suite. B, Hierarchical clustering dendrogram of HWIDE expression profile compared with FTC and PTC samples. C, Heatmap showing differential gene expression between HWIDE expression profile compared with FTC and PTC samples from GEO. Tumors are arranged along the top and genes along the left.