Cytologic and Molecular Assessment of Isthmus Thyroid Nodules and Carcinomas

<b><i>Background:</i></b> Isthmic thyroid nodules are more likely to be malignant and isthmic differentiated thyroid cancer demonstrates less favorable behavior compared with lobar locations. The goal of this study was to assess molecular differences of thyroid nodules and carcinomas from the isthmus relative to the lobes. <b><i>Methods:</i></b> The Afirma thyroid nodule database (<i>n</i> = 177,227) was assessed for cytologic and molecular differences between isthmus and lobar nodules in this observational cohort study. Genome-wide differential expression analysis was conducted to decipher transcriptomic differences. Histopathology reports (<i>n</i> = 583) of papillary thyroid cancer (PTC) (<i>n</i> = 389) and infiltrative follicular subtype of PTC (IF-PTC) (<i>n</i> = 194) from Afirma discovery cohorts and from thyroid cancer patients managed at an integrative endocrine surgery community care practice were analyzed for molecular differences between isthmic and lobar cancers. <b><i>Results:</i></b> In the Afirma database, 8527 (4.8%) isthmus nodules were identified. Bethesda V-VI nodules were almost twice as prevalent from the isthmus as compared with the lobes (8.2% vs. 4.3%, <i>p</i> < 0.0001). Isthmus nodules had twice the frequency of <i>BRAFp.^V600E</i> (21% vs. 10.6%, <i>p</i> < 0.0001), an increased frequency of <i>ALK</i>/<i>NTRK</i>/<i>RET</i> fusions (4.6% vs. 2.5%, <i>p</i> < 0.0001) and <i>SPOP</i> variants (1.5% vs. 0.8%, <i>p</i> < 0.0001), and a lower frequency of <i>NRAS</i> mutations (7.8% vs. 13.2%, <i>p</i> < 0.0001), and <i>PAX8::PPARy</i> fusions (1.1% vs. 2.3%, <i>p</i> < 0.0001) than lobar nodules. Transcriptome analysis of molecular signatures and genome-wide analysis showed that isthmus nodules have higher <i>BRAF</i>-like scores, ERK activity, follicular mesenchymal transition scores (FMT), and lower inflammation activity scores. Pathway enrichment analysis revealed genes downregulated in isthmus tumors are enriched in immune response regulation. IF-PTC from the isthmus (<i>n</i> = 13) were more <i>BRAF</i>-like and had increased ERK and FMT scores compared with those from the lobes (<i>n</i> = 181) (<i>p</i> < 0.01 for all). <b><i>Conclusions:</i></b> These data suggest isthmic nodules are more likely to have malignant cytology and increased rates of higher risk molecular alterations compared with lobar nodules. IF-PTC from the isthmus is molecularly different compared with IF-PTC from the lobes. More data are needed to know if a change in surgical therapy is warranted in isthmic thyroid cancers relative to lobar cancers and if this molecular data should influence isthmic thyroid cancer management and monitoring.