IDH2 R172 Mutations Across Poorly Differentiated Sinonasal Tract Malignancies: Forty Molecularly Homogenous and Histologically Variable Cases With Favorable Outcome

Abstract

IDH2 R172 mutations occur in sinonasal undifferentiated carcinoma (SNUC), large-cell neuroendocrine carcinoma (LCNEC), sinonasal adenocarcinomas, and olfactory neuroblastoma (ONB). We performed a clinical, pathologic, and genetic/epigenetic analysis of a large IDH2-mutated sinonasal tumor cohort to explore their distinct features. A total 165 sinonasal/skull base tumors included 40 IDH2 mutants studied by light microscopy, immunohistochemistry, and genome-wide DNA methylation, and 125 IDH2 wild-type tumors used for comparison. Methylation profiles were analyzed by unsupervised hierarchical clustering, t-distributed stochastic neighbor embedding dimensionality reduction and assessed for copy number alterations (CNA). Thirty-nine histologically assessable cases included 25 (64.1%) SNUC, 8 (20.5%) LCNEC, 2 (5.1%) poorly differentiated adenocarcinomas, 1 (2.7%) ONB, and 3 (7.7%) IDH2-mutated tumors with ONB features. All cases were high-grade showing necrosis (82.4%), prominent nucleoli (88.9%), and median 21 mitoses/10 HPFs. AE1/AE3 and/or CAM 5.2 were positive in all and insulinoma-associated protein 1 (INSM1) in 80% cases. All IDH2 mutants formed one distinct group by t-distributed stochastic neighbor embedding dimensionality reduction separating from all IDH2 wild-type tumors. There was no correlation between methylation clusters and histopathologic diagnoses. Recurrent CNA included 1q gain (79.3%), 17p loss (75.9%), and 17q gain (58.6%). No CNA differences were observed between SNUC and LCNEC. IDH2 mutants showed better disease-specific survival than SMARCB1-deficient (P=0.027) and IDH2 wild-type carcinomas overall (P=0.042). IDH2-mutated sinonasal tumors are remarkably homogeneous at the molecular level and distinct from IDH2 wild-type sinonasal malignancies. Biology of IDH2-mutated sinonasal tumors might be primarily defined by their unique molecular fingerprint rather than by their respective histopathologic diagnoses.

Figure 1.

IDH2 mutated SNUC tumors cells formed lobules and nests and show prominent nucleoli (A). A crisp, granular staining by 11C8B1 indicated the presence of IDH2 R172S or R172T mutation (B). SN_09 first presented as carcinoma in situ (C) and the tumor cells are seen to involve adjacent seromucinous glands (D) and to stand out among residual small, cytologically bland normal epithelial cells. The first recurrence shows surface involvement (left, E) and invasive nests of undifferentiated tumor cells (right, E); the surface component showed focal positive labeling for p40, although mostly in residual benign epithelial cells (left, F). The invasive component was entirely negative for p40 (right, F). Second recurrence showed squamous differentiation with keratinization (left, medium power and right, high power, G). Squamous cells were positive for p40 (left, H) and IDH2 R172S immunostains. Red arrow points to a keratinized focus (right, H). Abbreviations: SNUC, sinonasal undifferentiated carcinoma.

Figure 2.

LCNEC showing large tumor cells with prominent nucleoli (inset) and harboring IDH2 R172G mutation (A) was positive for 3C11 monoclonal antibody (B), INSM1 (H-score 85, C), and chromogranin (D).

Figure 3.

IDH2 mutated ONB, Hyams grade III-IV. A lobulated architecture (A) and focal necrosis (B) are depicted. The tumor was positive for IDH2 11C8B1 (C), S100 in sustentacular pattern (D), INSM1 (E), and very focally positive for synaptophysin (F). Abbreviations: ONB, olfactory neuroblastoma.

Figure 4.

Poorly differentiated carcinoma with ONB features (SN_116). Focally, the tumor showed rosettes (A) and otherwise undifferentiated tumor cells with inconspicuous nucleoli (B). IDH2 R172S variant was confirmed by IHC (C). Sustentacular labeling for S100 was very focal (D), EMA was positive in most tumor cells (E), INSM1 showed H-score 43 (F) and chromogranin (G) and synaptophysin (H) were entirely negative. Abbreviations: ONB, olfactory neuroblastoma.

Figure 5.

Neuroendocrine markers expression in IDH2 mutated sinonasal tumors. INSM1 expression based on H-score in synaptophysin/chromogranin negative and INSM1 positive cases (n=14) and either or both positive synaptophysin/chromogranin and INSM1 positive cases (n=12, A). Synaptophysin, chromogranin and INSM1 expression based on the tumor type (B). p values are displayed only for statistically significant differences. Abbreviations: SYN, synaptophysin; CHR, chromogranin; SNUC, sinonasal undifferentiated carcinoma; LCNEC, large cell neuroendocrine carcinoma; ONB, olfactory neuroblastoma; IDH2-ONBF, IDH2 mutated tumors with ONB features including one ONB Hyams grade III-IV.

Figure 6.

tSNE analysis of IDH2 mutant sinonasal malignancies compared with other morphologically similar small round cell tumors. Tumors are annotated and color coded according to the “Diagnosis” legend (lower right) and include sinonasal tumors with IDH2 mutation (n=30), SMARCB1-deficient carcinoma (n=15), sinonasal squamous cell carcinoma (n=23), sinonasal mucosal melanoma (n=8), pituitary adenoma (n=12), and olfactory neuroblastoma (n=36). Abbreviations: tSNE, t-distributed stochastic neighbor embedding.

Figure 7.

DNA methylation profiling of IDH2 mutated sinonasal malignancies. Unsupervised hierarchical clustering of DNA methylation profiles from 30 tumor samples, using the 2,000 most variably methylated probes fails to reveal any differences between the methylation clusters, histologic diagnosis, IDH2 R172 variant or CNA (A). Copy number profiles show broad chromosome (arm) level CNA are similar between SNUC (n=19) and LCNEC (n=6, B). Abbreviations: SNUC, sinonasal undifferentiated carcinoma; LCNEC, large cell neuroendocrine carcinoma; IDH2-ONBF, IDH2 mutated tumors with ONB features, ONB, olfactory neuroblastoma; PD non-ITAC, poorly differentiated non-intestinal type adenocarcinoma; PDCA-GL, poorly differentiated carcinoma with focal glandular/acinar features; CNA, copy number alterations.

Figure 8.

Outcome of IDH2 mutated and IDH2 wild-type sinonasal carcinomas. Overall survival (A), disease-specific survival (B) and disease-free survival (C; Log rank test) differences between IDH2 mutated tumors (n=28) and each IDH2 wild-type group are depicted on the left and comparison of IDH2 mutants and all IDH2 wild-type tumors (n=38) irrespective of SMARCB1 status are seen on the right. P-values compare each tumor group with IDH2-mutated tumors; * indicates p value between SMARCB1 def (n=18) and IDH2 wt/SMARCB1 wt (n=20). Abbreviations: wt, wild-type; def, deficient.