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Nuclear expression of AFF2 C-terminus is a sensitive and specific ancillary marker for DEK::AFF2 carcinoma of the sinonasal tract


DEK::AFF2 carcinoma of the sinonasal tract is an emerging entity. The tumor is typically characterized by papillary proliferation of non-keratinizing squamous epithelial cells with monotonous cytologic features, which may mimic other sinonasal tumors. The confirmation of this gene fusion has thus far relied solely on next-generation sequencing, fluorescence in situ hybridization (FISH), or reverse transcription polymerase chain reaction (RT-PCR). This current study aimed to validate an immunohistochemical assay for AFF2 C-terminus as an ancillary marker. We first analyzed publicly available RNA sequencing data of sinonasal tumors from the national center for biotechnology information (NCBI) sequence read archive and identified 3 DEK::AFF2 carcinomas out of 28 sinonasal tumors. The gene expression of AFF2 was significantly higher in the fusion-positive cases compared to the wild-type tumors (p < 0.001), while DEK was not. We then optimized an immunohistochemical assay with an anti-AFF2 C-terminus antibody for ancillary diagnosis. Seventeen DEK::AFF2 carcinomas, including 11 cases with predominantly low-grade morphology and one showing glandular differentiation, as well as 78 DEK FISH-negative sinonasal tumors were evaluated by AFF2 immunohistochemistry (IHC). Sixteen of the 17 DEK::AFF2 carcinomas showed nuclear AFF2 expression in ≥30% of tumor cells, including one decalcified case that failed FISH and RT-PCR confirmation. The one case that was negative for AFF2 IHC in the tumor cells also lacked expression in the internal positive control. It was thus considered a failure of the IHC rather than a truly negative case and was excluded from the statistical analysis. All DEK FISH-negative sinonasal tumors were negative for nuclear AFF2 expression. The nuclear expression of AFF2 IHC showed 100% sensitivity and specificity for DEK::AFF2 carcinoma. Accordingly, AFF2 IHC is a highly sensitive and specific ancillary marker that distinguishes DEK-AFF2 carcinoma from the other sinonasal tumors with overlapping morphological features and may be an especially useful alternative for decalcified specimens.

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Fig. 1: RNA sequencing data mining.
Fig. 2: Illustration of the AFF2 immunohistochemistry detection of the DEK::AFF2 fusion protein.
Fig. 3: Morphologic spectrum of DEK::AFF2 carcinoma and the AFF2 immunohistochemistry (IHC).
Fig. 4: Morphology and AFF2 immunohistochemistry (IHC) of the DEK fluorescence in situ hybridization-negative sinonasal tumors (H&E, 200X; inset: AFF2 IHC, 400X).

Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request.


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The authors would like to thank the Biobank, Taipei Veterans General Hospital for assistance with sample preparation in this study. This study was presented in part at the annual meeting of the United States and Canadian Academy of Pathology on March 21st, 2022, Los Angeles, CA, USA.


The study was supported by the research grants from Taipei Veterans General Hospital (V110B-019) and the Ministry of Science and Technology, Taiwan (MOST110-2320-B-075-003-MY3).

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Authors and Affiliations



Y.J.K. and J.F.H. performed the study concept and design, analyzed the data, and wrote the paper; Y.C.Y. and J.F.H. conducted bioinformatics analysis of the RNAseq data; Y.J.K., J.S.L., T.T., R.D.C., C.Z., Y.A.C., T.H., C.K.L., Q.S., J.M.V., A.B.G., Y.H.C., M.S.H., A.H., and J.F.H. provided specimen acquisition and clinical data; J.F.H. supported immunohistochemistry and molecular methodology; J.S.L., R.D.C., and I.W. performed critical review and editing. All authors read and approved the final paper.

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Correspondence to Jen-Fan Hang.

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The authors declare no competing interests.

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The study was approved by the institutional review board (IRB) of Taipei Veterans General Hospital (IRB no.: 2020-12-012CC).

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Kuo, YJ., Lewis, J.S., Truong, T. et al. Nuclear expression of AFF2 C-terminus is a sensitive and specific ancillary marker for DEK::AFF2 carcinoma of the sinonasal tract. Mod Pathol (2022).

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