DEK-AFF2 Carcinoma of the Sinonasal Region and Skull Base: Detailed Clinicopathologic Characterization of a Distinctive Entity

Lisa M. Rooper, Abbas Agaimy, Brendan C. Dickson, Julie C. Dueber, Charles G. Eberhart, Jeffrey Gagan, Arndt Hartmann, Armen Khararjian, Nyall R. London, Christina M. MacMillan, Doreen N. Palsgrove, J. Stephen Nix, Ann Sandison, Robert Stoehr, Tra Truong, Ilan Weinreb, Justin A. Bishop

Research output: Contribution to journalArticlepeer-review

37 Scopus citations


A novel DEK-AFF2 fusion was recently reported in 4 nonkeratinizing squamous cell carcinomas of the sinonasal region and skull base, including 1 with exceptional response to immunotherapy, but it is not yet clear if this rearrangement defines a unique clinicopathologic category or represents a rare event. This study aims to characterize a larger cohort of carcinomas with DEK-AFF2 fusions to assess whether they truly constitute a distinctive entity. Among 27 sinonasal and skull base nonkeratinizing squamous cell carcinoma that were negative for human papillomavirus and Epstein-Barr virus, RNA sequencing identified DEK-AFF2 fusions in 13 cases (48%). Nine were centered in the nasal cavity, 2 in the middle ear/temporal bone, 1 in the nasopharynx, and 1 in the orbit. These tumors displayed recurrent histologic features including (1) complex endophytic and exophytic, frequently papilloma-like growth, (2) transitional epithelium with eosinophilic to amphophilic cytoplasm, (3) absent or minimal keratinization with occasional compact keratin pearls, (4) monotonous nuclei, and (5) prominent tumor-infiltrating neutrophils or stromal lymphocytes. This appearance not only overlaps with high-grade basaloid sinonasal carcinomas but also with benign papillomas and tumors reported as low-grade papillary Schneiderian carcinoma. However, DEK-AFF2 carcinomas showed frequent local recurrence, cervical lymph node metastases, and distant metastasis with 2 deaths from disease, confirming they are aggressive malignancies despite relatively bland histology. Overall, the distinctive molecular, histologic, and clinical features of DEK-AFF2 carcinomas suggest they represent a unique entity in the sinonasal region. This tumor merits increased pathologic recognition to better understand its prognostic and therapeutic implications.

Original languageEnglish (US)
Pages (from-to)1682-1693
Number of pages12
JournalAmerican Journal of Surgical Pathology
Issue number12
StatePublished - Dec 1 2021


  • AFF2, sinonasal tract
  • DEK
  • DEK-AFF2
  • immunohistochemistry
  • molecular diagnostics
  • nasal neoplasms
  • skull base neoplasms

ASJC Scopus subject areas

  • Anatomy
  • Surgery
  • Pathology and Forensic Medicine


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