Fine needle aspiration cytology including the analysis of human papilloma virus (HPV) DNA enhances the diagnostic workup of solitary cystic neck lesions in a population with a high incidence of HPV positive oropharyngeal cancer

Background and purpose: Distinguishing branchial cleft cysts (BrCCs) from cystic metastases of human papillomavirus (HPV) positive tonsillar or base of tongue squamous cell carcinoma and cancer of unknown primary (CUP) is challenging. Fine needle aspiration cytology (FNAC) from cystic metastasis can be nonrepresentative, while reactive squamous cells from BrCC can be atypical. It is unclear whether benign characteristics and the absence of HPV-DNA in FNAC can enhance distinguishing BrCC from a cystic metastasis; therefore, we investigated here. Patients/materials and methods: Morphology and HPV-DNA in FNAC were reevaluated preoperatively and correlated to final diagnosis of 304 BrCC and CUP patients at Karolinska University Hospital during 2016-2023. Results and interpretation: All 176 cases finally diagnosed as BrCC were HPV-DNA negative in the preoperative FNAC. HPV-DNA was present in 100/128 (78.1%) of the FNAC with a solitary cystic neck metastasis and in 3/3 CUPs separately investigated on surgical specimens, which is distributed in 40/58 (69.0%) CUP, 40/41 (97.6%) tonsillar cancer, 21/22 (95.5%) base of tongue cancer, 2/2 uterine cervical cancer, and 0/5 non-HPV-related cancers. Interpretation: All cases with final BrCC diagnosis were HPV-DNA negative in FNAC. HPV-DNA was only present in FNAC of malignant cystic neck masses of HPV-related tumors or CUP. The data suggest that HPV-DNA analysis in FNAC enhances the diagnostics of cystic masses of the neck. A FNAC with a benign morphology and the absence of HPV-DNA indicated a BrCC, while an HPV-DNA positive aspirate irrespective of morphology suggested an HPV-DNA positive cancer or CUP.