Early Diagnosis of Oral Cancer and Lesions in Fanconi Anemia Patients: A Prospective and Longitudinal Study Using Saliva and Plasma

SIMPLE SUMMARY: Patients with Fanconi anemia (FA) have a very high risk of developing oral lesions and squamous carcinomas at early ages. As treatment strategies in this setting are very limited, new early diagnosis methods are urgently needed. We performed a pilot, prospective clinical study in which saliva and plasma samples were analyzed with the deep sequencing of cancer genes. The patients included had apparently normal oral mucosa when recruited. Mutations were detected in the liquid biopsies with allele frequencies of down to 0.07%. We found that patients with mutations displayed a higher risk of developing lesions/carcinomas after mutation detection. We propose that this non-invasive, highly sensitive technology could allow for the better management of these pathologies in FA individuals. ABSTRACT: Fanconi anemia (FA) patients display an exacerbated risk of oral squamous cell carcinoma (OSCC) and oral potentially malignant lesions (OPMLs) at early ages. As patients have defects in their DNA repair mechanisms, standard-of-care treatments for OSCC such as radiotherapy and chemotherapy, give rise to severe toxicities. New methods for early diagnosis are urgently needed to allow for treatment in early disease stages and achieve better clinical outcomes. We conducted a prospective, longitudinal study wherein liquid biopsies from sixteen patients with no clinical diagnoses of OPML and/or OSCC were analyzed for the presence of mutations in cancer genes. The DNA from saliva and plasma were sequentially collected and deep-sequenced, and the clinical evaluation followed over a median time of approximately 2 years. In 9/16 FA patients, we detected mutations in cancer genes (mainly TP53) with minor allele frequencies (MAF) of down to 0.07%. Importantly, all patients that had mutations and clinical follow-up data after mutation detection (n = 6) developed oral precursor lesions or OSCC. The lead-time between mutation detection and tumor diagnosis ranged from 23 to 630 days. Strikingly, FA patients without mutations displayed a significantly lower risk of developing precursor lesions or OSCCs. Therefore, our diagnostic approach could help to stratify FA patients into risk groups, which would allow for closer surveillance for OSCCs or precursor lesions.