POT1 genetic testing in melanoma-prone families in Sweden: germline variant prevalence and tumor spectrum in identified carriers

Abstract

Background and purpose: Approximately 5-10% of cutaneous melanoma occurs in individuals with a family history of the disease. While known high-penetrance genes, such as CDKN2A, explain some cases, a substantial proportion of hereditary melanoma remains genetically undefined. Recently, germline variants in genes involved in telomere regulation, including POT1, TERT, ACD, and TERF2IP, have been identified in melanoma-prone families. This study investigated the prevalence and pathogenicity of POT1 variants in a Swedish familial melanoma cohort. Patient/material and methods: A total of 168 familial melanoma cases were screened for CDKN2A, CDK4, BAP1, and POT1. The population frequency of pathogenic variants (PVs) was assessed using the SweGen and the gnomAD databases. Functional evaluation was performed using a saturation genome editing (SGE) assay. Telomere length analysis was performed using quantitative polymerase chain reaction (qPCR) on blood-derived DNA from melanoma patients and healthy controls. The melanomas of the carriers were reviewed by expert dermatopathologists.

Results: Among the 161 CDKN2A/CDK4/BAP1-negative melanoma families included in this cohort, only one likely PV in POT1 (c.676C > A, p.His226Asn) was identified (0.6%). Population data confirmed its rarity. The carrier family exhibited multiple early-onset melanomas, with two out of three invasive cases displaying spitzoid morphology, and several other tumors. No significant telomere length differences were observed between carriers and controls. Two additional POT1 variants of uncertain significance were detected; both were predicted to be benign.

Interpretation: POT1 PVs were rare in the studied Swedish familial melanoma cases, implying limited contribution to hereditary melanoma in this population. Nonetheless, the identification of a previously unknown likely PV further supports the need for continued genetic screening in selected cases. POT1 testing should be considered in families with multiple melanomas, early onset and spitzoid histopathology, and co-occurring with other syndromic tumors.

Figure 1

Schematic view of human POT1 protein functional domains. There are three oligonucleotide/oligosaccharide-binding (OB) fold domains, namely, OB1–3, with an embedded Holliday junction resolvase-like (HJRL) domain in the OB3 domain. The location of the likely pathogenic missense variant is indicated by the red arrow.

Figure 2

Histopathologic findings of cutaneous melanomas from an individual with a germline variant in POT1 (p.His226Asn). (A) Low magnification of spitzoid melanoma showing epidermal and dermal nests, growing adjacent to a nevus, marked by the arrows (hematoxylin and eosin, original magnification: X4). (B) Spitzoid morphology consisting of atypical enlarged epithelioid melanocytes with abundant eosinophilic cytoplasm. Some of the melanocytes are slightly pigmented (hematoxylin and eosin, original magnification: X20). (C) Superficial spreading melanoma with spitzoid features (hematoxylin and eosin, original magnification: X4). (D) Nests of enlarged spitzoid melanocytes including scattered multinucleated cells embedded in fibrosis (original magnification: X20).