Germline BAP1 Inactivation Is Preferentially Associated with Metastatic Ocular Melanoma and Cutaneous-Ocular Melanoma Families

Background: BAP1 has been shown to be a target of both somatic alteration in high-risk ocular melanomas (OM) and germline inactivation in a few individuals from cancer-prone families. These findings suggest that constitutional BAP1 changes may predispose individuals to metastatic OM and that familial permeation of deleterious alleles could delineate a new cancer syndrome. Design: To characterize BAP1’s contribution to melanoma risk, we sequenced BAP1 in a set of 100 patients with OM, including 50 metastatic OM cases and 50 matched non-metastatic OM controls, and 200 individuals with cutaneous melanoma (CM) including 7 CM patients from CM-OM families and 193 CM patients from CM-non-OM kindreds. Results: Germline BAP1 mutations were detected in 4/50 patients with metastatic OM and 0/50 cases of non-metastatic OM (8 % vs. 0%, p = 0.059). Since 2/4 of the BAP1 carriers reported a family history of CM, we analyzed 200 additional hereditary CM patients and found mutations in 2/7 CM probands from CM-OM families and 1/193 probands from CM-non-OM kindreds (29 % vs. 0.52%, p =.003). Germline mutations co-segregated with both CM and OM phenotypes and were associated with the presence of unique nevoid melanomas and highly atypical nevoid melanoma-like melanocytic proliferations (NEMMPs). Interestingly, 7/14 germline variants identified to date reside in C-terminus suggesting that the BRCA1 binding domain i

Cohorts and pedigrees.

<p>(<b>A</b>). Ocular melanoma and cutaneous melanoma cohorts used in this study. (<b>B</b>). Fam-562 pedigree and clinical images of two nevoid melanoma-like melanocytic proliferations (NEMMPs) diagnosed in Fam729. (<b>C</b>). Fam-729 pedigree. One carrier had a Spitz nevus, which has been reported to harbor somatic <i>BAP1</i> mutations <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035295#pone.0035295-Wiesner1" target="_blank">[4]</a>. Abbreviations: M, mutation carrier; wt, wildtype germline sequence; Ob, obligate carrier; OCMEL, ocular melanoma; MEL, cutaneous melanoma; NEMMPs, nevoid melanoma-like melanocytic proliferations; BR, breast cancer; CHL, cholangiocarcinoma; LG, lung cancer; KID, kidney cancer; UNP, melanoma of unknown primary site; CNS, central nervous system tumor; LK, leukemia. Crosses indicate CM with a nevoid pattern. The numbers next to the “MEL” indicate ages of diagnosis. <i>For the sake of confidentiality, the pedigrees have been masked for some non-affected individuals and siblings. Nonessential gender information has also been disguised by a diamond; the number of individuals collapsed into the diamond is indicated.</i></p

Distribution of <i>BAP1</i> mutations.

<p>Inactivating germline mutations identified in this study are indicated by the red arrows. Reported somatic missense mutations (blue bars) and indels (blue arrows) from ocular melanoma specimens (COSMIC database; <a href="http://www.sanger.ac.uk/genetics/CGP/cosmic/" target="_blank">http://www.sanger.ac.uk/genetics/CGP/cosmic/</a>) and germline variants (blue lines) from other families are also shown. Half of the germline variants occur in the terminal 150 amino acids while the somatic changes are more scattered.</p

BAP1 Mutations Identified In Study.

<p>Oc mel = ocular melanoma, Cut mel = cutaneous melanoma, NEMMP = nevoid melanoma-like melanocytic proliferation, SSM = superficial spreading melanoma; DCIS = breast ductal carcinoma-in-situ; DOD = died of disease; mat = maternal; pat = paternal; GM = grandmother.</p>*<p>found to be part of the same kindred.</p>#<p>see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035295#pone-0035295-g001" target="_blank">Figure 1</a>.</p

Histologic and molecular analyses of tumors from Fam-562.

<p>(<b>A</b>)–(<b>F</b>): Histology of 2 distinct NEMMPs. (<b>A</b>) Scanning view of the first lesion showing two expansile dermal nodules (H&E, 2×,) with a (<b>B</b>) benign nevoid appearance (H&E, 10×). (<b>C</b>) Atypical cytological features including nuclear pleomorphism and prominent nucleoli and a dermal mitotic figure (arrow) (H&E, 40×) along with focal increases in Ki67 staining (inset). (<b>D</b>) In the second lesion, there is an expansile dermal proliferation (H&E, 4×). (<b>E</b>) Detail of a field populated by dermal nevic cells with bland nuclear features (H&E,20×). (<b>F</b>) A proliferative area showing marked nuclear atypia and hyperchromasia along with elevated Ki 67 staining (inset). Biallelic inactivation of <i>BAP1</i> in two tumors through (<b>G</b>) loss of the wildtype allele in a nevoid melanoma (ie. LOH; arrow) or (<b>H</b>) a secondary mutation (p.Ser123Lysfs*3) in a NEMMP that did not exhibit LOH.</p