Melanoma Functional Genomics

Our vision is to focus on melanoma as a model system to resolve its genomic landscape and evaluate the functional effects of identified drivers. To this end, our lab has established, a unique asset, a bank of 200 low-passage melanoma cell lines, for which we also have fresh tumors, peripheral blood cells and tumor infiltrating lymphocytes (TILs). To further our understanding of the complex melanoma genomic landscape, we demonstrated that melanoma tumors can be subdivided into four main genetic landscapes (Cell 2015).

Our establishment of a robust database of melanoma drivers allowed us to perform an unbiased query for novel tumor suppressors, which led to our discovery that RASA2 is a novel melanoma tumor suppressor gene that regulates NRAS (Nature Genetics 2015). Further assessment of RASA2 mutations’ functional effects showed RASA2 and NF1, two-negative regulators of Ras, to have complementary functions in melanoma (Oncogene 2018, Nature Communications 2018). This discovery is part of our broader efforts to map mutual exclusivity and co-occurrence of melanoma drivers in order to identify melanoma-driving pathways, as well as the complexity of and inter-relationship within the network of melanoma drivers. 

Our current research aims to decipher the functional effects of discovered mutations in their physiological context, while utilizing statistical and bioinformatics tools, along with functional studies using overexpression, knockdown (siRNA and shRNA) and knockout (CRISPR) strategies to conclusively identify “driver” mutations.

Melanoma Functional Genomics

Figure legend. Distribution of somatic mutations in RASA2 in melanoma.
(A) The human RASA2 protein, with conserved domains indicated as blocks, including the C2 domain first repeat (C2 1), C2 domain second repeat (C2 2), RAS GTPase-activating domain (RasGAP), Plekstrin homology domain (PH) and Bruton’s tyrosine kinase cysteine-rich motif (BTK). Somatic alterations are represented by arrowheads and amino acid changes. Red triangles represent deleterious alterations. Underlined alterations were functionally assessed.
(B) Distribution of the somatic alterations encoded in BRAF, NRAS, NF1 and RASA2 in melanomas (n = 501).

Arafeh et al., Neture Genetics 2015