What is FuSiOn?
A challenge for biomedical research is the development of pharmaceuticals that appropriately target disease mechanisms. Natural products, specifically, are rich in chemical diversity with structure subject to co-evolution with biological systems, thus they may engage targets not currently recognized as chemically addressable. A significant barrier associated with natural products discovery is the purification of metabolites from producing organisms and discovery of chemical mechanism of action. With FuSiOn, we seek to help overcome these barriers through construction of a scalable high-throughput discovery approach to deliver statistically prioritized testable mechanism of action hypotheses for thousands of complex marine microbe-derived natural products fractions (3-6 bioactive compounds/fraction) in parallel.
How does FuSiOn work?
We measure expression of 6 highly variable ‘reporter genes’, whose collective expression is to serve as a quantitative indicator of cell state changes in response to perturbations from siRNA’s targeting the kinome, miRNA mimics, and natural products. Perturbation signatures from all three libraries are clustered together to produce ‘guilt by association’ hypotheses.
Evaluation of natural products fractions in this fashion allows for high-throughput iterative prioritization based on attractive functional consequences on the cells. In addition to stratification of samples for follow-up, this enables development of bio-assay guided purification schemes. This approach has successfully assigned function to previously uncharacterized miRNA’s and siRNA’s and linked natural products to cellular mechanism of action (Potts et al., 2013; Potts et al., 2015; Vaden et al., 2017).
How has FuSiOn expanded?
FuSiOn has expanded to a genome-scale inclusive of 14,272 distinct human gene perturbations, 725 human miRNA perturbations, and 2,847 chemicals consisting of 2776 marine-derived natural products fractions and 71 purified natural products and chemicals. We employed this comprehensive feature matrix to generate a map of functional associations between all genes in the genome and assess the overall topology of the functional network in a biological setting. FuSiOn was used to expand gene membership within known mechanistic processes and to discover previously unrecognized mechanistic relationships among gene networks. Finally, we integrated chemical perturbations with the genome-wide genetic functional network to assign biological mechanisms of action to a large number of natural products; a subset of which underwent experimental validation. All precomputed relationships are made available here as a queryable GUI to enable community-based hypothesis testing.
- Potts, M.B., Kim, H.S., Fisher, K.W., Hu, Y., Carrasco, Y.P., Bulut, G.B., Ou, Y.H., Herrera-Herrera, M.L., Cubillos, F., Mendiratta, S., et al. (2013). Using functional signature ontology (FUSION) to identify mechanisms of action for natural products. Sci Signal 6, ra90.
- Potts, M.B., McMillan, E.A., Rosales, T.I., Kim, H.S., Ou, Y.H., Toombs, J.E., Brekken, R.A., Minden, M.D., MacMillan, J.B., and White, M.A. (2015). Mode of action and pharmacogenomic biomarkers for exceptional responders to didemnin B. Nat Chem Biol 11, 401-408.
- Vaden, R.M., Oswald, N.W., Potts, M.B., MacMillan, J.B., and White, M.A. (2017). FUSION-Guided Hypothesis Development Leads to the Identification of N(6),N(6)-Dimethyladenosine, a Marine-Derived AKT Pathway Inhibitor. Mar Drugs 15.
- McMillan, E.A., Kwon, G., Clemenceau, J.R., Fisher, K.W., Vaden, R.M., Shakih, A.F., Neilsen, B.K., Kelly, D., Potts, M.B., Sung, Y-J, Mendiratta, S., Hight, S.K., Lee, Y., MacMillan, J.B., Lewis, R.E., Kim, H.S., White, M.A. (2019) A genome-wide functional signature ontology map (FuSiOn) and applications to natural product mechanism of action discovery. Cell Chem Biol, in press.