Using Functional Signature Ontology (FUSION) to Identify Mechanisms of Action for Natural Products

Abstract

A challenge for biomedical research is the development of pharmaceuticals that appropriately target disease mechanisms. Natural products can be a rich source of bioactive chemicals for medicinal applications but can act through unknown mechanisms and can be difficult to produce or obtain. To address these challenges, we developed a new marine-derived, renewable natural products resource and a method for linking bioactive derivatives of this library to the proteins and biological processes that they target in cells. We used cell-based screening and computational analysis to match gene expression signatures produced by natural products to those produced by siRNA and synthetic microRNA libraries. With this strategy, we matched proteins and microRNAs with diverse biological processes and also identified putative protein targets and mechanisms of action for several previously undescribed marine-derived natural products. We confirmed mechanistic relationships for selected short-interfering RNAs, microRNAs, and compounds with functional roles in autophagy, chemotaxis mediated by discoidin domain receptor 2, or activation of the kinase AKT. Thus, this approach may be an effective method for screening new drugs while simultaneously identifying their targets.

KSR1 and EPHB4 Regulate Myc and PGC1β To Promote Survival of Human Colon Tumors

“…The gene expression-based high-throughput screen has been described previously (16,19). The gene expression-based signature measured in the screen is based on six genes (ACSL5, BNIP3L, ALDOC, LOXL2, BNIP3, and NDRG1 genes) that are consistently affected by KSR1 depletion, as well as two housekeeping genes (PPIB and hypoxanthine phosphoribosyltransferase [HPRT] genes) that were included for normalization.…”

“…Given that KSR1 is dispensable for normal cells but indispensable for colorectal cancer cells, we sought to detect and exploit further vulnerabilities in human colon tumor cells. To do this, we developed a gene expression-based high-throughput screen and used functional signature ontology (FUSION) (16,19) to identify functional analogs of KSR1. From this screen, we identified EPH (erythropoietin-producing hepatocellular carcinoma) receptor B4 (EPHB4) as a KSR1-like, cancer-specific vulnerability that may be exploited by targeted therapies.…”

SIK2 Restricts Autophagic Flux To Support Triple-Negative Breast Cancer Survival

“…Furthermore, inhibition of CRTCs had no impact on the SIK2 phenotype in TNBC (not shown). Thus, our work, along with two prior reports, presents a strong case that SIK2 represents a novel autophagic regulatory pathway (18,21). The molecular mechanisms that activate SIK2 and its downstream substrates are poorly described outside of gluconeogenesis.…”

“…A number of recent reports have implicated SIK2 in the modulation of autophagy (18,21). Also, the expression of the tumor suppressor beclin-1 is lost in a subset of TNBC, suggesting that autophagy is altered in a subset of TNBC tumors (30).…”

“…Importantly, tissue-specific deletions of SIK proteins in mice can lead to altered glucose and lipid metabolism (14)(15)(16). Additional findings have also implicated SIK2 proteins in modulating autophagy and inflammatory responses (17)(18)(19)(20)(21). With respect to cancer, two reports have indicated that SIK2 is essential for centrosome splitting and mitotic progression, and SIK1 loss can inhibit anoikis and promotes metastases (22)(23)(24).…”