Identifying Cancer-Relevant Mutations in the DLC START Domain Using Evolutionary and Structure-Function Analyses.

Ashton S. Holub,Renee A. Bouley,Ruben C. Petreaca,Aman Y. Husbands

doi:10.3390/ijms21218175

Abstract

Rho GTPase signaling promotes proliferation, invasion, and metastasis in a broad spectrum of cancers. Rho GTPase activity is regulated by the deleted in liver cancer (DLC) family of bona fide tumor suppressors which directly inactivate Rho GTPases by stimulating GTP hydrolysis. In addition to a RhoGAP domain, DLC proteins contain a StAR-related lipid transfer (START) domain. START domains in other organisms bind hydrophobic small molecules and can regulate interacting partners or co-occurring domains through a variety of mechanisms. In the case of DLC proteins, their START domain appears to contribute to tumor suppressive activity. However, the nature of this START-directed mechanism, as well as the identities of relevant functional residues, remain virtually unknown. Using the Catalogue of Somatic Mutations in Cancer (COSMIC) dataset and evolutionary and structure-function analyses, we identify several conserved residues likely to be required for START-directed regulation of DLC-1 and DLC-2 tumor-suppressive capabilities. This pan-cancer analysis shows that conserved residues of both START domains are highly overrepresented in cancer cells from a wide range tissues. Interestingly, in DLC-1 and DLC-2, three of these residues form multiple interactions at the tertiary structural level. Furthermore, mutation of any of these residues is predicted to disrupt interactions and thus destabilize the START domain. As such, these mutations would not have emerged from traditional hotspot scans of COSMIC. We propose that evolutionary and structure-function analyses are an underutilized strategy which could be used to unmask cancer-relevant mutations within COSMIC. Our data also suggest DLC-1 and DLC-2 as high-priority candidates for development of novel therapeutics that target their START domain.

Highlights

Rho GTPases are a subfamily of G proteins involved in signal transduction
We focused on missense mutations, as the latter two are more likely to yield strong effects that confound specific contributions of the deleted in liver cancer (DLC) StAR-related lipid transfer (START) domain
We hypothesized that clustering occurs at the level of functional residues, which are distributed along the length of the DLC START domain

Summary

Introduction

Rho GTPases are a subfamily of G proteins involved in signal transduction. These proteins regulate multiple pathways, including the actin cytoskeleton, cell polarity, cell cycle progression, and microtubule dynamics [1]. Signaling is activated by GTP binding at their GTPase domain and is inactivated by its hydrolysis into GDP. This balance is mediated by the opposing activities of Rho guanine nucleotide exchange factors (RhoGEFs) and Rho GTPase-activating proteins (RhoGAPs), which promote GTP replacement and GTP hydrolysis, respectively (Figure 1). Rho GTPases, such as RhoA, Cdc, and Rac, or their respective RhoGEFs leads to tumor proliferation, migration, invasion, and metastasis in a number of cancers [2,3,4].

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Conclusion