Abstract 2628: Exploring synthetic lethality between VPS4A and VPS4B paralog enzymes in pancreatic and colon cancer
Authors: Nacarelli Timothy , Bechtel Nelisa , Gao Yanzhe , Auger Kurt 
Published: June 2022

Tumor suppressors can be inactivated through somatic gene deletions in cancer. Loss of the tumor suppressor SMAD4 is associated with 18q21 chromosomal deletion and frequently observed in pancreatic and colon cancers. The large-scale cancer dependency Broad and Sanger lethality screens revealed a synthetic lethal relationship between genomic loss of SMAD4 and vacuolar protein sorting 4 homolog A (VPS4A) with selectivity in pancreatic and colon cancer cell lines. VPS4A is a functional paralog to vacuolar protein sorting 4 homolog B (VPS4B), where VPS4B is located on 18q21 and correlates with SMAD4 copy number. VPS4A and VPS4B are paralog ATPases that function in the endosomal sorting complex required for vesicular transport and budding, which is required for cellular homeostasis and survival. As a consequence, collateral loss of VPS4B associated with SMAD4 loss results in a selective sensitivity for VPS4A deletion. Therefore, VPS4A is a possible therapeutic target in tumors deficient for VPS4B.We investigated the paralog synthetic lethality relationship between VPS4A and VPS4B in pancreatic and colon cancer cell lines. We rescued cell growth using ectopic wildtype VPS4A expression following combined knockdown of VPS4A and VPS4B. We further investigated if the ATPase activity of VPS4A was required to rescue paralog lethality using ectopic expression of mutant catalytically-dead VPS4A proteins. We discovered that the ATPase activity of VPS4A was required to rescue paralog lethality, as expression of the catalytically-dead VPS4A proteins did not support cell growth. However, it was noted that expression of the mutant proteins resulted in cell growth attenuation in addition to the inability to rescue. To investigate this observation, we expressed mutant and wild-type VPS4A proteins in cell lines without knock-down of endogenous protein. We found expressing either of the mutant VPS4A proteins, but not wild-type VPS4A protein, decreased cell growth in the presence of the endogenous protein. Decreased cell growth with the expression of the ATPase catalytic mutants suggest a potential dominant negative effect. This negative effect on cell growth with an ATPase inactive protein has the potential to translate to the effect observed with a selective VPS4A ATPase inhibitor. Additionally, the discovery of a selective ATPase inhibitor against VPS4A or VPS4B may be challenging due to the high sequence similarity within the ATPase domain. However, the microtubule interacting and trafficking (MIT) domain between VPS4A and VPS4B shows less sequence similarity and has a higher likelihood for selectivity. In summary, we confirmed the paralog lethality relationship between VPS4A and VPS4B and the dependence on the ATPase activity of VPS4A. However, the selective targeting of the VPS4A ATPase activity may result in unintended cell growth impairment, the lack of synthetic lethality, and potential for adverse toxicity.

Citation Format: Timothy Nacarelli, Nelisa Bechtel, Yanzhe Gao, Kurt Auger. Exploring synthetic lethality between VPS4A and VPS4B paralog enzymes in pancreatic and colon cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2628.