Identification of deubiquitinase targets of isothiocyanates using SILAC-assisted quantitative mass spectrometry

// Ann P. Lawson 1 , Daniel W. Bak 2 , D. Alexander Shannon 2 , Marcus J.C. Long 3, 7 , Tushara Vijaykumar 4, 8 , Runhan Yu 5 , Farid El Oualid 6 , Eranthie Weerapana 2 and Lizbeth Hedstrom 1, 5 1 Department of Biology, Brandeis University, Waltham, MA 02453-9110, USA 2 Department of Chemistry, Merkert Center, Boston College, Chestnut Hill, MA 02467-3860, USA 3 Graduate Program in Biochemistry and Biophysics, Brandeis University, Waltham, MA 02453-9110, USA 4 Graduate Program in Molecular and Cellular Biology, Brandeis University, Waltham, MA 02453-9110, USA 5 Department of Chemistry, Brandeis University, Waltham, MA 02453-9110, USA 6 UbiQ, 1098 XH Amsterdam, The Netherlands 7 Current address: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA 8 Current address: Sanofi Genzyme, Framingham, MA 01701, USA Correspondence to: Lizbeth Hedstrom, email: hedstrom@brandeis.edu Keywords: PEITC, USP1, cisplatin, deubiquitinase, cruciferous vegetable Received: June 20, 2016      Accepted: March 22, 2017      Published: April 20, 2017 ABSTRACT Cruciferous vegetables such as broccoli and kale have well documented chemopreventative and anticancer effects that are attributed to the presence of isothiocyanates (ITCs). ITCs modulate the levels of many oncogenic proteins, but the molecular mechanisms of ITC action are not understood. We previously reported that phenethyl isothiocyanate (PEITC) inhibits two deubiquitinases (DUBs), USP9x and UCH37. DUBs regulate many cellular processes and DUB dysregulation is linked to the pathogenesis of human diseases including cancer, neurodegeneration, and inflammation. Using SILAC assisted quantitative mass spectrometry, here we identify 9 new PEITC-DUB targets: USP1, USP3, USP10, USP11, USP16, USP22, USP40, USP48 and VCPIP1. Seven of these PEITC-sensitive DUBs have well-recognized roles in DNA repair or chromatin remodeling. PEITC both inhibits USP1 and increases its ubiquitination and degradation, thus decreasing USP1 activity by two mechanisms. The loss of USP1 activity increases the level of mono-ubiquitinated DNA clamp PCNA, impairing DNA repair. Both the inhibition/degradation of USP1 and the increase in mono-ubiquitinated PCNA are new activities for PEITC that can explain the previously recognized ability of ITCs to enhance cancer cell sensitivity to cisplatin treatment. Our work also demonstrates that PEITC reduces the mono-ubiquityl histones H2A and H2B. Understanding the mechanism of action of ITCs should facilitate their use as therapeutic agents.