title: Profiling human protein degradome delineates cellular responses to proteasomal inhibition and reveals a feedback mechanism in regulating proteasome homeostasis.
abstract: Global change in protein turnover (protein degradome) constitutes a central part of cellular responses to intrinsic or extrinsic stimuli. However, profiling protein degradome remains technically challenging. Recently, inhibition of the proteasome, e.g., by using bortezomib (BTZ), has emerged as a major chemotherapeutic strategy for treating multiple myeloma and other human malignancies, but systematic understanding of the mechanisms for BTZ drug action and tumor drug resistance is yet to be achieved. Here we developed and applied a dual-fluorescence-based Protein Turnover Assay (ProTA) to quantitatively profile global changes in human protein degradome upon BTZ-induced proteasomal inhibition. ProTA and subsequent network analyses delineate potential molecular basis for BTZ action and tumor drug resistance in BTZ chemotherapy. Finally, combined use of BTZ with drugs targeting the ProTA-identified key genes or pathways in BTZ action reduced BTZ resistance in multiple myeloma cells. Remarkably, BTZ stabilizes proteasome subunit PSMC1 and proteasome assembly factor PSMD10, suggesting a previously under-appreciated mechanism for regulating proteasome homeostasis. Therefore, ProTA is a novel tool for profiling human protein degradome to elucidate potential mechanisms of drug action and resistance, which might facilitate therapeutic development targeting proteostasis to treat human disorders.
authors.affiliation: 1] State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China [2] Graduate School, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Yu
authors.affiliation: 1] State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China [2] Graduate School, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
authors.forename: Yonghui
authors.initials: Y
authors.lastname: Tao
authors.affiliation: State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
authors.forename: Meiqiang
authors.initials: M
authors.lastname: Yang
authors.affiliation: 1] State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China [2] Graduate School, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Chen
authors.affiliation: 1] State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China [2] Graduate School, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Gao
authors.affiliation: 1] Graduate School, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China [2] State Key Laboratory of Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
authors.forename: Yanbo
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Laboratory Medicine, Hua-Shan Hospital, Fudan University, 12 Road Wulumuqi middle Road, Shanghai 200040, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Department of Hematology, Hua-Shan Hospital, Fudan University, 12 Road Wulumuqi middle Road, Shanghai 200040, China.
authors.forename: Zi
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Department of Hematology, Changzheng Hospital, The Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Hou
authors.affiliation: Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
authors.forename: Kangcheng
authors.initials: K
authors.lastname: Ruan
authors.affiliation: State Key Laboratory of Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
authors.forename: Hongyan
authors.initials: H
authors.lastname: Wang
authors.affiliation: 1] State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China [2] Cancer Research Center, SIBS-Xuhui Central Hospital, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
authors.forename: Ronggui
authors.initials: R
authors.lastname: Hu
mesh_terms: D017209:Apoptosis / Q000187:drug effects; D001897:Boronic Acids / Q000494:pharmacology / Q000627:therapeutic use; D000069286:Bortezomib; D019008:Drug Resistance, Neoplasm / Q000187:drug effects; D015723:Gene Library; D057809:HEK293 Cells; D006801:Humans; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism; D009369:Neoplasms / Q000188:drug therapy / Q000378:metabolism / Q000473:pathology; D046988:Proteasome Endopeptidase Complex / Q000737:chemistry / Q000378:metabolism*; D061988:Proteasome Inhibitors / Q000494:pharmacology / Q000627:therapeutic use; D040081:Protein Array Analysis; D060066:Protein Interaction Maps / Q000187:drug effects; D059748:Proteolysis / Q000187:drug effects; D011518:Proto-Oncogene Proteins / Q000378:metabolism; D011719:Pyrazines / Q000494:pharmacology / Q000627:therapeutic use; D059467:Transcriptome
chemical_list: D001897:Boronic Acids; D008164:Luminescent Proteins; C403591:PSMD10 protein, human; D061988:Proteasome Inhibitors; D011518:Proto-Oncogene Proteins; D011719:Pyrazines; D000069286:Bortezomib; D046988:Proteasome Endopeptidase Complex