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Varshavsky A. N-degron pathways. Proc Natl Acad Sci U S A 2024; 121:e2408697121. [PMID: 39264755 DOI: 10.1073/pnas.2408697121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2024] Open
Abstract
An N-degron is a degradation signal whose main determinant is a "destabilizing" N-terminal residue of a protein. Specific N-degrons, discovered in 1986, were the first identified degradation signals in short-lived intracellular proteins. These N-degrons are recognized by a ubiquitin-dependent proteolytic system called the Arg/N-degron pathway. Although bacteria lack the ubiquitin system, they also have N-degron pathways. Studies after 1986 have shown that all 20 amino acids of the genetic code can act, in specific sequence contexts, as destabilizing N-terminal residues. Eukaryotic proteins are targeted for the conditional or constitutive degradation by at least five N-degron systems that differ both functionally and mechanistically: the Arg/N-degron pathway, the Ac/N-degron pathway, the Pro/N-degron pathway, the fMet/N-degron pathway, and the newly named, in this perspective, GASTC/N-degron pathway (GASTC = Gly, Ala, Ser, Thr, Cys). I discuss these systems and the expanded terminology that now encompasses the entire gamut of known N-degron pathways.
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Affiliation(s)
- Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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2
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Zhou Y, Chen Y, Xuan C, Li X, Tan Y, Yang M, Cao M, Chen C, Huang X, Hu R. DPP9 regulates NQO1 and ROS to promote resistance to chemotherapy in liver cancer cells. Redox Biol 2024; 75:103292. [PMID: 39094401 PMCID: PMC11345690 DOI: 10.1016/j.redox.2024.103292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/23/2024] [Accepted: 07/27/2024] [Indexed: 08/04/2024] Open
Abstract
Chemotherapy has been the standard treatment for liver cancer. However, intrinsic or acquired drug resistance remains a major barrier to successful treatment. At present, the underlying molecular mechanisms of chemoresistance in liver cancer have not been elucidated. Dipeptidyl peptidase 9 (DPP9) is a member of the dipeptidyl peptidase IV family that has been found to be highly expressed in a variety of tumors, including liver cancer. It is unclear whether DPP9 affects chemoresistance in liver cancer. In this study, we find that DPP9 weakens the responses of liver cancer cells to chemotherapy drugs by up-regulating NQO1 and inhibiting intracellular ROS levels. In terms of mechanism, DPP9 inhibits ubiquitin-mediated degradation of NRF2 protein by binding to KEAP1, up-regulates NRF2 protein levels, promotes mRNA transcription of NQO1, and inhibits intracellular ROS levels. In addition, the NQO1 inhibitor dicoumarol can enhance the efficacy of chemotherapy drugs in liver cancer cells. Collectively, our findings suggest that inhibiting DPP9/NQO1 signaling can serve as a potential therapeutic strategy for liver cancer.
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Affiliation(s)
- Yunjiang Zhou
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yaxin Chen
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Chenyuan Xuan
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xingyan Li
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yingying Tan
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Mengdi Yang
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Mengran Cao
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Chi Chen
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xing Huang
- Department of Pathology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, 210009, China.
| | - Rong Hu
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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3
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Shimshon A, Dahan K, Israel-Gueta M, Olmayev-Yaakobov D, Timms RT, Bekturova A, Makaros Y, Elledge SJ, Koren I. Dipeptidyl peptidases and E3 ligases of N-degron pathways cooperate to regulate protein stability. J Cell Biol 2024; 223:e202311035. [PMID: 38874443 PMCID: PMC11178506 DOI: 10.1083/jcb.202311035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/21/2024] [Accepted: 04/30/2024] [Indexed: 06/15/2024] Open
Abstract
N-degrons are short sequences located at protein N-terminus that mediate the interaction of E3 ligases (E3s) with substrates to promote their proteolysis. It is well established that N-degrons can be exposed following protease cleavage to allow recognition by E3s. However, our knowledge regarding how proteases and E3s cooperate in protein quality control mechanisms remains minimal. Using a systematic approach to monitor the protein stability of an N-terminome library, we found that proline residue at the third N-terminal position (hereafter "P+3") promotes instability. Genetic perturbations identified the dipeptidyl peptidases DPP8 and DPP9 and the primary E3s of N-degron pathways, UBR proteins, as regulators of P+3 bearing substrate turnover. Interestingly, P+3 UBR substrates are significantly enriched for secretory proteins. We found that secretory proteins relying on a signal peptide (SP) for their targeting contain a "built-in" N-degron within their SP. This degron becomes exposed by DPP8/9 upon translocation failure to the designated compartments, thus enabling clearance of mislocalized proteins by UBRs to maintain proteostasis.
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Affiliation(s)
- Adi Shimshon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Karin Dahan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Mor Israel-Gueta
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Diana Olmayev-Yaakobov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Richard T Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre , Cambridge, UK
| | - Aizat Bekturova
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yaara Makaros
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Itay Koren
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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4
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Heß L, Aliar K, Grünwald BT, Griffin R, Lozan A, Knöller M, Khokha R, Brummer T, Reinheckel T. Dipeptidyl-peptidase 9 regulates the dynamics of tumorigenesis and metastasis in breast cancer. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167133. [PMID: 38531482 DOI: 10.1016/j.bbadis.2024.167133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024]
Abstract
The cytosolic dipeptidyl-aminopeptidase 9 (DPP9) cleaves protein N-termini post-proline or -alanine. Our analysis of DPP9 mRNA expression from the TCGA 'breast cancer' data set revealed that low/intermediate DPP9 levels are associated with poor overall survival of breast cancer patients. To unravel the impact of DPP9 on breast cancer development and progression, the transgenic MMTV-PyMT mouse model of metastasizing breast cancer was used. In addition, tissue- and time-controlled genetic deletion of DPP9 by the Cre-loxP recombination system was done. Despite a delay of tumor onset, a higher number of lung metastases were measured in DPP9-deficient mice compared to controls. In human mammary epithelial cells with oncogenic RAS pathway activation, DPP9 deficiency delayed tumorigenic transformation and accelerated TGF-β1 induced epithelial-to-mesenchymal transition (EMT) of spheroids. For further analysis of the mechanism, primary breast tumor cells were isolated from the MMTV-PyMT model. DPP9 deficiency in these cells caused cancer cell migration and invasion accompanied by EMT. In absence of DPP9, the EMT transcription factor ZEB1 was stabilized due to insufficient degradation by the proteasome. In summary, low expression of DPP9 appears to decelerate mammary tumorigenesis but favors EMT and metastasis, which establishes DPP9 as a novel dynamic regulator of breast cancer initiation and progression.
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Affiliation(s)
- Lisa Heß
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Kazeera Aliar
- Princess Margaret Cancer Centre, University Health Network, ON M5G 2G4, Toronto, Canada
| | - Barbara T Grünwald
- Princess Margaret Cancer Centre, University Health Network, ON M5G 2G4, Toronto, Canada
| | - Ricarda Griffin
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Alina Lozan
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; German Cancer Consortium (DKTK), partner site Freiburg, 79104 Freiburg, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mariel Knöller
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Rama Khokha
- Princess Margaret Cancer Centre, University Health Network, ON M5G 2G4, Toronto, Canada; Department of Medical Biophysics, University of Toronto, ON M5G 2G4, Toronto, Canada
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; German Cancer Consortium (DKTK), partner site Freiburg, 79104 Freiburg, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Centre for Biological Signalling Studies BIOSS, University of Freiburg, 79104 Freiburg, Germany; Comprehensive Cancer Center Freiburg (CCCF), University Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; German Cancer Consortium (DKTK), partner site Freiburg, 79104 Freiburg, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Centre for Biological Signalling Studies BIOSS, University of Freiburg, 79104 Freiburg, Germany; Comprehensive Cancer Center Freiburg (CCCF), University Medical Center, University of Freiburg, 79106 Freiburg, Germany.
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5
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Zolg S, Donzelli L, Geiss-Friedlander R. N-terminal processing by dipeptidyl peptidase 9: Cut and Go! Biochimie 2024:S0300-9084(24)00052-X. [PMID: 38461970 DOI: 10.1016/j.biochi.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
Dipeptidyl peptidase 9 (DPP9) is an intracellular amino-dipeptidase with physiological roles in the immune system, DNA repair and mitochondria homeostasis, while its deregulation is linked to cancer progression and immune-associated defects. Through its rare ability to cleave a peptide bond following the imino-acid proline, DPP9 acts as a molecular switch that regulates key proteins, such as the tumor-suppressor BRCA2. In this review we will discuss key concepts underlying the outcomes of protein processing by DPP9, including substrate turn-over by the N-degron pathway. Additionally, we will review non-enzymatic roles and the regulation of DPP9 by discussing the interactome of this protease, which includes SUMO1, Filamin A, NLRP1 and CARD8.
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Affiliation(s)
- Samuel Zolg
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
| | - Laura Donzelli
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
| | - Ruth Geiss-Friedlander
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany.
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Hua E, Xu D, Chen H, Zhang S, Feng J, Xu L. Development of the dipeptidyl peptidase 4 family and its association with lung diseases: a narrative review. J Thorac Dis 2023; 15:7024-7034. [PMID: 38249892 PMCID: PMC10797411 DOI: 10.21037/jtd-23-1158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/10/2023] [Indexed: 01/23/2024]
Abstract
Background and Objective Dipeptidyl peptidase (DPP)4 is a member of a subfamily of serine peptidase S9. DPP4, expressed as a type II transmembrane protein, has a wide tissue distribution and is most active in the lung and small intestine. Many substrates of DPP4 have been identified, including neuropeptides, chemokines, and glucagon-like peptide-1 (GLP-1) and gastric inhibitory polypeptides (GIPs). DPP4 inhibitors are clinically useful in the treatment of type 2 diabetes mellitus. DPP9, an N-terminal dipeptide targeting enzyme with proline or alanine, may have DPP4-like activity. DPP9 is ubiquitously expressed at human and rodent messenger RNA (mRNA) levels and therefore may play a role in the immune system and epithelial cells. It has been shown that DPP9 plays an important signaling role in the regulation of survival and proliferation pathways and is also involved in cell migration, apoptosis, and cell adhesion. In recent years, there has been further progress in DPP9 inhibition through activation of apoptosis by the inflammasome sensor protein Nlrp1b. This study aims to investigate the association of DPP4 family members and DPP9 with lung disease. Methods The literature search was initiated using the PubMed database. We searched for the content (DPP4) AND (Lung Diseases), (DPP9) AND (Lung Diseases), from which we filtered the literature we needed. Key Content and Findings Given the high biological activity of the DPP4 family, their involvement in various lung diseases is highly relevant. There is growing evidence for the importance of DPP4 and DPP9 of the DPP4 family in lung diseases, which are closely associated with diseases such as asthma, lung infections, pulmonary fibrosis (PF), and lung cancer. Conclusions This review summarizes most of the current evidence that DPP4/9 is associated with lung disease. Within the DPP4 family, the role of DPP4 in particular in respiratory disease is important.
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Affiliation(s)
- Ershi Hua
- Department of Pulmonary and Critical Care Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Department of Clinical Laboratory, Affiliated Nantong Hospital of Shanghai University (The Six People’s Hospital of Nantong), Nantong, China
| | - Dongmei Xu
- Department of Pulmonary and Critical Care Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Huamao Chen
- Department of Pulmonary and Critical Care Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Shuwen Zhang
- Department of Pulmonary and Critical Care Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Jian Feng
- Department of Pulmonary and Critical Care Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Liqin Xu
- Department of Pulmonary and Critical Care Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
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7
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Eldeeb MA, Zhou W, Esmaili M, Elgohary AM, Wei H, Fahlman RP. N-degron-mediated degradation of the proteolytically activated form of PKC-theta kinase attenuates its pro-apoptotic function. Cell Signal 2023; 110:110830. [PMID: 37516395 DOI: 10.1016/j.cellsig.2023.110830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/04/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Cellular signalling cues lead to the initiation of apoptotic pathways and often result in the activation of caspases which in turn cause the generation of proteolytically generated protein fragments with new or altered functions. Mounting number of studies reveal that the activity of these proteolytically activated protein fragments can be counteracted via their selective degradation by the N-degron degradation pathways. Here, we investigate the proteolytically generated fragment of the PKC theta kinase, where we demonstrate the first report on the stability of this pro-apoptotic protein fragment. We have determined that the pro-apoptotic cleaved fragment of PKC-theta is unstable in cells because its N-terminal lysine targets it for proteasomal degradation via the N-degron degradation pathway and this degradation is inhibited by mutating the destabilizing N-termini, knockdown of the UBR1 and UBR2 E3 ligases. Tellingly, we demonstrate that the metabolic stabilization of the cleaved fragment of PKC-theta or inhibition of the N-degron degradation augments the apoptosis-inducing effect of staurosporine in Jurkat cells. Notably, we have unveiled that the cleaved fragment of PKC theta, per se, can induce apoptotic cell death in Jurkat T-cell leukemia. Our results expand the functional scope of mammalian N-degron degradation pathways, and support the notion that targeting N-degron degradation machinery may have promising therapeutic implications in cancer cells.
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Affiliation(s)
- Mohamed A Eldeeb
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada; Department of Neurology, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.
| | - Wenbin Zhou
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, China
| | - Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Alaa M Elgohary
- Biophysics department, Faculty of science, Cairo University, Egypt
| | - Hai Wei
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
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8
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Bettecken A, Heß L, Hölzen L, Reinheckel T. Dipeptidyl-Aminopeptidases 8 and 9 Regulate Autophagy and Tamoxifen Response in Breast Cancer Cells. Cells 2023; 12:2031. [PMID: 37626841 PMCID: PMC10453625 DOI: 10.3390/cells12162031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
The cytosolic dipeptidyl-aminopeptidases 8 (DPP8) and 9 (DPP9) belong to the DPPIV serine proteases with the unique characteristic of cleaving off a dipeptide post-proline from the N-termini of substrates. To study the role of DPP8 and DPP9 in breast cancer, MCF-7 cells (luminal A-type breast cancer) and MDA.MB-231 cells (basal-like breast cancer) were used. The inhibition of DPP8/9 by 1G244 increased the number of lysosomes in both cell lines. This phenotype was more pronounced in MCF-7 cells, in which we observed a separation of autophagosomes and lysosomes in the cytosol upon DPP8/9 inhibition. Likewise, the shRNA-mediated knockdown of either DPP8 or DPP9 induced autophagy and increased lysosomes. DPP8/9 inhibition as well as the knockdown of the DPPs reduced the cell survival and proliferation of MCF-7 cells. Additional treatment of MCF-7 cells with tamoxifen, a selective estrogen receptor modulator (SERM) used to treat patients with luminal breast tumors, further decreased survival and proliferation, as well as increased cell death. In summary, both DPP8 and DPP9 activities confine macroautophagy in breast cancer cells. Thus, their inhibition or knockdown reduces cell viability and sensitizes luminal breast cancer cells to tamoxifen treatment.
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Affiliation(s)
- Aaron Bettecken
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Lisa Heß
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Lena Hölzen
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, 79104 Freiburg, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, 79104 Freiburg, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Centre of Biological Signalling Studies BIOSS, University of Freiburg, 79104 Freiburg, Germany
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9
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Kikuchi S, Wada A, Kamihara Y, Okazaki K, Jawaid P, Rehman MU, Kobayashi E, Susukida T, Minemura T, Nabe Y, Iwao N, Ozawa T, Hatano R, Yamada M, Kishi H, Matsuya Y, Mizuguchi M, Hayakawa Y, Dang NH, Sakamoto Y, Morimoto C, Sato T. DPP8 Selective Inhibitor Tominostat as a Novel and Broad-Spectrum Anticancer Agent against Hematological Malignancies. Cells 2023; 12:cells12071100. [PMID: 37048172 PMCID: PMC10093441 DOI: 10.3390/cells12071100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
DPP8/9 inhibition induces either pyroptotic or apoptotic cell death in hematological malignancies. We previously reported that treatment with the DPP8/9 inhibitor 1G244 resulted in apoptotic cell death in myeloma, and our current study further evaluates the mechanism of action of 1G244 in different blood cancer cell lines. Specifically, 1G244 inhibited DPP9 to induce GSDMD-mediated-pyroptosis at low concentrations and inhibited DPP8 to cause caspase-3-mediated-apoptosis at high concentrations. HCK expression is necessary to induce susceptibility to pyroptosis but does not participate in the induction of apoptosis. To further characterize this DPP8-dependent broad-spectrum apoptosis induction effect, we evaluated the potential antineoplastic role for an analog of 1G244 with higher DPP8 selectivity, tominostat (also known as 12 m). In vitro studies demonstrated that the cytotoxic effect of 1G244 at high concentrations was enhanced in tominostat. Meanwhile, in vivo work showed tominostat exhibited antitumor activity that was more effective on a cell line sensitive to 1G244, and at higher doses, it was also effective on a cell line resistant to 1G244. Importantly, the weight loss morbidity associated with increasing doses of 1G244 was not observed with tominostat. These results suggest the possible development of novel drugs with antineoplastic activity against selected hematological malignancies by refining and increasing the DPP8 selectivity of tominostat.
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Affiliation(s)
- Shohei Kikuchi
- Department of Hematology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Akinori Wada
- Department of Hematology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yusuke Kamihara
- Department of Hematology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Kosuke Okazaki
- Center for Clinical Research, Toyama University Hospital, 2630 Sugitani, Toyama 930-0194, Japan
| | - Paras Jawaid
- Department of Hematology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Mati Ur Rehman
- Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi 74800, Pakistan
| | - Eiji Kobayashi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Takeshi Susukida
- Section of Host Defences, Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Tomoki Minemura
- Department of Hematology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yoshimi Nabe
- Department of Hematology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Noriaki Iwao
- Department of Hematology, Juntendo University Shizuoka Hospital, 1129 Nagaoka, Izunokuni City, Shizuoka 410-2295, Japan
| | - Tatsuhiko Ozawa
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Ryo Hatano
- Department of Therapy Development and Innovation for Immune Disorders and Cancers, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo Bunkyo-ku, Tokyo 113-8421, Japan
| | - Mitsugu Yamada
- JEM Utilization Center Human Spaceflight Technology Directorate, Japan Aerospace Exploration Agency (JAXA), 2-1-1 Sengen, Tsukuba-shi 305-8505, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yuji Matsuya
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yoshihiro Hayakawa
- Section of Host Defences, Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Nam H Dang
- Division of Hematology/Oncology, University of Florida, Gainesville, FL 32610, USA
| | - Yasumitsu Sakamoto
- School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba 028-3694, Japan
| | - Chikao Morimoto
- Department of Therapy Development and Innovation for Immune Disorders and Cancers, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo Bunkyo-ku, Tokyo 113-8421, Japan
| | - Tsutomu Sato
- Department of Hematology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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10
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Donzelli L, Bolgi O, Geiss-Friedlander R. The amino-dipeptidyl peptidases DPP8 and DPP9: Purification and enzymatic assays. Methods Enzymol 2023; 684:289-323. [PMID: 37230592 DOI: 10.1016/bs.mie.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Proline residues highly impact protein stability when present either in the first or second N-terminal position. While the human genome encodes for more than 500 proteases, only few proteases are capable of hydrolyzing a proline-containing peptide bond. The two intra-cellular amino-dipeptidyl peptidases DPP8 and DPP9 are exceptional as they possess the rare ability to cleave post-proline. By removing N-terminal Xaa-Pro dipeptides, DPP8 and DPP9 expose a neo N-terminus of their substates, which can consequently alter inter- or intra-molecular interactions of the modified protein. Both DPP8 and DPP9 play key roles in the immune response and are linked to cancer progression, emerging as attractive drug targets. DPP9 is more abundant than DPP8 and is rate limiting for cleavage of cytosolic proline-containing peptides. Only few DPP9 substrates have been characterized; these include Syk, a central kinase for B-cell receptor mediated signaling; Adenylate Kinase 2 (AK2) which is important for cellular energy homeostasis; and the tumor suppressor Breast cancer type 2 susceptibility protein (BRCA2) that is critical for repair of DNA double strand breaks. N-terminal processing of these proteins by DPP9 triggers their rapid turn-over by the proteasome, highlighting a role for DPP9 as upstream components of the N-degron pathway. Whether N-terminal processing by DPP9 leads to substrate-degradation in all cases, or whether additional outcomes are possible, remains to be tested. In this chapter we will describe methods for purification of DPP8 and DPP9 as well as protocols for biochemical and enzymatic characterization of these proteases.
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Affiliation(s)
- Laura Donzelli
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Oguz Bolgi
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Ruth Geiss-Friedlander
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany.
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11
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Bhattacharjee A, Bachovchin DA. DPP8/9 are not Required to Cleave Most Proline-Containing Peptides. Isr J Chem 2023; 63:e202200117. [PMID: 37982048 PMCID: PMC10655806 DOI: 10.1002/ijch.202200117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Indexed: 02/16/2023]
Abstract
Small molecule inhibitors of the intracellular serine peptidases DPP8 and DPP9 (DPP8/9) activate the NLRP1 and CARD8 inflammasomes, but the key DPP8/9 substrates have not yet been identified. DPP8/9 cleave after proline to remove N-terminal dipeptides from peptides or proteins, and studies using pseudo-peptide reporter substrates have suggested that these enzymes may play key roles in the catabolism of many proline-containing peptides generated by the proteasome. Here, we evaluated the degradation of a wide array of actual peptides in cell lysates, and discovered that DPP8/9 are not in fact involved in the processing of the vast majority of proline-containing peptides. Overall, these results indicate that DPP8/9 have a much more limited substrate scope than previously thought, and likely specifically cleave some critically important, but as yet unknown, intracellular peptide or protein that regulates inflammasome activation.
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Affiliation(s)
- Abir Bhattacharjee
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
- Pharmacology Program of the Weill Cornell, Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
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12
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Carvalho LAR, Ross B, Fehr L, Bolgi O, Wöhrle S, Lum KM, Podlesainski D, Vieira AC, Kiefersauer R, Félix R, Rodrigues T, Lucas SD, Groß O, Geiss‐Friedlander R, Cravatt BF, Huber R, Kaiser M, Moreira R. Chemoproteomics-Enabled Identification of 4-Oxo-β-Lactams as Inhibitors of Dipeptidyl Peptidases 8 and 9. Angew Chem Int Ed Engl 2022; 61:e202210498. [PMID: 36089535 PMCID: PMC9828149 DOI: 10.1002/anie.202210498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 01/12/2023]
Abstract
Dipeptidyl peptidases 8 and 9 (DPP8/9) have gathered interest as drug targets due to their important roles in biological processes like immunity and tumorigenesis. Elucidation of their distinct individual functions remains an ongoing task and could benefit from the availability of novel, chemically diverse and selective chemical tools. Here, we report the activity-based protein profiling (ABPP)-mediated discovery of 4-oxo-β-lactams as potent, non-substrate-like nanomolar DPP8/9 inhibitors. X-ray crystallographic structures revealed different ligand binding modes for DPP8 and DPP9, including an unprecedented targeting of an extended S2' (eS2') subsite in DPP8. Biological assays confirmed inhibition at both target and cellular levels. Altogether, our integrated chemical proteomics and structure-guided small molecule design approach led to novel DPP8/9 inhibitors with alternative molecular inhibition mechanisms, delivering the highest selectivity index reported to date.
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Affiliation(s)
- Luís A. R. Carvalho
- Department of Pharmaceutical Sciences and MedicinesResearch Institute for Medicines (iMed.ULisboa)Faculdade de FarmáciaUniversidade de LisboaAv. Prof. Gama Pinto1649-003LisboaPortugal,Department of ChemistryThe Scripps Research InstituteLa JollaCalifornia92037USA
| | - Breyan Ross
- Max Planck Institut für Biochemie82152PlaneggMartinsriedGermany,Proteros Biostructures GmbH82152PlaneggMartinsriedGermany
| | - Lorenz Fehr
- Fakultät für BiologieZentrum für Medizinische BiotechnologieUniversität Duisburg-Essen45117EssenGermany
| | - Oguz Bolgi
- Center of Biochemistry and Molecular Cell ResearchAlbert-Ludwigs-Universität79104FreiburgGermany
| | - Svenja Wöhrle
- Institut für NeuropathologieUniversitätsklinikum Freiburg79106FreiburgGermany
| | - Kenneth M. Lum
- Department of ChemistryThe Scripps Research InstituteLa JollaCalifornia92037USA
| | - David Podlesainski
- Fakultät für BiologieZentrum für Medizinische BiotechnologieUniversität Duisburg-Essen45117EssenGermany
| | - Andreia C. Vieira
- Department of Pharmaceutical Sciences and MedicinesResearch Institute for Medicines (iMed.ULisboa)Faculdade de FarmáciaUniversidade de LisboaAv. Prof. Gama Pinto1649-003LisboaPortugal
| | | | - Rita Félix
- Department of Pharmaceutical Sciences and MedicinesResearch Institute for Medicines (iMed.ULisboa)Faculdade de FarmáciaUniversidade de LisboaAv. Prof. Gama Pinto1649-003LisboaPortugal
| | - Tiago Rodrigues
- Department of Pharmaceutical Sciences and MedicinesResearch Institute for Medicines (iMed.ULisboa)Faculdade de FarmáciaUniversidade de LisboaAv. Prof. Gama Pinto1649-003LisboaPortugal
| | - Susana D. Lucas
- Department of Pharmaceutical Sciences and MedicinesResearch Institute for Medicines (iMed.ULisboa)Faculdade de FarmáciaUniversidade de LisboaAv. Prof. Gama Pinto1649-003LisboaPortugal
| | - Olaf Groß
- Institut für NeuropathologieUniversitätsklinikum Freiburg79106FreiburgGermany,Signalling Research Centres BIOSS and CIBSSUniversity of Freiburg79104FreiburgGermany
| | - Ruth Geiss‐Friedlander
- Center of Biochemistry and Molecular Cell ResearchAlbert-Ludwigs-Universität79104FreiburgGermany
| | - Benjamin F. Cravatt
- Department of ChemistryThe Scripps Research InstituteLa JollaCalifornia92037USA
| | - Robert Huber
- Max Planck Institut für Biochemie82152PlaneggMartinsriedGermany,Fakultät für BiologieZentrum für Medizinische BiotechnologieUniversität Duisburg-Essen45117EssenGermany,Fakultät für ChemieTechnische Universität München85747GarchingGermany
| | - Markus Kaiser
- Fakultät für BiologieZentrum für Medizinische BiotechnologieUniversität Duisburg-Essen45117EssenGermany
| | - Rui Moreira
- Department of Pharmaceutical Sciences and MedicinesResearch Institute for Medicines (iMed.ULisboa)Faculdade de FarmáciaUniversidade de LisboaAv. Prof. Gama Pinto1649-003LisboaPortugal
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13
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Bolgi O, Silva-Garcia M, Ross B, Pilla E, Kari V, Killisch M, Spitzner M, Stark N, Lenz C, Weiss K, Donzelli L, Gorrell MD, Grade M, Riemer J, Urlaub H, Dobbelstein M, Huber R, Geiss-Friedlander R. Dipeptidyl peptidase 9 triggers BRCA2 degradation and promotes DNA damage repair. EMBO Rep 2022; 23:e54136. [PMID: 35912982 PMCID: PMC9535758 DOI: 10.15252/embr.202154136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/30/2022] Open
Abstract
N-terminal sequences are important sites for post-translational modifications that alter protein localization, activity, and stability. Dipeptidyl peptidase 9 (DPP9) is a serine aminopeptidase with the rare ability to cleave off N-terminal dipeptides with imino acid proline in the second position. Here, we identify the tumor-suppressor BRCA2 as a DPP9 substrate and show this interaction to be induced by DNA damage. We present crystallographic structures documenting intracrystalline enzymatic activity of DPP9, with the N-terminal Met1-Pro2 of a BRCA21-40 peptide captured in its active site. Intriguingly, DPP9-depleted cells are hypersensitive to genotoxic agents and are impaired in the repair of DNA double-strand breaks by homologous recombination. Mechanistically, DPP9 targets BRCA2 for degradation and promotes the formation of RAD51 foci, the downstream function of BRCA2. N-terminal truncation mutants of BRCA2 that mimic a DPP9 product phenocopy reduced BRCA2 stability and rescue RAD51 foci formation in DPP9-deficient cells. Taken together, we present DPP9 as a regulator of BRCA2 stability and propose that by fine-tuning the cellular concentrations of BRCA2, DPP9 alters the BRCA2 interactome, providing a possible explanation for DPP9's role in cancer.
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Affiliation(s)
- Oguz Bolgi
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany.,Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Maria Silva-Garcia
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Breyan Ross
- Max Planck Institut für Biochemie, Martinsried, Germany.,Proteros Biostructures GmbH, Martinsried, Germany
| | - Esther Pilla
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Vijayalakshmi Kari
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Markus Killisch
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Melanie Spitzner
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Nadine Stark
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Christof Lenz
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center, Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Konstantin Weiss
- Institute of Biochemistry, Redox Biochemistry, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Laura Donzelli
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Mark D Gorrell
- Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, NSW, Australia
| | - Marian Grade
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Jan Riemer
- Institute of Biochemistry, Redox Biochemistry, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Henning Urlaub
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center, Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Robert Huber
- Max Planck Institut für Biochemie, Martinsried, Germany.,Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, Essen, Germany.,Fakultät für Chemie, Technische Universität München, Garching, Germany
| | - Ruth Geiss-Friedlander
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany.,Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
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14
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Harapas CR, Robinson KS, Lay K, Wong J, Traspas RM, Nabavizadeh N, Rass-Rothschild A, Boisson B, Drutman SB, Laohamonthonkul P, Bonner D, Xiong JR, Gorrell MD, Davidson S, Yu CH, Fleming MD, Gudera J, Stein J, Ben-Harosh M, Groopman E, Shimamura A, Tamary H, Kayserili H, Hatipoğlu N, Casanova JL, Bernstein JA, Zhong FL, Masters SL, Reversade B. DPP9 deficiency: An inflammasomopathy that can be rescued by lowering NLRP1/IL-1 signaling. Sci Immunol 2022; 7:eabi4611. [PMID: 36112693 PMCID: PMC9844213 DOI: 10.1126/sciimmunol.abi4611] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Dipeptidyl peptidase 9 (DPP9) is a direct inhibitor of NLRP1, but how it affects inflammasome regulation in vivo is not yet established. Here, we report three families with immune-associated defects, poor growth, pancytopenia, and skin pigmentation abnormalities that segregate with biallelic DPP9 rare variants. Using patient-derived primary cells and biochemical assays, these variants were shown to behave as hypomorphic or knockout alleles that failed to repress NLRP1. The removal of a single copy of Nlrp1a/b/c, Asc, Gsdmd, or Il-1r, but not Il-18, was sufficient to rescue the lethality of Dpp9 mutant neonates in mice. Similarly, dpp9 deficiency was partially rescued by the inactivation of asc, an obligate downstream adapter of the NLRP1 inflammasome, in zebrafish. These experiments suggest that the deleterious consequences of DPP9 deficiency were mostly driven by the aberrant activation of the canonical NLRP1 inflammasome and IL-1β signaling. Collectively, our results delineate a Mendelian disorder of DPP9 deficiency driven by increased NLRP1 activity as demonstrated in patient cells and in two animal models of the disease.
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Affiliation(s)
- Cassandra R. Harapas
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Kim S. Robinson
- Skin Research Institute of Singapore (SRIS), A*STAR, Singapore
- Skin Research Laboratories (ASRL), A*STAR, Singapore
| | - Kenneth Lay
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore
| | - Jasmine Wong
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore
| | - Ricardo Moreno Traspas
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore
| | - Nasrin Nabavizadeh
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore
| | - Annick Rass-Rothschild
- The Institute for Rare Diseases, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, USA
- Paris University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Disease, Necker Branch, INSERM U1163, Paris, France
| | - Scott B. Drutman
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, USA
| | - Pawat Laohamonthonkul
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Devon Bonner
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Mark D. Gorrell
- Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Sophia Davidson
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Chien-Hsiung Yu
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Mark D. Fleming
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonas Gudera
- Dana Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, LMU Klinikum Munich, Munich, Germany
| | - Jerry Stein
- The Rina Zaizov Hematology-Oncology Division, Schneider Children’s Medical Center of Israel, Felsenstain Medical Research Center, Tel-Aviv University, Israel
| | - Miriam Ben-Harosh
- Department of Pediatric Hemato-Oncology, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Emily Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
| | - Akiko Shimamura
- Dana Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Hannah Tamary
- The Rina Zaizov Hematology-Oncology Division, Schneider Children’s Medical Center of Israel, Felsenstain Medical Research Center, Tel-Aviv University, Israel
| | - Hülya Kayserili
- Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey
| | - Nevin Hatipoğlu
- Department of Pediatric Infection, Health Science University, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, Istanbul, Turkey
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, USA
- Paris University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Disease, Necker Branch, INSERM U1163, Paris, France
- Pediatric Immunology-Hematology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, USA
| | | | - Franklin L. Zhong
- Skin Research Institute of Singapore (SRIS), A*STAR, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Seth L. Masters
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Bruno Reversade
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore
- Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey
- Laboratory of Human Genetics & Therapeutics, Institute of Molecular and Cellular Biology (IMCB), A*STAR, Singapore
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15
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Cui C, Tian X, Wei L, Wang Y, Wang K, Fu R. New insights into the role of dipeptidyl peptidase 8 and dipeptidyl peptidase 9 and their inhibitors. Front Pharmacol 2022; 13:1002871. [PMID: 36172198 PMCID: PMC9510841 DOI: 10.3389/fphar.2022.1002871] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Dipeptidyl peptidase 8 (DPP8) and 9 (DPP9) are widely expressed in mammals including humans, mainly locate in the cytoplasm. The DPP8 and DPP9 (DPP8/9) belong to serine proteolytic enzymes, they can recognize and cleave N-terminal dipeptides of specific substrates if proline is at the penultimate position. Because the localization of DPP8/9 is different from that of DPP4 and the substrates for DPP8/9 are not yet completely clear, their physiological and pathological roles are still being further explored. In this article, we will review the recent research advances focusing on the expression, regulation, and functions of DPP8/9 in physiology and pathology status. Emerging research results have shown that DPP8/9 is involved in various biological processes such as cell behavior, energy metabolism, and immune regulation, which plays an essential role in maintaining normal development and physiological functions of the body. DPP8/9 is also involved in pathological processes such as tumorigenesis, inflammation, and organ fibrosis. In recent years, related research on immune cell pyroptosis has made DPP8/9 a new potential target for the treatment of hematological diseases. In addition, DPP8/9 inhibitors also have great potential in the treatment of tumors and chronic kidney disease.
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Affiliation(s)
- Chenkai Cui
- Department of Nephrology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xuefei Tian
- Section of Nephrology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Linting Wei
- Department of Nephrology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yinhong Wang
- Department of Nephrology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Kexin Wang
- Department of Nephrology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Rongguo Fu
- Department of Nephrology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Rongguo Fu,
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16
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Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates. Proc Natl Acad Sci U S A 2022; 119:e2209597119. [PMID: 35878037 PMCID: PMC9351520 DOI: 10.1073/pnas.2209597119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
N-degron pathways are proteolytic systems that target proteins bearing N-terminal (Nt) degradation signals (degrons) called N-degrons. Nt-Arg of a protein is among Nt-residues that can be recognized as destabilizing ones by the Arg/N-degron pathway. A proteolytic cleavage of a protein can generate Arg at the N terminus of a resulting C-terminal (Ct) fragment either directly or after Nt-arginylation of that Ct-fragment by the Ate1 arginyl-tRNA-protein transferase (R-transferase), which uses Arg-tRNAArg as a cosubstrate. Ate1 can Nt-arginylate Nt-Asp, Nt-Glu, and oxidized Nt-Cys* (Cys-sulfinate or Cys-sulfonate) of proteins or short peptides. Ate1 genes of fungi, animals, and plants have been cloned decades ago, but a three-dimensional structure of Ate1 remained unknown. A detailed mechanism of arginylation is unknown as well. We describe here the crystal structure of the Ate1 R-transferase from the budding yeast Kluyveromyces lactis. The 58-kDa R-transferase comprises two domains that recognize, together, an acidic Nt-residue of an acceptor substrate, the Arg residue of Arg-tRNAArg, and a 3'-proximal segment of the tRNAArg moiety. The enzyme's active site is located, at least in part, between the two domains. In vitro and in vivo arginylation assays with site-directed Ate1 mutants that were suggested by structural results yielded inferences about specific binding sites of Ate1. We also analyzed the inhibition of Nt-arginylation activity of Ate1 by hemin (Fe3+-heme), and found that hemin induced the previously undescribed disulfide-mediated oligomerization of Ate1. Together, these results advance the understanding of R-transferase and the Arg/N-degron pathway.
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17
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BAFF promotes heightened BCR responsiveness and manifestations of chronic GVHD after allogeneic stem cell transplantation. Blood 2021; 137:2544-2557. [PMID: 33534893 PMCID: PMC8109011 DOI: 10.1182/blood.2020008040] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 01/21/2021] [Indexed: 12/25/2022] Open
Abstract
Patients with chronic graft-versus-host disease (cGVHD) have increased B cell-activating factor (BAFF) levels, but whether BAFF promotes disease after allogeneic bone marrow transplantation (allo-BMT) remains unknown. In a major histocompatibility complex-mismatched model with cGVHD-like manifestations, we first examined B-lymphopenic μMT allo-BMT recipients and found that increased BAFF levels in cGVHD mice were not merely a reflection of B-cell number. Mice that later developed cGVHD had significantly increased numbers of recipient fibroblastic reticular cells with higher BAFF transcript levels. Increased BAFF production by donor cells also likely contributed to cGVHD, because BAFF transcript in CD4+ T cells from diseased mice and patients was increased. cGVHD manifestations in mice were associated with high BAFF/B-cell ratios and persistence of B-cell receptor (BCR)-activated B cells in peripheral blood and lesional tissue. By employing BAFF transgenic (Tg) mice donor cells, we addressed whether high BAFF contributed to BCR activation in cGVHD. BAFF increased NOTCH2 expression on B cells, augmenting BCR responsiveness to surrogate antigen and NOTCH ligand. BAFF Tg B cells had significantly increased protein levels of the proximal BCR signaling molecule SYK, and high SYK protein was maintained by BAFF after in vitro BCR activation or when alloantigen was present in vivo. Using T cell-depleted (BM only) BAFF Tg donors, we found that BAFF promoted cGVHD manifestations, circulating GL7+ B cells, and alloantibody production. We demonstrate that pathologic production of BAFF promotes an altered B-cell compartment and augments BCR responsiveness. Our findings compel studies of therapeutic targeting of BAFF and BCR pathways in patients with cGVHD.
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18
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Gudipati RK, Braun K, Gypas F, Hess D, Schreier J, Carl SH, Ketting RF, Großhans H. Protease-mediated processing of Argonaute proteins controls small RNA association. Mol Cell 2021; 81:2388-2402.e8. [PMID: 33852894 DOI: 10.1016/j.molcel.2021.03.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/13/2022]
Abstract
Small RNA pathways defend the germlines of animals against selfish genetic elements, yet pathway activities need to be contained to prevent silencing of self genes. Here, we reveal a proteolytic mechanism that controls endogenous small interfering (22G) RNA activity in the Caenorhabditis elegans germline to protect genome integrity and maintain fertility. We find that DPF-3, a P-granule-localized N-terminal dipeptidase orthologous to mammalian dipeptidyl peptidase (DPP) 8/9, processes the unusually proline-rich N termini of WAGO-1 and WAGO-3 Argonaute (Ago) proteins. Without DPF-3 activity, these WAGO proteins lose their proper complement of 22G RNAs. Desilencing of repeat-containing and transposon-derived transcripts, DNA damage, and acute sterility ensue. These phenotypes are recapitulated when WAGO-1 and WAGO-3 are rendered resistant to DPF-3-mediated processing, identifying them as critical substrates of DPF-3. We conclude that N-terminal processing of Ago proteins regulates their activity and promotes silencing of selfish genetic elements by ensuring Ago association with appropriate small RNAs.
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Affiliation(s)
- Rajani Kanth Gudipati
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland.
| | - Kathrin Braun
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
| | - Foivos Gypas
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
| | - Jan Schreier
- Biology of Non-coding RNA, Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany; International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
| | - René F Ketting
- Biology of Non-coding RNA, Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland; University of Basel, Petersplatz 1, 4056 Basel, Switzerland.
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19
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Huang JC, Emran AA, Endaya JM, McCaughan GW, Gorrell MD, Zhang HE. DPP9: Comprehensive In Silico Analyses of Loss of Function Gene Variants and Associated Gene Expression Signatures in Human Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:1637. [PMID: 33915844 PMCID: PMC8037973 DOI: 10.3390/cancers13071637] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Dipeptidyl peptidase (DPP) 9, DPP8, DPP4 and fibroblast activation protein (FAP) are the four enzymatically active members of the S9b protease family. Associations of DPP9 with human liver cancer, exonic single nucleotide polymorphisms (SNPs) in DPP9 and loss of function (LoF) variants have not been explored. Human genomic databases, including The Cancer Genome Atlas (TCGA), were interrogated to identify DPP9 LoF variants and associated cancers. Survival and gene signature analyses were performed on hepatocellular carcinoma (HCC) data. We found that DPP9 and DPP8 are intolerant to LoF variants. DPP9 exonic LoF variants were most often associated with uterine carcinoma and lung carcinoma. All four DPP4-like genes were overexpressed in liver tumors and their joint high expression was associated with poor survival in HCC. Increased DPP9 expression was associated with obesity in HCC patients. High expression of genes that positively correlated with overexpression of DPP4, DPP8, and DPP9 were associated with very poor survival in HCC. Enriched pathways analysis of these positively correlated genes featured Toll-like receptor and SUMOylation pathways. This comprehensive data mining suggests that DPP9 is important for survival and that the DPP4 protease family, particularly DPP9, is important in the pathogenesis of human HCC.
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Affiliation(s)
- Jiali Carrie Huang
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.H.); (A.A.E.); (J.M.E.); (G.W.M.)
| | - Abdullah Al Emran
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.H.); (A.A.E.); (J.M.E.); (G.W.M.)
| | - Justine Moreno Endaya
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.H.); (A.A.E.); (J.M.E.); (G.W.M.)
| | - Geoffrey W. McCaughan
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.H.); (A.A.E.); (J.M.E.); (G.W.M.)
- AW Morrow GE & Liver Centre, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Mark D. Gorrell
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.H.); (A.A.E.); (J.M.E.); (G.W.M.)
| | - Hui Emma Zhang
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.H.); (A.A.E.); (J.M.E.); (G.W.M.)
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20
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Dunaevsky YE, Tereshchenkova VF, Oppert B, Belozersky MA, Filippova IY, Elpidina EN. Human proline specific peptidases: A comprehensive analysis. Biochim Biophys Acta Gen Subj 2020; 1864:129636. [DOI: 10.1016/j.bbagen.2020.129636] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/05/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
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21
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Leboeuf D, Pyatkov M, Zatsepin TS, Piatkov K. The Arg/N-Degron Pathway-A Potential Running Back in Fine-Tuning the Inflammatory Response? Biomolecules 2020; 10:biom10060903. [PMID: 32545869 PMCID: PMC7356051 DOI: 10.3390/biom10060903] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022] Open
Abstract
Recognition of danger signals by a cell initiates a powerful cascade of events generally leading to inflammation. Inflammatory caspases and several other proteases become activated and subsequently cleave their target proinflammatory mediators. The irreversible nature of this process implies that the newly generated proinflammatory fragments need to be sequestered, inhibited, or degraded in order to cancel the proinflammatory program or prevent chronic inflammation. The Arg/N-degron pathway is a ubiquitin-dependent proteolytic pathway that specifically degrades protein fragments bearing N-degrons, or destabilizing residues, which are recognized by the E3 ligases of the pathway. Here, we report that the Arg/N-degron pathway selectively degrades a number of proinflammatory fragments, including some activated inflammatory caspases, contributing in tuning inflammatory processes. Partial ablation of the Arg/N-degron pathway greatly increases IL-1β secretion, indicating the importance of this ubiquitous pathway in the initiation and resolution of inflammation. Thus, we propose a model wherein the Arg/N-degron pathway participates in the control of inflammation in two ways: in the generation of inflammatory signals by the degradation of inhibitory anti-inflammatory domains and as an “off switch” for inflammatory responses through the selective degradation of proinflammatory fragments.
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Affiliation(s)
- Dominique Leboeuf
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (D.L.); (T.S.Z.)
| | - Maxim Pyatkov
- Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia;
| | - Timofei S. Zatsepin
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (D.L.); (T.S.Z.)
| | - Konstantin Piatkov
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (D.L.); (T.S.Z.)
- Correspondence:
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22
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Recognition of nonproline N-terminal residues by the Pro/N-degron pathway. Proc Natl Acad Sci U S A 2020; 117:14158-14167. [PMID: 32513738 DOI: 10.1073/pnas.2007085117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Eukaryotic N-degron pathways are proteolytic systems whose unifying feature is their ability to recognize proteins containing N-terminal (Nt) degradation signals called N-degrons, and to target these proteins for degradation by the 26S proteasome or autophagy. GID4, a subunit of the GID ubiquitin ligase, is the main recognition component of the proline (Pro)/N-degron pathway. GID4 targets proteins through their Nt-Pro residue or a Pro at position 2, in the presence of specific downstream sequence motifs. Here we show that human GID4 can also recognize hydrophobic Nt-residues other than Pro. One example is the sequence Nt-IGLW, bearing Nt-Ile. Nt-IGLW binds to wild-type human GID4 with a K d of 16 μM, whereas the otherwise identical Nt-Pro-bearing sequence PGLW binds to GID4 more tightly, with a K d of 1.9 μM. Despite this difference in affinities of GID4 for Nt-IGLW vs. Nt-PGLW, we found that the GID4-mediated Pro/N-degron pathway of the yeast Saccharomyces cerevisiae can target an Nt-IGLW-bearing protein for rapid degradation. We solved crystal structures of human GID4 bound to a peptide bearing Nt-Ile or Nt-Val. We also altered specific residues of human GID4 and measured the affinities of resulting mutant GID4s for Nt-IGLW and Nt-PGLW, thereby determining relative contributions of specific GID4 residues to the GID4-mediated recognition of Nt-Pro vs. Nt-residues other than Pro. These and related results advance the understanding of targeting by the Pro/N-degron pathway and greatly expand the substrate recognition range of the GID ubiquitin ligase in both human and yeast cells.
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23
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Eldeeb MA, Fahlman RP, Esmaili M, Fon EA. When Degradation Elicits the Alarm: N-Terminal Degradation of NLRP1B Unleashes Its Inflammasome Activity. Mol Cell 2019; 74:637-639. [PMID: 31100244 DOI: 10.1016/j.molcel.2019.04.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Despite being among the first discovered mammalian innate immune sensor, NLRP1B (NLR pyrin domain-containing1B) activation and its molecular basis have remained elusive. Two recent studies have unveiled N-terminal degradation as a common mechanism for pathogen-mediated NLRP1B inflammasome activation in mammals.
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Affiliation(s)
- Mohamed A Eldeeb
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Edward A Fon
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
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24
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Haataja TJK, Capoulade R, Lecointe S, Hellman M, Merot J, Permi P, Pentikäinen U. Critical Structural Defects Explain Filamin A Mutations Causing Mitral Valve Dysplasia. Biophys J 2019; 117:1467-1475. [PMID: 31542223 DOI: 10.1016/j.bpj.2019.08.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/15/2019] [Accepted: 08/28/2019] [Indexed: 11/16/2022] Open
Abstract
Mitral valve diseases affect ∼3% of the population and are the most common reasons for valvular surgery because no drug-based treatments exist. Inheritable genetic mutations have now been established as the cause of mitral valve insufficiency, and four different missense mutations in the filamin A gene (FLNA) have been found in patients suffering from nonsyndromic mitral valve dysplasia (MVD). The filamin A (FLNA) protein is expressed, in particular, in endocardial endothelia during fetal valve morphogenesis and is key in cardiac development. The FLNA-MVD-causing mutations are clustered in the N-terminal region of FLNA. How the mutations in FLNA modify its structure and function has mostly remained elusive. In this study, using NMR spectroscopy and interaction assays, we investigated FLNA-MVD-causing V711D and H743P mutations. Our results clearly indicated that both mutations almost completely destroyed the folding of the FLNA5 domain, where the mutation is located, and also affect the folding of the neighboring FLNA4 domain. The structure of the neighboring FLNA6 domain was not affected by the mutations. These mutations also completely abolish FLNA's interactions with protein tyrosine phosphatase nonreceptor type 12, which has been suggested to contribute to the pathogenesis of FLNA-MVD. Taken together, our results provide an essential structural and molecular framework for understanding the molecular bases of FLNA-MVD, which is crucial for the development of new therapies to replace surgery.
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Affiliation(s)
- Tatu J K Haataja
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland; Institute of Biomedicine, University of Turku, Turku, Finland; Turku Bioscience Centre, University of Turku, 20520 Turku, Finland
| | - Romain Capoulade
- l'institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - Simon Lecointe
- l'institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - Maarit Hellman
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland; Department of Chemistry and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Jean Merot
- l'institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - Perttu Permi
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland; Department of Chemistry and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Ulla Pentikäinen
- Institute of Biomedicine, University of Turku, Turku, Finland; Turku Bioscience Centre, University of Turku, 20520 Turku, Finland.
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25
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Melnykov A, Chen SJ, Varshavsky A. Gid10 as an alternative N-recognin of the Pro/N-degron pathway. Proc Natl Acad Sci U S A 2019; 116:15914-15923. [PMID: 31337681 PMCID: PMC6689949 DOI: 10.1073/pnas.1908304116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In eukaryotes, N-degron pathways (formerly "N-end rule pathways") comprise a set of proteolytic systems whose unifying feature is their ability to recognize proteins containing N-terminal degradation signals called N-degrons, thereby causing degradation of these proteins by the 26S proteasome or autophagy. Gid4, a subunit of the GID ubiquitin ligase in the yeast Saccharomyces cerevisiae, is the recognition component (N-recognin) of the GID-mediated Pro/N-degron pathway. Gid4 targets proteins by recognizing their N-terminal Pro residues or a Pro at position 2, in the presence of distinct adjoining sequence motifs. Under conditions of low or absent glucose, cells make it through gluconeogenesis. When S. cerevisiae grows on a nonfermentable carbon source, its gluconeogenic enzymes Fbp1, Icl1, Mdh2, and Pck1 are expressed and long-lived. Transition to a medium containing glucose inhibits the synthesis of these enzymes and induces their degradation by the Gid4-dependent Pro/N-degron pathway. While studying yeast Gid4, we identified a similar but uncharacterized yeast protein (YGR066C), which we named Gid10. A screen for N-terminal peptide sequences that can bind to Gid10 showed that substrate specificities of Gid10 and Gid4 overlap but are not identical. Gid10 is not expressed under usual (unstressful) growth conditions, but is induced upon starvation or osmotic stresses. Using protein binding analyses and degradation assays with substrates of GID, we show that Gid10 can function as a specific N-recognin of the Pro/N-degron pathway.
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Affiliation(s)
- Artem Melnykov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Shun-Jia Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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26
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Gall MG, Zhang HE, Lee Q, Jolly CJ, McCaughan GW, Cook A, Roediger B, Gorrell MD. Immune regeneration in irradiated mice is not impaired by the absence of DPP9 enzymatic activity. Sci Rep 2019; 9:7292. [PMID: 31086209 PMCID: PMC6513830 DOI: 10.1038/s41598-019-43739-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 04/29/2019] [Indexed: 01/21/2023] Open
Abstract
The ubiquitous intracellular protease dipeptidyl peptidase 9 (DPP9) has roles in antigen presentation and B cell signaling. To investigate the importance of DPP9 in immune regeneration, primary and secondary chimeric mice were created in irradiated recipients using fetal liver cells and adult bone marrow cells, respectively, using wild-type (WT) and DPP9 gene-knockin (DPP9S729A) enzyme-inactive mice. Immune cell reconstitution was assessed at 6 and 16 weeks post-transplant. Primary chimeric mice successfully regenerated neutrophils, natural killer, T and B cells, irrespective of donor cell genotype. There were no significant differences in total myeloid cell or neutrophil numbers between DPP9-WT and DPP9S729A-reconstituted mice. In secondary chimeric mice, cells of DPP9S729A-origin cells displayed enhanced engraftment compared to WT. However, we observed no differences in myeloid or lymphoid lineage reconstitution between WT and DPP9S729A donors, indicating that hematopoietic stem cell (HSC) engraftment and self-renewal is not diminished by the absence of DPP9 enzymatic activity. This is the first report on transplantation of bone marrow cells that lack DPP9 enzymatic activity.
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Affiliation(s)
- Margaret G Gall
- Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Hui Emma Zhang
- Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Quintin Lee
- Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Christopher J Jolly
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Geoffrey W McCaughan
- Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Adam Cook
- Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Ben Roediger
- Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Mark D Gorrell
- Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia.
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27
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Griswold AR, Cifani P, Rao SD, Axelrod AJ, Miele MM, Hendrickson RC, Kentsis A, Bachovchin DA. A Chemical Strategy for Protease Substrate Profiling. Cell Chem Biol 2019; 26:901-907.e6. [PMID: 31006619 DOI: 10.1016/j.chembiol.2019.03.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 02/14/2019] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
Abstract
The dipeptidyl peptidases (DPPs) regulate hormones, cytokines, and neuropeptides by cleaving dipeptides after proline from their amino termini. Due to technical challenges, many DPP substrates remain unknown. Here, we introduce a simple method, termed CHOPS (chemical enrichment of protease substrates), for the discovery of protease substrates. CHOPS exploits a 2-pyridinecarboxaldehyde (2PCA)-biotin probe, which selectively biotinylates protein N-termini except those with proline in the second position. CHOPS can, in theory, discover substrates for any protease, but is particularly well suited to discover canonical DPP substrates, as cleaved but not intact DPP substrates can be identified by gel electrophoresis or mass spectrometry. Using CHOPS, we show that DPP8 and DPP9, enzymes that control the Nlrp1 inflammasome through an unknown mechanism, do not directly cleave Nlrp1. We further show that DPP9 robustly cleaves short peptides but not full-length proteins. More generally, this work delineates a practical technology for identifying protease substrates, which we anticipate will complement available "N-terminomic" approaches.
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Affiliation(s)
- Andrew R Griswold
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA; Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sahana D Rao
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Abram J Axelrod
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew M Miele
- Proteomics Core Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ronald C Hendrickson
- Proteomics Core Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alex Kentsis
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center and Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Daniel A Bachovchin
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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28
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Abstract
This perspective is partly review and partly proposal. N-degrons and C-degrons are degradation signals whose main determinants are, respectively, the N-terminal and C-terminal residues of cellular proteins. N-degrons and C-degrons include, to varying extents, adjoining sequence motifs, and also internal lysine residues that function as polyubiquitylation sites. Discovered in 1986, N-degrons were the first degradation signals in short-lived proteins. A particularly large set of C-degrons was discovered in 2018. We describe multifunctional proteolytic systems that target N-degrons and C-degrons. We also propose to denote these systems as "N-degron pathways" and "C-degron pathways." The former notation replaces the earlier name "N-end rule pathways." The term "N-end rule" was introduced 33 years ago, when only some N-terminal residues were thought to be destabilizing. However, studies over the last three decades have shown that all 20 amino acids of the genetic code can act, in cognate sequence contexts, as destabilizing N-terminal residues. Advantages of the proposed terms include their brevity and semantic uniformity for N-degrons and C-degrons. In addition to being topologically analogous, N-degrons and C-degrons are related functionally. A proteolytic cleavage of a subunit in a multisubunit complex can create, at the same time, an N-degron (in a C-terminal fragment) and a spatially adjacent C-degron (in an N-terminal fragment). Consequently, both fragments of a subunit can be selectively destroyed through attacks by the N-degron and C-degron pathways.
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29
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Enz N, Vliegen G, De Meester I, Jungraithmayr W. CD26/DPP4 - a potential biomarker and target for cancer therapy. Pharmacol Ther 2019; 198:135-159. [PMID: 30822465 DOI: 10.1016/j.pharmthera.2019.02.015] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
CD26/dipeptidyl peptidase (DPP)4 is a membrane-bound protein found in many cell types of the body, and a soluble form is present in body fluids. There is longstanding evidence that various primary tumors and also metastases express CD26/DPP4 to a variable extent. By cleaving dipeptides from peptides with a proline or alanine in the penultimate position at the N-terminus, it regulates the activity of incretin hormones, chemokines and many other peptides. Due to these effects and interactions with other molecules, a tumor promoting or suppressing role can be attributed to CD26/DPP4. In this review, we discuss the existing evidence on the expression of soluble or membrane-bound CD26/DPP4 in malignant diseases, along with the most recent findings on CD26/DPP4 as a therapeutic target in specific malignancies. The expression and possible involvement of the related DPP8 and DPP9 in cancer are also reviewed. A higher expression of CD26/DPP4 is found in a wide variety of tumor entities, however more research on CD26/DPP4 in the tumor microenvironment is needed to fully explore its use as a tumor biomarker. Circulating soluble CD26/DPP4 has also been studied as a cancer biomarker, however, the observed decrease in most cancer patients does not seem to be cancer specific. Encouraging results from experimental work and a recently reported first phase clinical trial targeting CD26/DPP4 in mesothelioma, renal and urological tumors pave the way for follow-up clinical studies, also in other tumor entities, possibly leading to the development of more effective complementary therapies against cancer.
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Affiliation(s)
- Njanja Enz
- Department of Thoracic Surgery, University Hospital Rostock, Schillingallee 35, 18057 Rostock, Germany
| | - Gwendolyn Vliegen
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Ingrid De Meester
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.
| | - Wolfgang Jungraithmayr
- Department of Thoracic Surgery, University Hospital Rostock, Schillingallee 35, 18057 Rostock, Germany.
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30
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Jia Y, Tao Y, Lv C, Xia Y, Wei Z, Dai Y. Tetrandrine enhances the ubiquitination and degradation of Syk through an AhR-c-src-c-Cbl pathway and consequently inhibits osteoclastogenesis and bone destruction in arthritis. Cell Death Dis 2019; 10:38. [PMID: 30674869 PMCID: PMC6427010 DOI: 10.1038/s41419-018-1286-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/10/2018] [Accepted: 12/14/2018] [Indexed: 12/27/2022]
Abstract
Recently, we reported that tetrandrine, a natural alkaloid, could inhibit the osteoclastogenesis and bone erosion through enhancing the ubiquitination and degradation of spleen tyrosine kinase (Syk). Herein, we addressed whether and how aryl hydrocarbon receptor (AhR) mediate the effect of tetrandrine. In vitro, tetrandrine was shown to repress RANKL-induced osteoclastogenesis and the expression of osteoclast-related marker genes, which was almost completely reversed by either AhR antagonist CH223191 or siRNA. In pre-osteoclasts, tetrandrine enhanced the ubiquitination and degradation of Syk through the AhR/c-src/c-Cbl signaling pathway, downregulated the expression of phospho-Syk and phospho-PLCγ2, and inhibited the nuclear translocation of NFATc1, a master transcription factor for osteoclastogenesis. Notably, tetrandrine acted through the non-genomic pathway of the ligand-activated AhR, as evidenced by the fact that the effect of tetrandrine did not change in the absence of AhR nuclear translocator. In collagen-induced arthritis rats, oral administration of tetrandrine decreased the number of phospho-Syk-positive cells and osteoclasts, and reduced the bone erosion in the areas of the proximal tibial epiphysis excluding the cortical bone. A combined use with CH223191 almost abolished the effect of tetrandrine. These findings revealed that tetrandrine enhanced the ubiquitination and degradation of Syk and consequently repressed the osteoclastogenesis and bone destruction through the AhR-c-src-c-Cbl pathway.
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Affiliation(s)
- Yugai Jia
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China.,Department of Pharmacology, Hebei University of Chinese Medicine, No. 326 South Xinshi Road, Shijiazhuang, 050091, Hebei, China
| | - Yu Tao
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China
| | - Changjun Lv
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China
| | - Yufeng Xia
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China
| | - Zhifeng Wei
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China.
| | - Yue Dai
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China.
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Unsworth AJ, Bombik I, Pinto-Fernandez A, McGouran JF, Konietzny R, Zahedi RP, Watson SP, Kessler BM, Pears CJ. Human Platelet Protein Ubiquitylation and Changes following GPVI Activation. Thromb Haemost 2018; 119:104-116. [PMID: 30597505 PMCID: PMC6327716 DOI: 10.1055/s-0038-1676344] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Platelet activators stimulate post-translational modification of signalling proteins to change their activity or their molecular interactions leading to signal propagation. One covalent modification is attachment of the small protein ubiquitin to lysine residues in target proteins. Modification by ubiquitin can either target proteins for degradation by the proteasome or act as a scaffold for other proteins. Pharmacological inhibition of deubiquitylases or the proteasome inhibition of platelet activation by collagen, demonstrating a role for ubiquitylation, but relatively few substrates for ubiquitin have been identified and the molecular basis of inhibition is not established. Here, we report the ubiquitome of human platelets and changes in ubiquitylated proteins following stimulation by collagen-related peptide (CRP-XL). Using platelets from six individuals over three independent experiments, we identified 1,634 ubiquitylated peptides derived from 691 proteins, revealing extensive ubiquitylation in resting platelets. Note that 925 of these peptides show an increase of more than twofold following stimulation with CRP-XL. Multiple sites of ubiquitylation were identified on several proteins including Syk, filamin and integrin heterodimer sub-units. This work reveals extensive protein ubiquitylation during activation of human platelets and opens the possibility of novel therapeutic interventions targeting the ubiquitin machinery.
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Affiliation(s)
- Amanda J Unsworth
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.,Institute for Cardiovascular and Metabolic Research, University of Reading, Reading, United Kingdom
| | - Izabela Bombik
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Adan Pinto-Fernandez
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Joanna F McGouran
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Rebecca Konietzny
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - René P Zahedi
- JGH Proteomics Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Steve P Watson
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.,Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, The Midlands, United Kingdom
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Catherine J Pears
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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32
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Zhong FL, Robinson K, Teo DET, Tan KY, Lim C, Harapas CR, Yu CH, Xie WH, Sobota RM, Au VB, Hopkins R, D'Osualdo A, Reed JC, Connolly JE, Masters SL, Reversade B. Human DPP9 represses NLRP1 inflammasome and protects against autoinflammatory diseases via both peptidase activity and FIIND domain binding. J Biol Chem 2018; 293:18864-18878. [PMID: 30291141 PMCID: PMC6295727 DOI: 10.1074/jbc.ra118.004350] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/25/2018] [Indexed: 12/17/2022] Open
Abstract
The inflammasome is a critical molecular complex that activates interleukin-1 driven inflammation in response to pathogen- and danger-associated signals. Germline mutations in the inflammasome sensor NLRP1 cause Mendelian systemic autoimmunity and skin cancer susceptibility, but its endogenous regulation remains less understood. Here we use a proteomics screen to uncover dipeptidyl dipeptidase DPP9 as a novel interacting partner with human NLRP1 and a related inflammasome regulator, CARD8. DPP9 functions as an endogenous inhibitor of NLRP1 inflammasome in diverse primary cell types from human and mice. DPP8/9 inhibition via small molecule drugs and CRISPR/Cas9-mediated genetic deletion specifically activate the human NLRP1 inflammasome, leading to ASC speck formation, pyroptotic cell death, and secretion of cleaved interleukin-1β. Mechanistically, DPP9 interacts with a unique autoproteolytic domain (Function to Find Domain (FIIND)) found in NLRP1 and CARD8. This scaffolding function of DPP9 and its catalytic activity act synergistically to maintain NLRP1 in its inactive state and repress downstream inflammasome activation. We further identified a single patient-derived germline missense mutation in the NLRP1 FIIND domain that abrogates DPP9 binding, leading to inflammasome hyperactivation seen in the Mendelian autoinflammatory disease Autoinflammation with Arthritis and Dyskeratosis. These results unite recent findings on the regulation of murine Nlrp1b by Dpp8/9 and uncover a new regulatory mechanism for the NLRP1 inflammasome in primary human cells. Our results further suggest that DPP9 could be a multifunctional inflammasome regulator involved in human autoinflammatory diseases.
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Affiliation(s)
- Franklin L Zhong
- From the Institute of Molecular and Cell Biology, A*STAR, Proteos, Singapore 138673,
- the Institute of Medical Biology, A*STAR, Immunos, Singapore 138648
- the Skin Research Institute of Singapore, Immunos, Singapore 138648
- the Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921
| | - Kim Robinson
- the Institute of Medical Biology, A*STAR, Immunos, Singapore 138648
- the Skin Research Institute of Singapore, Immunos, Singapore 138648
| | - Daniel Eng Thiam Teo
- From the Institute of Molecular and Cell Biology, A*STAR, Proteos, Singapore 138673
- the Institute of Medical Biology, A*STAR, Immunos, Singapore 138648
- the Skin Research Institute of Singapore, Immunos, Singapore 138648
| | - Kiat-Yi Tan
- From the Institute of Molecular and Cell Biology, A*STAR, Proteos, Singapore 138673
| | - Chrissie Lim
- From the Institute of Molecular and Cell Biology, A*STAR, Proteos, Singapore 138673
| | - Cassandra R Harapas
- the Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Chien-Hsiung Yu
- the Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - William H Xie
- the Institute of Medical Biology, A*STAR, Immunos, Singapore 138648
| | - Radoslaw M Sobota
- From the Institute of Molecular and Cell Biology, A*STAR, Proteos, Singapore 138673
| | - Veonice Bijin Au
- From the Institute of Molecular and Cell Biology, A*STAR, Proteos, Singapore 138673
| | - Richard Hopkins
- From the Institute of Molecular and Cell Biology, A*STAR, Proteos, Singapore 138673
| | - Andrea D'Osualdo
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - John C Reed
- the Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, California 92037
| | - John E Connolly
- From the Institute of Molecular and Cell Biology, A*STAR, Proteos, Singapore 138673
- the Institute of Biomedical Studies, Baylor University, Waco, Texas 76712
- the Department of Microbiology and Immunology, National University of Singapore, Singapore 117545
| | - Seth L Masters
- the Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010 Australia
| | - Bruno Reversade
- From the Institute of Molecular and Cell Biology, A*STAR, Proteos, Singapore 138673,
- the Institute of Medical Biology, A*STAR, Immunos, Singapore 138648
- the Reproductive Biology Laboratory, Obstetrics and Gynaecology, Amsterdam UMC, 1105 AZ Amsterdam-Zuidoost, The Netherlands
- the Department of Paediatrics, National University of Singapore, Singapore 119228
- the Medical Genetics Department, Koç University School of Medicine, 34010 Istanbul, Turkey, and
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33
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Jia Y, Miao Y, Yue M, Shu M, Wei Z, Dai Y. Tetrandrine attenuates the bone erosion in collagen-induced arthritis rats by inhibiting osteoclastogenesis via spleen tyrosine kinase. FASEB J 2018; 32:3398-3410. [PMID: 29401630 DOI: 10.1096/fj.201701148rr] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Tetrandrine, a bisbenzylisoquinoline alkaloid, was previously demonstrated to attenuate inflammation and cartilage destruction in the ankles of mice with collagen-induced arthritis (CIA). Here, we explored the underlying mechanism by which tetrandrine prevented arthritis-induced bone erosion by focusing on the differentiation and function of osteoclasts. We found that daily administration of tetrandrine (30 mg/kg) markedly reduced the bone damage and decreased the number of osteoclasts in CIA rats. In vitro, tetrandrine inhibited receptor activator of NF-κB ligand (RANKL)-induced osteoclastogenesis at the early stage and reduced the expressions of osteoclast-related marker genes. In bone marrow-derived macrophages and RAW264.7 cells, tetrandrine inhibited RANKL-induced translocation of NF-κB-p65 and nuclear factor of activated T cell 1 (NFATc1) through suppressing spleen tyrosine kinase (Syk)-Bruton's tyrosine kinase-PLCγ2-Ca2+ signaling. Of interest, tetrandrine did not affect the phosphorylation of immunoreceptor tyrosine-based activation motifs, the conventional upstream of Syk, but it inhibited the activity of Syk by enhancing its ubiquitination and degradation. The anti-osteoclastogenesis effect of tetrandrine nearly disappeared when it was used in combination with the Syk inhibitor piceatannol or in constitutively activated Syk-overexpressing cells. Taken together, tetrandrine attenuated CIA-induced bone destruction by inhibiting osteoclastogenesis through hindering the translocation of NF-κB-p65 and NFATc1 via reducing the activation of Syk.-Jia, Y., Miao, Y., Yue, M., Shu, M., Wei, Z., Dai, Y. Tetrandrine attenuates the bone erosion in collagen-induced arthritis rats by inhibiting osteoclastogenesis via spleen tyrosine kinase.
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Affiliation(s)
- Yugai Jia
- Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| | - Yumeng Miao
- Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| | - Mengfan Yue
- Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| | - Mei Shu
- Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| | - Zhifeng Wei
- Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| | - Yue Dai
- Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
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Structures and mechanism of dipeptidyl peptidases 8 and 9, important players in cellular homeostasis and cancer. Proc Natl Acad Sci U S A 2018; 115:E1437-E1445. [PMID: 29382749 DOI: 10.1073/pnas.1717565115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Dipeptidyl peptidases 8 and 9 are intracellular N-terminal dipeptidyl peptidases (preferentially postproline) associated with pathophysiological roles in immune response and cancer biology. While the DPP family member DPP4 is extensively characterized in molecular terms as a validated therapeutic target of type II diabetes, experimental 3D structures and ligand-/substrate-binding modes of DPP8 and DPP9 have not been reported. In this study we describe crystal and molecular structures of human DPP8 (2.5 Å) and DPP9 (3.0 Å) unliganded and complexed with a noncanonical substrate and a small molecule inhibitor, respectively. Similar to DPP4, DPP8 and DPP9 molecules consist of one β-propeller and α/β hydrolase domain, forming a functional homodimer. However, they differ extensively in the ligand binding site structure. In intriguing contrast to DPP4, where liganded and unliganded forms are closely similar, ligand binding to DPP8/9 induces an extensive rearrangement at the active site through a disorder-order transition of a 26-residue loop segment, which partially folds into an α-helix (R-helix), including R160/133, a key residue for substrate binding. As vestiges of this helix are also seen in one of the copies of the unliganded form, conformational selection may contributes to ligand binding. Molecular dynamics simulations support increased flexibility of the R-helix in the unliganded state. Consistently, enzyme kinetics assays reveal a cooperative allosteric mechanism. DPP8 and DPP9 are closely similar and display few opportunities for targeted ligand design. However, extensive differences from DPP4 provide multiple cues for specific inhibitor design and development of the DPP family members as therapeutic targets or antitargets.
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35
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Eldeeb MA, Leitao LCA, Fahlman RP. Emerging branches of the N-end rule pathways are revealing the sequence complexities of N-termini dependent protein degradation. Biochem Cell Biol 2017; 96:289-294. [PMID: 29253354 DOI: 10.1139/bcb-2017-0274] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The N-end rule links the identity of the N-terminal amino acid of a protein to its in vivo half-life, as some N-terminal residues confer metabolic instability to a protein via their recognition by the cellular machinery that targets them for degradation. Since its discovery, the N-end rule has generally been defined as set of rules of whether an N-terminal residue is stabilizing or not. However, recent studies are revealing that the N-terminal code of amino acids conferring protein instability is more complex than previously appreciated, as recent investigations are revealing that the identity of adjoining downstream residues can also influence the metabolic stability of N-end rule substrate. This is exemplified by the recent discovery of a new branch of N-end rule pathways that target proteins bearing N-terminal proline. In addition, recent investigations are demonstrating that the molecular machinery in N-termini dependent protein degradation may also target proteins for lysosomal degradation, in addition to proteasome-dependent degradation. Herein, we describe some of the recent advances in N-end rule pathways and discuss some of the implications regarding the emerging additional sequence requirements.
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Affiliation(s)
- Mohamed A Eldeeb
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.,b Department of Chemistry, Faculty of Science, Cairo University, Giza, Cairo, Egypt
| | - Luana C A Leitao
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Richard P Fahlman
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.,c Department of Oncology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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36
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Vliegen G, Raju TK, Adriaensen D, Lambeir AM, De Meester I. The expression of proline-specific enzymes in the human lung. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:130. [PMID: 28462210 DOI: 10.21037/atm.2017.03.36] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The pathophysiology of lung diseases is very complex and proteolytic enzymes may play a role or could be used as biomarkers. In this review, the literature was searched to make an overview of what is known on the expression of the proline-specific peptidases dipeptidyl peptidase (DPP) 4, 8, 9, prolyl oligopeptidase (PREP) and fibroblast activation protein α (FAP) in the healthy and diseased lung. Search terms included asthma, chronic obstructive pulmonary disease (COPD), lung cancer, fibrosis, ischemia reperfusion injury and pneumonia. Knowledge on the loss or gain of protein expression and activity during disease might tie these enzymes to certain cell types, substrates or interaction partners that are involved in the pathophysiology of the disease, ultimately leading to the elucidation of their functional roles and a potential therapeutic target. Most data could be found on DPP4, while the other enzymes are less explored. Published data however often appear to be conflicting, the applied methods divers and the specificity of the assays used questionable. In conclusion, information on the expression of the proline-specific peptidases in the healthy and diseased lung is lacking, begging for further well-designed research.
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Affiliation(s)
- Gwendolyn Vliegen
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, 2610 Wilrijk, Belgium
| | - Tom K Raju
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, 2610 Wilrijk, Belgium
| | - Dirk Adriaensen
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium
| | - Anne-Marie Lambeir
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, 2610 Wilrijk, Belgium
| | - Ingrid De Meester
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, 2610 Wilrijk, Belgium
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