1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Scucchia F, Wong K, Zaslansky P, Putnam HM, Goodbody-Gringley G, Mass T. Morphological and genetic mechanisms underlying the plasticity of the coral Porites astreoides across depths in Bermuda. J Struct Biol 2023; 215:108036. [PMID: 37832837 DOI: 10.1016/j.jsb.2023.108036] [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: 06/21/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
The widespread decline of shallow-water coral reefs has fueled interest in assessing whether mesophotic reefs can act as refugia replenishing deteriorated shallower reefs through larval exchange. Here we explore the morphological and molecular basis facilitating survival of planulae and adults of the coral Porites astreoides (Lamarck, 1816; Hexacorallia: Poritidae) along the vertical depth gradient in Bermuda. We found differences in micro-skeletal features such as bigger calyxes and coarser surface of the skeletal spines in shallow corals. Yet, tomographic reconstructions reveal an analogous mineral distribution between shallow and mesophotic adults, pointing to similar skeleton growth dynamics. Our study reveals patterns of host genetic connectivity and minimal symbiont depth-zonation across a broader depth range than previously known for this species in Bermuda. Transcriptional variations across life stages showed different regulation of metabolism and stress response functions, unraveling molecular responses to environmental conditions at different depths. Overall, these findings increase our understanding of coral acclimatory capability across broad vertical gradients, ultimately allowing better evaluation of the refugia potential of mesophotic reefs.
Collapse
Affiliation(s)
- Federica Scucchia
- Department of Marine Biology, Leon H. Charney School of Marine Sciences University of Haifa, Israel; The Interuniversity Institute of Marine Sciences, Eilat, Israel.
| | - Kevin Wong
- Department of Biological Sciences, University of Rhode Island, Kingston, United States
| | - Paul Zaslansky
- Department for Operative, Preventive and Pediatric Dentistry, Charité-Universitätsmedizin, Berlin, Germany
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, United States
| | - Gretchen Goodbody-Gringley
- Central Caribbean Marine Institute, Little Cayman, Cayman Islands; Bermuda Institute of Ocean Sciences, St. George's, Bermuda
| | - Tali Mass
- Department of Marine Biology, Leon H. Charney School of Marine Sciences University of Haifa, Israel.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Kalogeropoulos K, Bundgaard L, Auf dem Keller U. Sensitive and High-Throughput Exploration of Protein N-Termini by TMT-TAILS N-Terminomics. Methods Mol Biol 2023; 2718:111-135. [PMID: 37665457 DOI: 10.1007/978-1-0716-3457-8_7] [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] [Indexed: 09/05/2023]
Abstract
Terminal amine isotopic labeling of substrates (TAILS) is a sensitive and robust quantitative mass spectrometry (MS)-based proteomics method used for the characterization of physiological or proteolytically processed protein N-termini, as well as other N-terminal posttranslational modifications (PTMs). TAILS is a well-established, high-throughput, negative enrichment workflow that enables system-wide exploration of N-terminomes independent of sample complexity. TAILS makes use of amine reactivity of free N-termini and a highly efficient aldehyde-functionalized polymer to deplete internal peptides generated after proteolytic digestion during sample preparation. Thereby, it enriches for natural N-termini, allowing for unbiased and complete investigation of differential proteolysis, protease substrate discovery, and analysis of N-terminal PTMs. In this chapter, we provide a state-of-the-art protocol, with detailed steps in all parts of the TAILS sample preparation, MS analysis, and post-processing of acquired data.
Collapse
Affiliation(s)
| | - Louise Bundgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
| |
Collapse
|
6
|
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.
Collapse
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,
| |
Collapse
|
7
|
Powell DR, Revelli JP, Doree DD, DaCosta CM, Desai U, Shadoan MK, Rodriguez L, Mullens M, Yang QM, Ding ZM, Kirkpatrick LL, Vogel P, Zambrowicz B, Sands AT, Platt KA, Hansen GM, Brommage R. High-Throughput Screening of Mouse Gene Knockouts Identifies Established and Novel High Body Fat Phenotypes. Diabetes Metab Syndr Obes 2021; 14:3753-3785. [PMID: 34483672 PMCID: PMC8409770 DOI: 10.2147/dmso.s322083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/04/2021] [Indexed: 01/05/2023] Open
Abstract
PURPOSE Obesity is a major public health problem. Understanding which genes contribute to obesity may better predict individual risk and allow development of new therapies. Because obesity of a mouse gene knockout (KO) line predicts an association of the orthologous human gene with obesity, we reviewed data from the Lexicon Genome5000TM high throughput phenotypic screen (HTS) of mouse gene KOs to identify KO lines with high body fat. MATERIALS AND METHODS KO lines were generated using homologous recombination or gene trapping technologies. HTS body composition analyses were performed on adult wild-type and homozygous KO littermate mice from 3758 druggable mouse genes having a human ortholog. Body composition was measured by either DXA or QMR on chow-fed cohorts from all 3758 KO lines and was measured by QMR on independent high fat diet-fed cohorts from 2488 of these KO lines. Where possible, comparisons were made to HTS data from the International Mouse Phenotyping Consortium (IMPC). RESULTS Body fat data are presented for 75 KO lines. Of 46 KO lines where independent external published and/or IMPC KO lines are reported as obese, 43 had increased body fat. For the remaining 29 novel high body fat KO lines, Ksr2 and G2e3 are supported by data from additional independent KO cohorts, 6 (Asnsd1, Srpk2, Dpp8, Cxxc4, Tenm3 and Kiss1) are supported by data from additional internal cohorts, and the remaining 21 including Tle4, Ak5, Ntm, Tusc3, Ankk1, Mfap3l, Prok2 and Prokr2 were studied with HTS cohorts only. CONCLUSION These data support the finding of high body fat in 43 independent external published and/or IMPC KO lines. A novel obese phenotype was identified in 29 additional KO lines, with 27 still lacking the external confirmation now provided for Ksr2 and G2e3 KO mice. Undoubtedly, many mammalian obesity genes remain to be identified and characterized.
Collapse
Affiliation(s)
- David R Powell
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Jean-Pierre Revelli
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Deon D Doree
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Christopher M DaCosta
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Urvi Desai
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Melanie K Shadoan
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Lawrence Rodriguez
- Department of Information Technology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Michael Mullens
- Department of Information Technology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Qi M Yang
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Zhi-Ming Ding
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Laura L Kirkpatrick
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Peter Vogel
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Brian Zambrowicz
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
- Department of Information Technology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Arthur T Sands
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
- Department of Information Technology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Kenneth A Platt
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Gwenn M Hansen
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Robert Brommage
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| |
Collapse
|
8
|
Mintoo M, Chakravarty A, Tilvawala R. N-Terminomics Strategies for Protease Substrates Profiling. Molecules 2021; 26:molecules26154699. [PMID: 34361849 PMCID: PMC8348681 DOI: 10.3390/molecules26154699] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 01/02/2023] Open
Abstract
Proteases play a central role in various biochemical pathways catalyzing and regulating key biological events. Proteases catalyze an irreversible post-translational modification called proteolysis by hydrolyzing peptide bonds in proteins. Given the destructive potential of proteolysis, protease activity is tightly regulated. Dysregulation of protease activity has been reported in numerous disease conditions, including cancers, neurodegenerative diseases, inflammatory conditions, cardiovascular diseases, and viral infections. The proteolytic profile of a cell, tissue, or organ is governed by protease activation, activity, and substrate specificity. Thus, identifying protease substrates and proteolytic events under physiological conditions can provide crucial information about how the change in protease regulation can alter the cellular proteolytic landscape. In recent years, mass spectrometry-based techniques called N-terminomics have become instrumental in identifying protease substrates from complex biological mixtures. N-terminomics employs the labeling and enrichment of native and neo-N-termini peptides, generated upon proteolysis followed by mass spectrometry analysis allowing protease substrate profiling directly from biological samples. In this review, we provide a brief overview of N-terminomics techniques, focusing on their strengths, weaknesses, limitations, and providing specific examples where they were successfully employed to identify protease substrates in vivo and under physiological conditions. In addition, we explore the current trends in the protease field and the potential for future developments.
Collapse
|
9
|
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.
Collapse
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.)
| |
Collapse
|
10
|
Suski M, Wiśniewska A, Kuś K, Kiepura A, Stachowicz A, Stachyra K, Czepiel K, Madej J, Olszanecki R. Decrease of the pro-inflammatory M1-like response by inhibition of dipeptidyl peptidases 8/9 in THP-1 macrophages - quantitative proteomics of the proteome and secretome. Mol Immunol 2020; 127:193-202. [PMID: 32998073 DOI: 10.1016/j.molimm.2020.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/29/2020] [Accepted: 09/07/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Cellular peptidases are an emerging target of novel pharmacological strategies in inflammatory diseases and cancer. In this context, the dipeptidyl peptidases 8 and 9 (DPP8/9) have gained special attention due to their activities in the immune cells. However, in spite of more than hundred protein substrates identified to date by mass spectrometry-based analysis, the cellular DPP8/9 functions are still elusive. METHODS We applied the proteomic approach (iTRAQ-2DLC-MS/MS) to comprehensively analyze the role of DPP8/9 in the regulation of macrophage activation by in-depth protein quantitation of THP-1 proteome and secretome. RESULTS Cells pre-incubated with DPP8/9 inhibitor (1G244) prior activation (LPS or IL-4/IL-13) diminished the expression levels of M1-like response markers, but not M2-like phenotype features. This was accompanied by multiple intra- and extra-cellular protein abundance changes in THP-1 cells, related to cellular metabolism, mitochondria and endoplasmic reticulum function, as well as those engaged with inflammatory and apoptotic processes, including previously reported and novel DPP8/9 targets. CONCLUSIONS Inhibition of DPP 8/9 had a profound effect on the THP-1 macrophage proteome and secretome, evidencing the decrease of the pro-inflammatory M1-like response. Presented results are to our best knowledge the first which, among others, highlight the metabolic effects of DPP8/9 inhibition in macrophages.
Collapse
Affiliation(s)
- Maciej Suski
- Chair of Pharmacology Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegorzecka str., 31-531, Krakow, Poland.
| | - Anna Wiśniewska
- Chair of Pharmacology Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegorzecka str., 31-531, Krakow, Poland
| | - Katarzyna Kuś
- Chair of Pharmacology Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegorzecka str., 31-531, Krakow, Poland
| | - Anna Kiepura
- Chair of Pharmacology Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegorzecka str., 31-531, Krakow, Poland
| | - Aneta Stachowicz
- Chair of Pharmacology Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegorzecka str., 31-531, Krakow, Poland
| | - Kamila Stachyra
- Chair of Pharmacology Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegorzecka str., 31-531, Krakow, Poland
| | - Klaudia Czepiel
- Chair of Pharmacology Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegorzecka str., 31-531, Krakow, Poland
| | - Józef Madej
- Chair of Pharmacology Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegorzecka str., 31-531, Krakow, Poland
| | - Rafał Olszanecki
- Chair of Pharmacology Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegorzecka str., 31-531, Krakow, Poland
| |
Collapse
|
11
|
Finger Y, Habich M, Gerlich S, Urbanczyk S, van de Logt E, Koch J, Schu L, Lapacz KJ, Ali M, Petrungaro C, Salscheider SL, Pichlo C, Baumann U, Mielenz D, Dengjel J, Brachvogel B, Hofmann K, Riemer J. Proteasomal degradation induced by DPP9-mediated processing competes with mitochondrial protein import. EMBO J 2020; 39:e103889. [PMID: 32815200 PMCID: PMC7527813 DOI: 10.15252/embj.2019103889] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/14/2022] Open
Abstract
Plasticity of the proteome is critical to adapt to varying conditions. Control of mitochondrial protein import contributes to this plasticity. Here, we identified a pathway that regulates mitochondrial protein import by regulated N-terminal processing. We demonstrate that dipeptidyl peptidases 8/9 (DPP8/9) mediate the N-terminal processing of adenylate kinase 2 (AK2) en route to mitochondria. We show that AK2 is a substrate of the mitochondrial disulfide relay, thus lacking an N-terminal mitochondrial targeting sequence and undergoing comparatively slow import. DPP9-mediated processing of AK2 induces its rapid proteasomal degradation and prevents cytosolic accumulation of enzymatically active AK2. Besides AK2, we identify more than 100 mitochondrial proteins with putative DPP8/9 recognition sites and demonstrate that DPP8/9 influence the cellular levels of a number of these proteins. Collectively, we provide in this study a conceptual framework on how regulated cytosolic processing controls levels of mitochondrial proteins as well as their dual localization to mitochondria and other compartments.
Collapse
Affiliation(s)
- Yannik Finger
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Markus Habich
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Sarah Gerlich
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Sophia Urbanczyk
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Erik van de Logt
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Julian Koch
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Laura Schu
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Kim Jasmin Lapacz
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Muna Ali
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Carmelina Petrungaro
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | | | - Christian Pichlo
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Joern Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Bent Brachvogel
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Faculty of Medicine, University of Cologne, Cologne, Germany.,Center for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Kay Hofmann
- Institute of Genetics, University of Cologne, Cologne, Germany
| | - Jan Riemer
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| |
Collapse
|
12
|
Taabazuing CY, Griswold AR, Bachovchin DA. The NLRP1 and CARD8 inflammasomes. Immunol Rev 2020; 297:13-25. [PMID: 32558991 PMCID: PMC7483925 DOI: 10.1111/imr.12884] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/06/2020] [Accepted: 05/14/2020] [Indexed: 12/28/2022]
Abstract
Inflammasomes are multiprotein complexes that activate inflammatory cytokines and induce pyroptosis in response to intracellular danger-associated signals. NLRP1 and CARD8 are related germline-encoded pattern recognition receptors that form inflammasomes, but their activation mechanisms and biological purposes have not yet been fully established. Both NLRP1 and CARD8 undergo post-translational autoproteolysis to generate two non-covalently associated polypeptide chains. NLRP1 and CARD8 activators induce the proteasome-mediated destruction of the N-terminal fragment, liberating the C-terminal fragment to form an inflammasome. Here, we review the danger-associated stimuli that have been reported to activate NLRP1 and/or CARD8, including anthrax lethal toxin, Toxoplasma gondii, Shigella flexneri and the small molecule DPP8/9 inhibitor Val-boroPro, focusing on recent mechanistic insights and highlighting unresolved questions. In addition, we discuss the recently identified disease-associated mutations in NLRP1 and CARD8, the potential role that DPP9's protein structure plays in inflammasome regulation, and the emerging link between NLRP1 and metabolism. Finally, we summarize all of this latest research and consider the possible biological purposes of these enigmatic inflammasomes.
Collapse
Affiliation(s)
| | - Andrew R Griswold
- Weill Cornell, Rockefeller, Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA.,Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
13
|
Identification of unexplored substrates of the serine protease, thrombin, using N-terminomics strategy. Int J Biol Macromol 2019; 144:449-459. [PMID: 31862363 DOI: 10.1016/j.ijbiomac.2019.12.137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/15/2019] [Accepted: 12/15/2019] [Indexed: 12/13/2022]
Abstract
The function and regulation of thrombin is a complex as well as an intriguing aspect of evolution and has captured the interest of many investigators over the years. The reported substrates of thrombin are coagulation factors V, VIII, XI, XIII, protein C and fibrinogen. However, these may not be all the substrate of thrombin and therefore its functional role(s), may not have been completely comprehended. The purpose of our study was to identify hitherto unreported substrates of thrombin from human plasma using a N-terminomics protease substrate identification method. We identified 54 putative substrates of thrombin of which 12 are already known and 42 are being reported for the first time. Amongst the proteins identified, recombinant siglec-6 and purified serum alpha-1-acid glycoprotein were validated by cleavage with thrombin. We have discussed the probable relevance of siglec-6 cleavage by thrombin in human placenta mostly because an upregulation in the expression of siglec-6 and thrombin has been reported in the placenta of preeclampsia patients. We also speculate the role of alpha-1-acid glycoprotein cleavage by thrombin in the acute phase as alpha-1-acid glycoprotein is known to be an inhibitor of platelet aggregation whereas thrombin is known to trigger platelet aggregation.
Collapse
|
14
|
Lualdi M, Ronci M, Zilocchi M, Corno F, Turilli ES, Sponchiado M, Aceto A, Alberio T, Fasano M. Exploring the Mitochondrial Degradome by the TAILS Proteomics Approach in a Cellular Model of Parkinson's Disease. Front Aging Neurosci 2019; 11:195. [PMID: 31417398 PMCID: PMC6685049 DOI: 10.3389/fnagi.2019.00195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/15/2019] [Indexed: 12/11/2022] Open
Abstract
Parkinson’s disease (PD) is the second most frequent neurodegenerative disease worldwide and the availability of early biomarkers and novel biotargets represents an urgent medical need. The main pathogenetic hallmark of PD is the specific loss of nigral dopaminergic neurons, in which mitochondrial dysfunction plays a crucial role. Mitochondrial proteases are central to the maintenance of healthy mitochondria and they have recently emerged as drug targets. However, an exhaustive characterization of these enzymes and their targets is still lacking, due to difficulties in analyzing proteolytic fragments by bottom-up proteomics approaches. Here, we propose the “mitochondrial dimethylation-TAILS” strategy, which combines the isolation of mitochondria with the enrichment of N-terminal peptides to analyze the mitochondrial N-terminome. We applied this method in a cellular model of altered dopamine homeostasis in neuroblastoma SH-SY5Y cells, which recapitulates early steps of PD pathogenesis. The main aim was to identify candidate mitochondrial proteases aberrantly activated by dopamine dysregulation and their cleaved targets. The proposed degradomics workflow was able to improve the identification of mitochondrial proteins if compared to classical shotgun analysis. In detail, 40% coverage of the mitochondrial proteome was obtained, the sequences of the transit peptides of two mitochondrial proteins were unveiled, and a consensus cleavage sequence for proteases involved in the processing of mitochondrial proteins was depicted. Mass spectrometry proteomics data have been submitted to ProteomeXchange with the identifier PXD013900. Moreover, sixty-one N-terminal peptides whose levels were affected by dopamine treatment were identified. By an in-depth analysis of the proteolytic peptides included in this list, eleven mitochondrial proteins showed altered proteolytic processing. One of these proteins (i.e., the 39S ribosomal protein L49 – MRPL49) was cleaved by the neprilysin protease, already exploited in clinics as a biotarget. We eventually demonstrated a mitochondrial subcellular localization of neprilysin in human cells for the first time. Collectively, these results shed new light on mitochondrial dysfunction linked to dopamine imbalance in PD and opened up the possibility to explore the mitochondrial targets of neprilysin as candidate biomarkers.
Collapse
Affiliation(s)
- Marta Lualdi
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Maurizio Ronci
- Department of Pharmacy, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Mara Zilocchi
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Federica Corno
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Emily S Turilli
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Mauro Sponchiado
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Antonio Aceto
- Department of Medical, Oral and Biotechnological Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Tiziana Alberio
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Mauro Fasano
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| |
Collapse
|
15
|
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: 47] [Impact Index Per Article: 9.4] [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.
Collapse
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.
| |
Collapse
|
16
|
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: 83] [Impact Index Per Article: 16.6] [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.
Collapse
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.
| |
Collapse
|
17
|
Zhang HE, Hamson EJ, Koczorowska MM, Tholen S, Chowdhury S, Bailey CG, Lay AJ, Twigg SM, Lee Q, Roediger B, Biniossek ML, O'Rourke MB, McCaughan GW, Keane FM, Schilling O, Gorrell MD. Identification of Novel Natural Substrates of Fibroblast Activation Protein-alpha by Differential Degradomics and Proteomics. Mol Cell Proteomics 2019; 18:65-85. [PMID: 30257879 PMCID: PMC6317473 DOI: 10.1074/mcp.ra118.001046] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Indexed: 01/10/2023] Open
Abstract
Fibroblast activation protein-alpha (FAP) is a cell-surface transmembrane-anchored dimeric protease. This unique, constitutively active serine protease has both dipeptidyl aminopeptidase and endopeptidase activities and can hydrolyze the post-proline bond. FAP expression is very low in adult organs but is upregulated by activated fibroblasts in sites of tissue remodeling, including fibrosis, atherosclerosis, arthritis and tumors. To identify the endogenous substrates of FAP, we immortalized primary mouse embryonic fibroblasts (MEFs) from FAP gene knockout embryos and then stably transduced them to express either enzymatically active or inactive FAP. The MEF secretomes were then analyzed using degradomic and proteomic techniques. Terminal amine isotopic labeling of substrates (TAILS)-based degradomics identified cleavage sites in collagens, many other extracellular matrix (ECM) and associated proteins, and lysyl oxidase-like-1, CXCL-5, CSF-1, and C1qT6, that were confirmed in vitro In addition, differential metabolic labeling coupled with quantitative proteomic analysis also implicated FAP in ECM-cell interactions, as well as with coagulation, metabolism and wound healing associated proteins. Plasma from FAP-deficient mice exhibited slower than wild-type clotting times. This study provides a significant expansion of the substrate repertoire of FAP and provides insight into the physiological and potential pathological roles of this enigmatic protease.
Collapse
Affiliation(s)
- Hui Emma Zhang
- From the ‡Centenary Institute, the University of Sydney, Locked Bag No.6, Newtown, New South Wales, 2042, Australia;; §Sydney Medical School, the University of Sydney Faculty of Medicine and Health, New South Wales, 2006, Australia
| | - Elizabeth J Hamson
- From the ‡Centenary Institute, the University of Sydney, Locked Bag No.6, Newtown, New South Wales, 2042, Australia;; §Sydney Medical School, the University of Sydney Faculty of Medicine and Health, New South Wales, 2006, Australia
| | | | - Stefan Tholen
- ¶Institute for Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Sumaiya Chowdhury
- From the ‡Centenary Institute, the University of Sydney, Locked Bag No.6, Newtown, New South Wales, 2042, Australia;; §Sydney Medical School, the University of Sydney Faculty of Medicine and Health, New South Wales, 2006, Australia
| | - Charles G Bailey
- From the ‡Centenary Institute, the University of Sydney, Locked Bag No.6, Newtown, New South Wales, 2042, Australia;; §Sydney Medical School, the University of Sydney Faculty of Medicine and Health, New South Wales, 2006, Australia
| | - Angelina J Lay
- From the ‡Centenary Institute, the University of Sydney, Locked Bag No.6, Newtown, New South Wales, 2042, Australia;; §Sydney Medical School, the University of Sydney Faculty of Medicine and Health, New South Wales, 2006, Australia
| | - Stephen M Twigg
- §Sydney Medical School, the University of Sydney Faculty of Medicine and Health, New South Wales, 2006, Australia;; ‖Charles Perkins Centre, the University of Sydney, New South Wales, 2006, Australia
| | - Quintin Lee
- From the ‡Centenary Institute, the University of Sydney, Locked Bag No.6, Newtown, New South Wales, 2042, Australia;; §Sydney Medical School, the University of Sydney Faculty of Medicine and Health, New South Wales, 2006, Australia
| | - Ben Roediger
- From the ‡Centenary Institute, the University of Sydney, Locked Bag No.6, Newtown, New South Wales, 2042, Australia;; §Sydney Medical School, the University of Sydney Faculty of Medicine and Health, New South Wales, 2006, Australia
| | - Martin L Biniossek
- ¶Institute for Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Matthew B O'Rourke
- ‖Charles Perkins Centre, the University of Sydney, New South Wales, 2006, Australia;; **Proteomics Core Facility, University of Technology Sydney, New South Wales, 2007, Australia
| | - Geoffrey W McCaughan
- From the ‡Centenary Institute, the University of Sydney, Locked Bag No.6, Newtown, New South Wales, 2042, Australia;; §Sydney Medical School, the University of Sydney Faculty of Medicine and Health, New South Wales, 2006, Australia
| | - Fiona M Keane
- From the ‡Centenary Institute, the University of Sydney, Locked Bag No.6, Newtown, New South Wales, 2042, Australia;; §Sydney Medical School, the University of Sydney Faculty of Medicine and Health, New South Wales, 2006, Australia
| | - Oliver Schilling
- ‡‡Institute of Surgical Pathology, University Medical Center - University of Freiburg, Freiburg, Germany;; §§BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany;; ¶¶German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Mark D Gorrell
- From the ‡Centenary Institute, the University of Sydney, Locked Bag No.6, Newtown, New South Wales, 2042, Australia;; §Sydney Medical School, the University of Sydney Faculty of Medicine and Health, New South Wales, 2006, Australia;; ‖Charles Perkins Centre, the University of Sydney, New South Wales, 2006, Australia;.
| |
Collapse
|
18
|
Borghetti G, von Lewinski D, Eaton DM, Sourij H, Houser SR, Wallner M. Diabetic Cardiomyopathy: Current and Future Therapies. Beyond Glycemic Control. Front Physiol 2018; 9:1514. [PMID: 30425649 PMCID: PMC6218509 DOI: 10.3389/fphys.2018.01514] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/09/2018] [Indexed: 12/14/2022] Open
Abstract
Diabetes mellitus and the associated complications represent a global burden on human health and economics. Cardiovascular diseases are the leading cause of death in diabetic patients, who have a 2–5 times higher risk of developing heart failure than age-matched non-diabetic patients, independent of other comorbidities. Diabetic cardiomyopathy is defined as the presence of abnormal cardiac structure and performance in the absence of other cardiac risk factors, such coronary artery disease, hypertension, and significant valvular disease. Hyperglycemia, hyperinsulinemia, and insulin resistance mediate the pathological remodeling of the heart, characterized by left ventricle concentric hypertrophy and perivascular and interstitial fibrosis leading to diastolic dysfunction. A change in the metabolic status, impaired calcium homeostasis and energy production, increased inflammation and oxidative stress, as well as an accumulation of advanced glycation end products are among the mechanisms implicated in the pathogenesis of diabetic cardiomyopathy. Despite a growing interest in the pathophysiology of diabetic cardiomyopathy, there are no specific guidelines for diagnosing patients or structuring a treatment strategy in clinical practice. Anti-hyperglycemic drugs are crucial in the management of diabetes by effectively reducing microvascular complications, preventing renal failure, retinopathy, and nerve damage. Interestingly, several drugs currently in use can improve cardiac health beyond their ability to control glycemia. GLP-1 receptor agonists and sodium-glucose co-transporter 2 inhibitors have been shown to have a beneficial effect on the cardiovascular system through a direct effect on myocardium, beyond their ability to lower blood glucose levels. In recent years, great improvements have been made toward the possibility of modulating the expression of specific cardiac genes or non-coding RNAs in vivo for therapeutic purpose, opening up the possibility to regulate the expression of key players in the development/progression of diabetic cardiomyopathy. This review summarizes the pathogenesis of diabetic cardiomyopathy, with particular focus on structural and molecular abnormalities occurring during its progression, as well as both current and potential future therapies.
Collapse
Affiliation(s)
- Giulia Borghetti
- Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Dirk von Lewinski
- Division of Cardiology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Deborah M Eaton
- Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Harald Sourij
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Steven R Houser
- Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Markus Wallner
- Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States.,Division of Cardiology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| |
Collapse
|
19
|
Kim M, von Muenchow L, Le Meur T, Kueng B, Gapp B, Weber D, Dietrich W, Kovarik J, Rolink AG, Ksiazek I. DPP9 enzymatic activity in hematopoietic cells is dispensable for mouse hematopoiesis. Immunol Lett 2018; 198:60-65. [PMID: 29709545 DOI: 10.1016/j.imlet.2018.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/09/2018] [Accepted: 04/25/2018] [Indexed: 02/07/2023]
Abstract
Dipeptidyl peptidase 9 (DPP9) is a ubiquitously expressed intracellular prolyl peptidase implicated in immunoregulation. However, its physiological relevance in the immune system remains largely unknown. We investigated the role of DPP9 enzyme in immune system by characterizing DPP9 knock-in mice expressing a catalytically inactive S729A mutant of DPP9 enzyme (DPP9ki/ki mice). DPP9ki/ki mice show reduced number of lymphoid and myeloid cells in fetal liver and postnatal blood but their hematopoietic cells are fully functional and able to reconstitute lymphoid and myeloid lineages even in competitive mixed chimeras. These studies demonstrate that inactivation of DPP9 enzymatic activity does not lead to any perturbations in mouse hematopoiesis.
Collapse
Affiliation(s)
- Munkyung Kim
- Novartis Institute for Biomedical Research, CH-4056, Basel, Switzerland
| | - Lilly von Muenchow
- Developmental and Molecular Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Thomas Le Meur
- Novartis Institute for Biomedical Research, CH-4056, Basel, Switzerland
| | - Benjamin Kueng
- Novartis Institute for Biomedical Research, CH-4056, Basel, Switzerland
| | - Berangere Gapp
- Novartis Institute for Biomedical Research, CH-4056, Basel, Switzerland
| | - Delphine Weber
- Novartis Institute for Biomedical Research, CH-4056, Basel, Switzerland
| | | | - Jiri Kovarik
- Novartis Institute for Biomedical Research, CH-4056, Basel, Switzerland
| | - Antonius G Rolink
- Developmental and Molecular Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Iwona Ksiazek
- Novartis Institute for Biomedical Research, CH-4056, Basel, Switzerland.
| |
Collapse
|
20
|
Kim M, Minoux M, Piaia A, Kueng B, Gapp B, Weber D, Haller C, Barbieri S, Namoto K, Lorenz T, Wirsching J, Bassilana F, Dietrich W, Rijli FM, Ksiazek I. DPP9 enzyme activity controls survival of mouse migratory tongue muscle progenitors and its absence leads to neonatal lethality due to suckling defect. Dev Biol 2017; 431:297-308. [PMID: 28887018 DOI: 10.1016/j.ydbio.2017.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 08/16/2017] [Accepted: 09/03/2017] [Indexed: 01/23/2023]
Abstract
Dipeptidyl peptidase 9 (DPP9) is an intracellular N-terminal post-proline-cleaving enzyme whose physiological function remains largely unknown. We investigated the role of DPP9 enzyme in vivo by characterizing knock-in mice expressing a catalytically inactive mutant form of DPP9 (S729A; DPP9ki/ki mice). We show that DPP9ki/ki mice die within 12-18h after birth. The neonatal lethality can be rescued by manual feeding, indicating that a suckling defect is the primary cause of neonatal lethality. The suckling defect results from microglossia, and is characterized by abnormal formation of intrinsic muscles at the distal tongue. In DPP9ki/ki mice, the number of occipital somite-derived migratory muscle progenitors, forming distal tongue intrinsic muscles, is reduced due to increased apoptosis. In contrast, intrinsic muscles of the proximal tongue and extrinsic tongue muscles, which derive from head mesoderm, develop normally in DPP9ki/ki mice. Thus, lack of DPP9 activity in mice leads to impaired tongue development, suckling defect and subsequent neonatal lethality due to impaired survival of a specific subset of migratory tongue muscle progenitors.
Collapse
Affiliation(s)
- Munkyung Kim
- Novartis Institute for Biomedical Research, CH-4056 Basel, Switzerland
| | - Maryline Minoux
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Alessandro Piaia
- Novartis Institute for Biomedical Research, CH-4056 Basel, Switzerland
| | - Benjamin Kueng
- Novartis Institute for Biomedical Research, CH-4056 Basel, Switzerland
| | - Berangere Gapp
- Novartis Institute for Biomedical Research, CH-4056 Basel, Switzerland
| | - Delphine Weber
- Novartis Institute for Biomedical Research, CH-4056 Basel, Switzerland
| | - Corinne Haller
- Novartis Institute for Biomedical Research, CH-4056 Basel, Switzerland
| | - Samuel Barbieri
- Novartis Institute for Biomedical Research, CH-4056 Basel, Switzerland
| | - Kenji Namoto
- Novartis Institute for Biomedical Research, CH-4056 Basel, Switzerland
| | - Thorsten Lorenz
- Novartis Institute for Biomedical Research, CH-4056 Basel, Switzerland
| | - Johann Wirsching
- Novartis Institute for Biomedical Research, CH-4056 Basel, Switzerland
| | | | | | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Iwona Ksiazek
- Novartis Institute for Biomedical Research, CH-4056 Basel, Switzerland.
| |
Collapse
|
21
|
Coradin M, Karch KR, Garcia BA. Monitoring proteolytic processing events by quantitative mass spectrometry. Expert Rev Proteomics 2017; 14:409-418. [PMID: 28395554 DOI: 10.1080/14789450.2017.1316977] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Protease activity plays a key role in a wide variety of biological processes including gene expression, protein turnover and development. misregulation of these proteins has been associated with many cancer types such as prostate, breast, and skin cancer. thus, the identification of protease substrates will provide key information to understand proteolysis-related pathologies. Areas covered: Proteomics-based methods to investigate proteolysis activity, focusing on substrate identification, protease specificity and their applications in systems biology are reviewed. Their quantification strategies, challenges and pitfalls are underlined and the biological implications of protease malfunction are highlighted. Expert commentary: Dysregulated protease activity is a hallmark for some disease pathologies such as cancer. Current biochemical approaches are low throughput and some are limited by the amount of sample required to obtain reliable results. Mass spectrometry based proteomics provides a suitable platform to investigate protease activity, providing information about substrate specificity and mapping cleavage sites.
Collapse
Affiliation(s)
- Mariel Coradin
- a Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Kelly R Karch
- a Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Benjamin A Garcia
- a Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| |
Collapse
|
22
|
Tani S, Yuki S, Kunitake E, Sumitani JI, Kawaguchi T. Dipeptidyl peptidase IV is involved in the cellulose-responsive induction of cellulose biomass-degrading enzyme genes in Aspergillus aculeatus. Biosci Biotechnol Biochem 2017; 81:1227-1234. [PMID: 28290772 DOI: 10.1080/09168451.2017.1295800] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We screened for factors involved in the cellulose-responsive induction of cellulose biomass-degrading enzyme genes from approximately 12,000 Aspergillus aculeatus T-DNA insertion mutants harboring a transcriptional fusion between the FIII-avicelase gene (cbhI) promoter and the orotidine 5'-monophosphate decarboxylase gene. Analysis of 5-fluoroorodic acid (5-FOA) sensitivity, cellulose utilization, and cbhI expression of the mutants revealed that a mutant harboring T-DNA at the dipeptidyl peptidase IV (dppIV) locus had acquired 5-FOA resistance and was deficient in cellulose utilization and cbhI expression. The deletion of dppIV resulted in a significant reduction in the cellulose-responsive expression of both cbhI as well as genes controlled by XlnR-independent and XlnR-dependent signaling pathways at an early phase in A. aculeatus. In contrast, the dppIV deletion did not affect the xylose-responsive expression of genes under the control of XlnR. These results demonstrate that DppIV participates in cellulose-responsive induction in A. aculeatus.
Collapse
Affiliation(s)
- Shuji Tani
- a Graduate School of Life and Environmental Sciences , Osaka Prefecture University , Sakai , Japan
| | - Shota Yuki
- a Graduate School of Life and Environmental Sciences , Osaka Prefecture University , Sakai , Japan
| | - Emi Kunitake
- a Graduate School of Life and Environmental Sciences , Osaka Prefecture University , Sakai , Japan
| | - Jun-Ichi Sumitani
- a Graduate School of Life and Environmental Sciences , Osaka Prefecture University , Sakai , Japan
| | - Takashi Kawaguchi
- a Graduate School of Life and Environmental Sciences , Osaka Prefecture University , Sakai , Japan
| |
Collapse
|
23
|
Zapletal E, Cupic B, Gabrilovac J. Expression, subcellular localisation, and possible roles of dipeptidyl peptidase 9 (DPP9) in murine macrophages. Cell Biochem Funct 2017; 35:124-137. [DOI: 10.1002/cbf.3256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 01/23/2017] [Accepted: 01/26/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Emilija Zapletal
- Laboratory for Experimental Haematology, Immunology and Oncology, Division of Molecular Medicine; Rudjer Boskovic Institute; Zagreb Croatia
| | - Barbara Cupic
- Laboratory for Experimental Haematology, Immunology and Oncology, Division of Molecular Medicine; Rudjer Boskovic Institute; Zagreb Croatia
| | - Jelka Gabrilovac
- Laboratory for Experimental Haematology, Immunology and Oncology, Division of Molecular Medicine; Rudjer Boskovic Institute; Zagreb Croatia
| |
Collapse
|
24
|
Marshall NC, Finlay BB, Overall CM. Sharpening Host Defenses during Infection: Proteases Cut to the Chase. Mol Cell Proteomics 2017; 16:S161-S171. [PMID: 28179412 PMCID: PMC5393396 DOI: 10.1074/mcp.o116.066456] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/03/2017] [Indexed: 01/14/2023] Open
Abstract
The human immune system consists of an intricate network of tightly controlled pathways, where proteases are essential instigators and executioners at multiple levels. Invading microbial pathogens also encode proteases that have evolved to manipulate and dysregulate host proteins, including host proteases during the course of disease. The identification of pathogen proteases as well as their substrates and mechanisms of action have empowered significant developments in therapeutics for infectious diseases. Yet for many pathogens, there remains a great deal to be discovered. Recently, proteomic techniques have been developed that can identify proteolytically processed proteins across the proteome. These “degradomics” approaches can identify human substrates of microbial proteases during infection in vivo and expose the molecular-level changes that occur in the human proteome during infection as an operational network to develop hypotheses for further research as well as new therapeutics. This Perspective Article reviews how proteases are utilized during infection by both the human host and invading bacterial pathogens, including archetypal virulence-associated microbial proteases, such as the Clostridia spp. botulinum and tetanus neurotoxins. We highlight the potential knowledge that degradomics studies of host–pathogen interactions would uncover, as well as how degradomics has been successfully applied in similar contexts, including use with a viral protease. We review how microbial proteases have been targeted in current therapeutic approaches and how microbial proteases have shaped and even contributed to human therapeutics beyond infectious disease. Finally, we discuss how, moving forward, degradomics research can greatly contribute to our understanding of how microbial pathogens cause disease in vivo and lead to the identification of novel substrates in vivo, and the development of improved therapeutics to counter these pathogens.
Collapse
Affiliation(s)
- Natalie C Marshall
- From the ‡Department of Microbiology & Immunology.,§Michael Smith Laboratories
| | - B Brett Finlay
- From the ‡Department of Microbiology & Immunology.,§Michael Smith Laboratories.,¶Department of Biochemistry & Molecular Biology
| | - Christopher M Overall
- ¶Department of Biochemistry & Molecular Biology, .,**Department of Oral Biological & Medical Sciences, Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
25
|
Gabrilovac J, Čupić B, Zapletal E, Kraus O, Jakić-Razumović J. Dipeptidyl peptidase 9 (DPP9) in human skin cells. Immunobiology 2017; 222:327-342. [DOI: 10.1016/j.imbio.2016.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 09/11/2016] [Accepted: 09/17/2016] [Indexed: 12/20/2022]
|
26
|
Okondo MC, Johnson DC, Sridharan R, Go EB, Chui AJ, Wang MS, Poplawski SE, Wu W, Liu Y, Lai JH, Sanford DG, Arciprete MO, Golub TR, Bachovchin WW, Bachovchin DA. DPP8 and DPP9 inhibition induces pro-caspase-1-dependent monocyte and macrophage pyroptosis. Nat Chem Biol 2016; 13:46-53. [PMID: 27820798 DOI: 10.1038/nchembio.2229] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022]
Abstract
Val-boroPro (Talabostat, PT-100), a nonselective inhibitor of post-proline cleaving serine proteases, stimulates mammalian immune systems through an unknown mechanism of action. Despite this lack of mechanistic understanding, Val-boroPro has attracted substantial interest as a potential anticancer agent, reaching phase 3 trials in humans. Here we show that Val-boroPro stimulates the immune system by triggering a proinflammatory form of cell death in monocytes and macrophages known as pyroptosis. We demonstrate that the inhibition of two serine proteases, DPP8 and DPP9, activates the pro-protein form of caspase-1 independent of the inflammasome adaptor ASC. Activated pro-caspase-1 does not efficiently process itself or IL-1β but does cleave and activate gasdermin D to induce pyroptosis. Mice lacking caspase-1 do not show immune stimulation after treatment with Val-boroPro. Our data identify what is to our knowledge the first small molecule that induces pyroptosis and reveals a new checkpoint that controls the activation of the innate immune system.
Collapse
Affiliation(s)
- Marian C Okondo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Darren C Johnson
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ramya Sridharan
- Graduate Program in Pharmacology, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Eun Bin Go
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ashley J Chui
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mitchell S Wang
- Graduate Program in Pharmacology, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Sarah E Poplawski
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Wengen Wu
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Yuxin Liu
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Jack H Lai
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - David G Sanford
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Michael O Arciprete
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Todd R Golub
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - William W Bachovchin
- Department of Developmental, Chemical &Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA.,Arisaph Pharmaceuticals, Boston, Massachusetts, USA
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Graduate Program in Pharmacology, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| |
Collapse
|
27
|
Wilson CH, Zhang HE, Gorrell MD, Abbott CA. Dipeptidyl peptidase 9 substrates and their discovery: current progress and the application of mass spectrometry-based approaches. Biol Chem 2016; 397:837-56. [DOI: 10.1515/hsz-2016-0174] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/04/2016] [Indexed: 12/16/2022]
Abstract
Abstract
The enzyme members of the dipeptidyl peptidase 4 (DPP4) gene family have the very unusual capacity to cleave the post-proline bond to release dipeptides from the N-terminus of peptide/protein substrates. DPP4 and related enzymes are current and potential therapeutic targets in the treatment of type II diabetes, inflammatory conditions and cancer. Despite this, the precise biological function of individual dipeptidyl peptidases (DPPs), other than DPP4, and knowledge of their in vivo substrates remains largely unknown. For many years, identification of physiological DPP substrates has been difficult due to limitations in the available tools. Now, with advances in mass spectrometry based approaches, we can discover DPP substrates on a system wide-scale. Application of these approaches has helped reveal some of the in vivo natural substrates of DPP8 and DPP9 and their unique biological roles. In this review, we provide a general overview of some tools and approaches available for protease substrate discovery and their applicability to the DPPs with a specific focus on DPP9 substrates. This review provides comment upon potential approaches for future substrate elucidation.
Collapse
|
28
|
Affiliation(s)
- Ralph Kettritz
- Experimental and Clinical Research Center; A joint cooperation between the Charité and the Max-Delbrück Center for Molecular Medicine (MDC) and Department of Nephrology and Intensive Care Medicine; Charité University Health Services; Berlin Germany
| |
Collapse
|
29
|
Rueda EM, Johnson JE, Giddabasappa A, Swaroop A, Brooks MJ, Sigel I, Chaney SY, Fox DA. The cellular and compartmental profile of mouse retinal glycolysis, tricarboxylic acid cycle, oxidative phosphorylation, and ~P transferring kinases. Mol Vis 2016; 22:847-85. [PMID: 27499608 PMCID: PMC4961465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 07/21/2016] [Indexed: 10/26/2022] Open
Abstract
PURPOSE The homeostatic regulation of cellular ATP is achieved by the coordinated activity of ATP utilization, synthesis, and buffering. Glucose is the major substrate for ATP synthesis through glycolysis and oxidative phosphorylation (OXPHOS), whereas intermediary metabolism through the tricarboxylic acid (TCA) cycle utilizes non-glucose-derived monocarboxylates, amino acids, and alpha ketoacids to support mitochondrial ATP and GTP synthesis. Cellular ATP is buffered by specialized equilibrium-driven high-energy phosphate (~P) transferring kinases. Our goals were twofold: 1) to characterize the gene expression, protein expression, and activity of key synthesizing and regulating enzymes of energy metabolism in the whole mouse retina, retinal compartments, and/or cells and 2) to provide an integrative analysis of the results related to function. METHODS mRNA expression data of energy-related genes were extracted from our whole retinal Affymetrix microarray data. Fixed-frozen retinas from adult C57BL/6N mice were used for immunohistochemistry, laser scanning confocal microscopy, and enzymatic histochemistry. The immunoreactivity levels of well-characterized antibodies, for all major retinal cells and their compartments, were obtained using our established semiquantitative confocal and imaging techniques. Quantitative cytochrome oxidase (COX) and lactate dehydrogenase (LDH) activity was determined histochemically. RESULTS The Affymetrix data revealed varied gene expression patterns of the ATP synthesizing and regulating enzymes found in the muscle, liver, and brain. Confocal studies showed differential cellular and compartmental distribution of isozymes involved in glucose, glutamate, glutamine, lactate, and creatine metabolism. The pattern and intensity of the antibodies and of the COX and LDH activity showed the high capacity of photoreceptors for aerobic glycolysis and OXPHOS. Competition assays with pyruvate revealed that LDH-5 was localized in the photoreceptor inner segments. The combined results indicate that glycolysis is regulated by the compartmental expression of hexokinase 2, pyruvate kinase M1, and pyruvate kinase M2 in photoreceptors, whereas the inner retinal neurons exhibit a lower capacity for glycolysis and aerobic glycolysis. Expression of nucleoside diphosphate kinase, mitochondria-associated adenylate kinase, and several mitochondria-associated creatine kinase isozymes was highest in the outer retina, whereas expression of cytosolic adenylate kinase and brain creatine kinase was higher in the cones, horizontal cells, and amacrine cells indicating the diversity of ATP-buffering strategies among retinal neurons. Based on the antibody intensities and the COX and LDH activity, Müller glial cells (MGCs) had the lowest capacity for glycolysis, aerobic glycolysis, and OXPHOS. However, they showed high expression of glutamate dehydrogenase, alpha-ketoglutarate dehydrogenase, succinate thiokinase, GABA transaminase, and ~P transferring kinases. This suggests that MGCs utilize TCA cycle anaplerosis and cataplerosis to generate GTP and ~P transferring kinases to produce ATP that supports MGC energy requirements. CONCLUSIONS Our comprehensive and integrated results reveal that the adult mouse retina expresses numerous isoforms of ATP synthesizing, regulating, and buffering genes; expresses differential cellular and compartmental levels of glycolytic, OXPHOS, TCA cycle, and ~P transferring kinase proteins; and exhibits differential layer-by-layer LDH and COX activity. New insights into cell-specific and compartmental ATP and GTP production, as well as utilization and buffering strategies and their relationship with known retinal and cellular functions, are discussed. Developing therapeutic strategies for neuroprotection and treating retinal deficits and degeneration in a cell-specific manner will require such knowledge. This work provides a platform for future research directed at identifying the molecular targets and proteins that regulate these processes.
Collapse
Affiliation(s)
- Elda M. Rueda
- College of Optometry, University of Houston, Houston TX
| | - Jerry E. Johnson
- Department of Natural Sciences, University of Houston-Downtown, Houston TX
- Department of Biology and Biochemistry, University of Houston, Houston TX
| | - Anand Giddabasappa
- Department of Biology and Biochemistry, University of Houston, Houston TX
| | | | | | - Irena Sigel
- College of Optometry, University of Houston, Houston TX
| | - Shawnta Y. Chaney
- Department of Biology and Biochemistry, University of Houston, Houston TX
| | - Donald A. Fox
- College of Optometry, University of Houston, Houston TX
- Department of Biology and Biochemistry, University of Houston, Houston TX
- Department of Pharmacology and Pharmaceutical Sciences, University of Houston, Houston TX
| |
Collapse
|
30
|
Wagner L, Klemann C, Stephan M, von Hörsten S. Unravelling the immunological roles of dipeptidyl peptidase 4 (DPP4) activity and/or structure homologue (DASH) proteins. Clin Exp Immunol 2016; 184:265-83. [PMID: 26671446 DOI: 10.1111/cei.12757] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/01/2015] [Accepted: 12/14/2015] [Indexed: 12/31/2022] Open
Abstract
Dipeptidyl peptidase (DPP) 4 (CD26, DPP4) is a multi-functional protein involved in T cell activation by co-stimulation via its association with adenosine deaminase (ADA), caveolin-1, CARMA-1, CD45, mannose-6-phosphate/insulin growth factor-II receptor (M6P/IGFII-R) and C-X-C motif receptor 4 (CXC-R4). The proline-specific dipeptidyl peptidase also modulates the bioactivity of several chemokines. However, a number of enzymes displaying either DPP4-like activities or representing structural homologues have been discovered in the past two decades and are referred to as DPP4 activity and/or structure homologue (DASH) proteins. Apart from DPP4, DASH proteins include fibroblast activation protein alpha (FAP), DPP8, DPP9, DPP4-like protein 1 (DPL1, DPP6, DPPX L, DPPX S), DPP4-like protein 2 (DPL2, DPP10) from the DPP4-gene family S9b and structurally unrelated enzyme DPP2, displaying DPP4-like activity. In contrast, DPP6 and DPP10 lack enzymatic DPP4-like activity. These DASH proteins play important roles in the immune system involving quiescence (DPP2), proliferation (DPP8/DPP9), antigen-presenting (DPP9), co-stimulation (DPP4), T cell activation (DPP4), signal transduction (DPP4, DPP8 and DPP9), differentiation (DPP4, DPP8) and tissue remodelling (DPP4, FAP). Thus, they are involved in many pathophysiological processes and have therefore been proposed for potential biomarkers or even drug targets in various cancers (DPP4 and FAP) and inflammatory diseases (DPP4, DPP8/DPP9). However, they also pose the challenge of drug selectivity concerning other DASH members for better efficacy and/or avoidance of unwanted side effects. Therefore, this review unravels the complex roles of DASH proteins in immunology.
Collapse
Affiliation(s)
- L Wagner
- Deutschsprachige Selbsthilfegruppe für Alkaptonurie (DSAKU) e.V, Stuttgart.,Department for Experimental Therapy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - C Klemann
- Centre of Paediatric Surgery.,Centre for Paediatrics and Adolescent Medicine
| | - M Stephan
- Clinic for Psychosomatics and Psychotherapy, Hannover Medical School, Hannover
| | - S von Hörsten
- Department for Experimental Therapy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
31
|
Chen Y, Gall MG, Zhang H, Keane FM, McCaughan GW, Yu DMT, Gorrell MD. Dipeptidyl peptidase 9 enzymatic activity influences the expression of neonatal metabolic genes. Exp Cell Res 2016; 342:72-82. [PMID: 26930324 DOI: 10.1016/j.yexcr.2016.02.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 02/07/2023]
Abstract
The success of dipeptidyl peptidase 4 (DPP4) inhibition as a type 2 diabetes therapy has encouraged deeper examination of the post-proline DPP enzymes. DPP9 has been implicated in immunoregulation, disease pathogenesis and metabolism. The DPP9 enzyme-inactive (Dpp9 gene knock-in; Dpp9 gki) mouse displays neonatal lethality, suggesting that DPP9 enzyme activity is essential in neonatal development. Here we present gene expression patterns in these Dpp9 gki neonatal mice. Taqman PCR arrays and sequential qPCR assays on neonatal liver and gut revealed differential expression of genes involved in cell growth, innate immunity and metabolic pathways including long-chain-fatty-acid uptake and esterification, long-chain fatty acyl-CoA binding, trafficking and transport into mitochondria, lipoprotein metabolism, adipokine transport and gluconeogenesis in the Dpp9 gki mice compared to wild type. In a liver cell line, Dpp9 knockdown increased AMP-activated protein kinase phosphorylation, which suggests a potential mechanism. DPP9 protein levels in liver cells were altered by treatment with EGF, HGF, insulin or palmitate, suggesting potential natural DPP9 regulators. These gene expression analyses of a mouse strain deficient in DPP9 enzyme activity show, for the first time, that DPP9 enzyme activity regulates metabolic pathways in neonatal liver and gut.
Collapse
Affiliation(s)
- Yiqian Chen
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Margaret G Gall
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Hui Zhang
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Fiona M Keane
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Geoffrey W McCaughan
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Denise M T Yu
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Mark D Gorrell
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.
| |
Collapse
|
32
|
Eckhard U, Huesgen PF, Schilling O, Bellac CL, Butler GS, Cox JH, Dufour A, Goebeler V, Kappelhoff R, auf dem Keller U, Klein T, Lange PF, Marino G, Morrison CJ, Prudova A, Rodriguez D, Starr AE, Wang Y, Overall CM. Active site specificity profiling datasets of matrix metalloproteinases (MMPs) 1, 2, 3, 7, 8, 9, 12, 13 and 14. Data Brief 2016; 7:299-310. [PMID: 26981551 PMCID: PMC4777984 DOI: 10.1016/j.dib.2016.02.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 02/12/2016] [Accepted: 02/15/2016] [Indexed: 11/19/2022] Open
Abstract
The data described provide a comprehensive resource for the family-wide active site specificity portrayal of the human matrix metalloproteinase family. We used the high-throughput proteomic technique PICS (Proteomic Identification of protease Cleavage Sites) to comprehensively assay 9 different MMPs. We identified more than 4300 peptide cleavage sites, spanning both the prime and non-prime sides of the scissile peptide bond allowing detailed subsite cooperativity analysis. The proteomic cleavage data were expanded by kinetic analysis using a set of 6 quenched-fluorescent peptide substrates designed using these results. These datasets represent one of the largest specificity profiling efforts with subsequent structural follow up for any protease family and put the spotlight on the specificity similarities and differences of the MMP family. A detailed analysis of this data may be found in Eckhard et al. (2015) [1]. The raw mass spectrometry data and the corresponding metadata have been deposited in PRIDE/ProteomeXchange with the accession number PXD002265.
Collapse
Affiliation(s)
- Ulrich Eckhard
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Pitter F. Huesgen
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Oliver Schilling
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Caroline L. Bellac
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Georgina S. Butler
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jennifer H. Cox
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Antoine Dufour
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Verena Goebeler
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ulrich auf dem Keller
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Theo Klein
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Philipp F. Lange
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Giada Marino
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Charlotte J. Morrison
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Anna Prudova
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - David Rodriguez
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Amanda E. Starr
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Yili Wang
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Christopher M. Overall
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
- Corresponding author at: Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada.Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British ColumbiaVancouverBCCanada
| |
Collapse
|
33
|
Wagner L, Wolf R, Zeitschel U, Rossner S, Petersén Å, Leavitt BR, Kästner F, Rothermundt M, Gärtner UT, Gündel D, Schlenzig D, Frerker N, Schade J, Manhart S, Rahfeld JU, Demuth HU, von Hörsten S. Proteolytic degradation of neuropeptide Y (NPY) from head to toe: Identification of novel NPY-cleaving peptidases and potential drug interactions in CNS and Periphery. J Neurochem 2015; 135:1019-37. [PMID: 26442809 DOI: 10.1111/jnc.13378] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/09/2015] [Accepted: 09/14/2015] [Indexed: 01/24/2023]
Abstract
The bioactivity of neuropeptide Y (NPY) is either N-terminally modulated with respect to receptor selectivity by dipeptidyl peptidase 4 (DP4)-like enzymes or proteolytic degraded by neprilysin or meprins, thereby abrogating signal transduction. However, neither the subcellular nor the compartmental differentiation of these regulatory mechanisms is fully understood. Using mass spectrometry, selective inhibitors and histochemistry, studies across various cell types, body fluids, and tissues revealed that most frequently DP4-like enzymes, aminopeptidases P, secreted meprin-A (Mep-A), and cathepsin D (CTSD) rapidly hydrolyze NPY, depending on the cell type and tissue under study. Novel degradation of NPY by cathepsins B, D, L, G, S, and tissue kallikrein could also be identified. The expression of DP4, CTSD, and Mep-A at the median eminence indicates that the bioactivity of NPY is regulated by peptidases at the interphase between the periphery and the CNS. Detailed ex vivo studies on human sera and CSF samples recognized CTSD as the major NPY-cleaving enzyme in the CSF, whereas an additional C-terminal truncation by angiotensin-converting enzyme could be detected in serum. The latter finding hints to potential drug interaction between antidiabetic DP4 inhibitors and anti-hypertensive angiotensin-converting enzyme inhibitors, while it ablates suspected hypertensive side effects of only antidiabetic DP4-inhibitors application. The bioactivity of neuropeptide Y (NPY) is either N-terminally modulated with respect to receptor selectivity by dipeptidyl peptidase 4 (DP4)-like enzymes or proteolytic degraded by neprilysin or meprins, thereby abrogating signal transduction. However, neither the subcellular nor the compartmental differentiation of these regulatory mechanisms is fully understood. Using mass spectrometry, selective inhibitors and histochemistry, studies across various cell types, body fluids, and tissues revealed that most frequently DP4-like enzymes, aminopeptidases P, secreted meprin-A (Mep-A), and cathepsin D (CTSD) rapidly hydrolyze NPY, depending on the cell type and tissue under study. Novel degradation of NPY by cathepsins B, D, L, G, S, and tissue kallikrein could also be identified. The expression of DP4, CTSD, and Mep-A at the median eminence indicates that the bioactivity of NPY is regulated by peptidases at the interphase between the periphery and the CNS. Detailed ex vivo studies on human sera and CSF samples recognized CTSD as the major NPY-cleaving enzyme in the CSF, whereas an additional C-terminal truncation by angiotensin-converting enzyme could be detected in serum. The latter finding hints to potential drug interaction between antidiabetic DP4 inhibitors and anti-hypertensive angiotensin-converting enzyme inhibitors, while it ablates suspected hypertensive side effects of only antidiabetic DP4-inhibitors application.
Collapse
Affiliation(s)
- Leona Wagner
- Deutschsprachige Selbsthilfegruppe für Alkaptonurie (DSAKU) e.V., Stuttgart, Germany.,Probiodrug AG, Halle, Germany.,Department of Experimental Therapy, Preclinical Experimental Center, Universitätsklinikum Erlangen, Erlangen, Germany
| | | | - Ulrike Zeitschel
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Steffen Rossner
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Åsa Petersén
- Translational Neuroendocrine Research Unit, Lund University, Lund, Sweden
| | - Blair R Leavitt
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia and Children's and Women's Hospital, Vancouver, BC, Canada
| | - Florian Kästner
- Department of Psychiatry, University of Muenster, Muenster, Germany
| | - Matthias Rothermundt
- Department of Psychiatry, University of Muenster, Muenster, Germany.,St. Rochus-Hospital Telgte, Telgte, Germany
| | | | - Daniel Gündel
- Julius Bernstein Institute for Physiology, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Dagmar Schlenzig
- Fraunhofer-Institute for Cell Therapy and Immunology, Department of Drug Design and Target Validation, Halle, Germany
| | - Nadine Frerker
- Department of Experimental Therapy, Preclinical Experimental Center, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Jutta Schade
- Department of Experimental Therapy, Preclinical Experimental Center, Universitätsklinikum Erlangen, Erlangen, Germany
| | | | - Jens-Ulrich Rahfeld
- Fraunhofer-Institute for Cell Therapy and Immunology, Department of Drug Design and Target Validation, Halle, Germany
| | - Hans-Ulrich Demuth
- Fraunhofer-Institute for Cell Therapy and Immunology, Department of Drug Design and Target Validation, Halle, Germany
| | - Stephan von Hörsten
- Department of Experimental Therapy, Preclinical Experimental Center, Universitätsklinikum Erlangen, Erlangen, Germany
| |
Collapse
|
34
|
Waumans Y, Baerts L, Kehoe K, Lambeir AM, De Meester I. The Dipeptidyl Peptidase Family, Prolyl Oligopeptidase, and Prolyl Carboxypeptidase in the Immune System and Inflammatory Disease, Including Atherosclerosis. Front Immunol 2015; 6:387. [PMID: 26300881 PMCID: PMC4528296 DOI: 10.3389/fimmu.2015.00387] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 07/13/2015] [Indexed: 12/19/2022] Open
Abstract
Research from over the past 20 years has implicated dipeptidyl peptidase (DPP) IV and its family members in many processes and different pathologies of the immune system. Most research has been focused on either DPPIV or just a few of its family members. It is, however, essential to consider the entire DPP family when discussing any one of its members. There is a substantial overlap between family members in their substrate specificity, inhibitors, and functions. In this review, we provide a comprehensive discussion on the role of prolyl-specific peptidases DPPIV, FAP, DPP8, DPP9, dipeptidyl peptidase II, prolyl carboxypeptidase, and prolyl oligopeptidase in the immune system and its diseases. We highlight possible therapeutic targets for the prevention and treatment of atherosclerosis, a condition that lies at the frontier between inflammation and cardiovascular disease.
Collapse
Affiliation(s)
- Yannick Waumans
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp , Antwerp , Belgium
| | - Lesley Baerts
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp , Antwerp , Belgium
| | - Kaat Kehoe
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp , Antwerp , Belgium
| | - Anne-Marie Lambeir
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp , Antwerp , Belgium
| | - Ingrid De Meester
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp , Antwerp , Belgium
| |
Collapse
|
35
|
Han R, Wang X, Bachovchin W, Zukowska Z, Osborn JW. Inhibition of dipeptidyl peptidase 8/9 impairs preadipocyte differentiation. Sci Rep 2015; 5:12348. [PMID: 26242871 PMCID: PMC4525143 DOI: 10.1038/srep12348] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/26/2015] [Indexed: 12/23/2022] Open
Abstract
Adipocytes are the primary cells in adipose tissue, and adipocyte dysfunction causes lipodystrophy, obesity and diabetes. The dipeptidyl peptidase (DPP) 4 family includes four enzymes, DPP4, DPP8, DPP9 and fibroblast activation protein (FAP). DPP4 family inhibitors have been used for the treatment of type 2 diabetes patients, but their role in adipocyte formation are poorly understood. Here we demonstrate that the DPP8/9 selective inhibitor 1G244 blocks adipogenesis in preadipocyte 3T3-L1 and 3T3-F422A, while DPP4 and FAP inhibitors have no effect. In addition, knockdown of DPP8 or DPP9 significantly impairs adipocyte differentiation in preadipocytes. We further uncovered that blocking the expression or activities of DPP8 and DPP9 attenuates PPARγ2 induction during preadipocyte differentiation. Addition of PPARγ agonist thiazolidinediones (TZDs), or ectopic expression of PPARγ2, is able to rescue the adipogenic defect caused by DPP8/9 inhibition in preadipocytes. These results indicate the importance of DPP8 and DPP9 on adipogenesis.
Collapse
Affiliation(s)
- Ruijun Han
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Xinying Wang
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - William Bachovchin
- Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Zofia Zukowska
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - John W Osborn
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
36
|
Zhang H, Maqsudi S, Rainczuk A, Duffield N, Lawrence J, Keane FM, Justa-Schuch D, Geiss-Friedlander R, Gorrell MD, Stephens AN. Identification of novel dipeptidyl peptidase 9 substrates by two-dimensional differential in-gel electrophoresis. FEBS J 2015; 282:3737-57. [PMID: 26175140 DOI: 10.1111/febs.13371] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/22/2015] [Accepted: 07/07/2015] [Indexed: 12/26/2022]
Abstract
Dipeptidyl peptidase 9 (DPP9) is a member of the S9B/DPPIV (DPP4) serine protease family, which cleaves N-terminal dipeptides at an Xaa-Pro consensus motif. Cytoplasmic DPP9 has roles in epidermal growth factor signalling and in antigen processing, whilst the role of the recently discovered nuclear form of DPP9 is unknown. Mice lacking DPP9 proteolytic activity die as neonates. We applied a modified 2D differential in-gel electrophoresis approach to identify novel DPP9 substrates, using mouse embryonic fibroblasts lacking endogenous DPP9 activity. A total of 111 potential new DPP9 substrates were identified, with nine proteins/peptides confirmed as DPP9 substrates by MALDI-TOF or immunoblotting. Moreover, we also identified the dipeptide Val-Ala as a consensus site for DPP9 cleavage that was not recognized by DPP8, suggesting different in vivo roles for these closely related enzymes. The relative kinetics for the cleavage of these nine candidate substrates by DPP9, DPP8 and DPP4 were determined. This is the first identification of DPP9 substrates from cells lacking endogenous DPP9 activity. These data greatly expand the potential roles of DPP9 and suggest different in vivo roles for DPP9 and DPP8.
Collapse
Affiliation(s)
- Hui Zhang
- Molecular Hepatology, Liver Injury and Cancer Group, Centenary Institute, Sydney Medical School, University of Sydney, Australia
| | - Sadiqa Maqsudi
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, Australia
| | - Adam Rainczuk
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, Australia
| | - Nadine Duffield
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, Australia
| | - Josie Lawrence
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, Australia
| | - Fiona M Keane
- Molecular Hepatology, Liver Injury and Cancer Group, Centenary Institute, Sydney Medical School, University of Sydney, Australia
| | - Daniela Justa-Schuch
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Goettingen, Germany
| | - Ruth Geiss-Friedlander
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Goettingen, Germany
| | - Mark D Gorrell
- Molecular Hepatology, Liver Injury and Cancer Group, Centenary Institute, Sydney Medical School, University of Sydney, Australia
| | - Andrew N Stephens
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, Australia.,Epworth Research Institute, Epworth HealthCare, Richmond, Victoria, Australia
| |
Collapse
|
37
|
Gong Q, Rajagopalan S, Zhong J. Dpp4 inhibition as a therapeutic strategy in cardiometabolic disease: Incretin-dependent and -independent function. Int J Cardiol 2015; 197:170-9. [PMID: 26142202 PMCID: PMC7114201 DOI: 10.1016/j.ijcard.2015.06.076] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 06/03/2015] [Accepted: 06/20/2015] [Indexed: 12/25/2022]
Abstract
Cardiometabolic disorders including obesity, diabetes and cardiovascular disease are among the most severe health problems worldwide. DPP4 enzymatic inhibitors were first developed as anti-diabetic reagents which preserve incretin hormones and promote post-prandial insulin secretion. It's been shown in animal studies that incretin-based therapy has a beneficial effect on cardiovascular disease. Recent studies demonstrated novel non-catalytic functions of DPP4 that may play a role in cardiometabolic disease. Although the role of DPP4 inhibition-mediated incretin effects has been well-reviewed, little information of its incretin-independent actions was introduced in cardiometabolic disease. In the current review, we will summarize the catalytic dependent and independent effects of DPP4 inhibition on cardiometabolic disease. Discuss the findings from recent large scale clinical trials (EXAMINE and SAVOR-TIMI 53) Summarize the catalytic dependent and independent effects of DPP4 inhibition on cardiometabolic disease Focus on recent evidence linking DPP4 inhibition therapy with cardiovascular disease Provide mechanistic insights into the cardiovascular effect of DPP4
Collapse
Affiliation(s)
- Quan Gong
- Department of Immunology, School of Medicine, Yangtze University, Jingzhou, Hubei 434023, PR China
| | - Sanjay Rajagopalan
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Jixin Zhong
- Department of Immunology, School of Medicine, Yangtze University, Jingzhou, Hubei 434023, PR China; Division of Cardiovascular Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| |
Collapse
|
38
|
Jerke U, Hernandez DP, Beaudette P, Korkmaz B, Dittmar G, Kettritz R. Neutrophil serine proteases exert proteolytic activity on endothelial cells. Kidney Int 2015; 88:764-75. [PMID: 26061547 DOI: 10.1038/ki.2015.159] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/17/2015] [Accepted: 04/09/2015] [Indexed: 12/12/2022]
Abstract
Neutrophil serine proteases (NSPs) are released from activated neutrophils during inflammation. Here we studied the transfer of the three major NSPs, namely proteinase 3, human neutrophil elastase, and cathepsin G, from neutrophils to endothelial cells and used an unbiased approach to identify novel endothelial NSP substrates. Enzymatically active NSPs were released from stimulated neutrophils and internalized by endothelial cells in a dose- and time-dependent manner as shown by immunoblotting, flow cytometry, and the Boc-Ala substrate assay. Using terminal-amine isotopic labeling of substrates in endothelial cells, we identified 121 peptides from 82 different proteins consisting of 36 substrates for proteinase 3, 30 for neutrophil elastase, and 28 for cathepsin G, respectively. We characterized the extended cleavage pattern and provide corresponding IceLogos. Gene ontology analysis showed significant cytoskeletal substrate enrichment and confirmed several cytoskeletal protein substrates by immunoblotting. Finally, ANCA-stimulated neutrophils released all three active NSPs into the supernatant. Supernatants increased endothelial albumin flux and disturbed the endothelial cell cytoskeletal architecture. Serine protease inhibition abrogated this effect. Longer exposure to NSPs reduced endothelial cell viability and increased apoptosis. Thus, we identified novel NSP substrates and suggest NSP inhibition as a therapeutic measure to inhibit neutrophil-mediated inflammatory vascular diseases.
Collapse
Affiliation(s)
- Uwe Jerke
- Experimental and Clinical Research Center, a joint cooperation between the Charité and the Max-Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | | | | | - Brice Korkmaz
- INSERM U-1100 Universite Francois Rabelais, Tours, France
| | | | - Ralph Kettritz
- Experimental and Clinical Research Center, a joint cooperation between the Charité and the Max-Delbrück Center for Molecular Medicine (MDC), Berlin, Germany.,Nephrology and Intensive Care Medicine, Charité Campus Virchow, Berlin, Germany
| |
Collapse
|
39
|
Pagel O, Loroch S, Sickmann A, Zahedi RP. Current strategies and findings in clinically relevant post-translational modification-specific proteomics. Expert Rev Proteomics 2015; 12:235-53. [PMID: 25955281 PMCID: PMC4487610 DOI: 10.1586/14789450.2015.1042867] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry-based proteomics has considerably extended our knowledge about the occurrence and dynamics of protein post-translational modifications (PTMs). So far, quantitative proteomics has been mainly used to study PTM regulation in cell culture models, providing new insights into the role of aberrant PTM patterns in human disease. However, continuous technological and methodical developments have paved the way for an increasing number of PTM-specific proteomic studies using clinical samples, often limited in sample amount. Thus, quantitative proteomics holds a great potential to discover, validate and accurately quantify biomarkers in body fluids and primary tissues. A major effort will be to improve the complete integration of robust but sensitive proteomics technology to clinical environments. Here, we discuss PTMs that are relevant for clinical research, with a focus on phosphorylation, glycosylation and proteolytic cleavage; furthermore, we give an overview on the current developments and novel findings in mass spectrometry-based PTM research.
Collapse
Affiliation(s)
- Oliver Pagel
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| | | | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| |
Collapse
|
40
|
Huan Y, Jiang Q, Liu JL, Shen ZF. Establishment of a dipeptidyl peptidases (DPP) 8/9 expressing cell model for evaluating the selectivity of DPP4 inhibitors. J Pharmacol Toxicol Methods 2015; 71:8-12. [DOI: 10.1016/j.vascn.2014.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 11/05/2014] [Accepted: 11/09/2014] [Indexed: 01/25/2023]
|
41
|
Zhang H, Chen Y, Wadham C, McCaughan GW, Keane FM, Gorrell MD. Dipeptidyl peptidase 9 subcellular localization and a role in cell adhesion involving focal adhesion kinase and paxillin. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:470-80. [PMID: 25486458 DOI: 10.1016/j.bbamcr.2014.11.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/24/2014] [Accepted: 11/26/2014] [Indexed: 12/12/2022]
Abstract
Dipeptidyl peptidase 9 (DPP9) is a ubiquitously expressed member of the DPP4 gene and protease family. Deciphering the biological functions of DPP9 and its roles in pathogenesis has implicated DPP9 in tumor biology, the immune response, apoptosis, intracellular epidermal growth factor-dependent signaling and cell adhesion and migration. We investigated the intracellular distribution of DPP9 chimeric fluorescent proteins and consequent functions of DPP9. We showed that while some DPP9 is associated with mitochondria, the strongest co-localization was with microtubules. Under steady state conditions, DPP9 was not seen at the plasma membrane, but upon stimulation with either phorbol 12-myristate 13-acetate or epidermal growth factor, some DPP9 re-distributed towards the ruffling membrane. DPP9 was seen at the leading edge of the migrating cell and co-localized with the focal adhesion proteins, integrin-β1 and talin. DPP9 gene silencing and treatment with a DPP8/DPP9 specific inhibitor both reduced cell adhesion and migration. Expression of integrin-β1 and talin was decreased in DPP9-deficient and DPP9-enzyme-inactive cells. There was a concomitant decrease in the phosphorylation of focal adhesion kinase and paxillin, indicating that DPP9 knockdown or enzyme inhibition suppressed the associated adhesion signaling pathway, causing impaired cell movement. These novel findings provide mechanistic insights into the regulatory role of DPP9 in cell movement, and may thus implicate DPP9 in tissue and tumor growth and metastasis.
Collapse
Affiliation(s)
- Hui Zhang
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Yiqian Chen
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Carol Wadham
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Geoffrey W McCaughan
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Fiona M Keane
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Mark D Gorrell
- Centenary Institute and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.
| |
Collapse
|
42
|
Hartmann EM, Armengaud J. N-terminomics and proteogenomics, getting off to a good start. Proteomics 2014; 14:2637-46. [PMID: 25116052 DOI: 10.1002/pmic.201400157] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 04/23/2014] [Accepted: 08/08/2014] [Indexed: 12/11/2022]
Abstract
Proteogenomics consists of the annotation or reannotation of protein-coding nucleic acid sequences based on the empirical observation of their gene products. While functional annotation of predicted genes is increasingly feasible given the multiplicity of genomes available for many branches of the tree of life, the accurate annotation of the translational start sites is still a point of contention. Extensive coverage of the proteome, including specifically the N-termini, is now possible, thanks to next-generation mass spectrometers able to record data from thousands of proteins at once. Efforts to increase the peptide coverage of protein sequences and to detect low abundance proteins are important to make proteomic and proteogenomic studies more comprehensive. In this review, we present the panoply of N-terminus-oriented strategies that have been developed over the last decade.
Collapse
Affiliation(s)
- Erica M Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | | |
Collapse
|
43
|
Justa-Schuch D, Möller U, Geiss-Friedlander R. The amino terminus extension in the long dipeptidyl peptidase 9 isoform contains a nuclear localization signal targeting the active peptidase to the nucleus. Cell Mol Life Sci 2014; 71:3611-26. [PMID: 24562348 PMCID: PMC11113674 DOI: 10.1007/s00018-014-1591-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 02/11/2014] [Accepted: 02/13/2014] [Indexed: 12/25/2022]
Abstract
The intracellular prolyl peptidase DPP9 is implied to be involved in various cellular pathways including amino acid recycling, antigen maturation, cellular homeostasis, and viability. Interestingly, the major RNA transcript of DPP9 contains two possible translation initiation sites, which could potentially generate a longer (892 aa) and a shorter version (863 aa) of DPP9. Although the endogenous expression of the shorter DPP9 form has been previously verified, it is unknown whether the longer version is expressed, and what is its biological significance. By developing specific antibodies against the amino-terminal extension of the putative DPP9-long form, we demonstrate for the first time the endogenous expression of this longer isoform within cells. Furthermore, we show that DPP9-long represents a significant fraction of total DPP9 in cells, under steady-state conditions. Using biochemical cell fractionation assays in combination with immunofluorescence studies, we find the two isoforms localize to separate subcellular compartments. Whereas DPP9-short is present in the cytosol, DPP9-long localizes preferentially to the nucleus. This differential localization is attributed to a classical monopartite nuclear localization signal (K(K/R)X(K/R)) in the N-terminal extension of DPP9-long. Furthermore, we detect prolyl peptidase activity in nuclear fractions, which can be inhibited by specific DPP8/9 inhibitors. In conclusion, a considerable fraction of DPP9, which was previously considered as a purely cytosolic peptidase, localizes to the nucleus and is active there, raising the intriguing possibility that the longer DPP9 isoform may regulate the activity or stability of nuclear proteins, such as transcription factors.
Collapse
Affiliation(s)
- Daniela Justa-Schuch
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Goettingen, Humboldtallee 23, 37073 Goettingen, Germany
| | - Ulrike Möller
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Goettingen, Humboldtallee 23, 37073 Goettingen, Germany
| | - Ruth Geiss-Friedlander
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Goettingen, Humboldtallee 23, 37073 Goettingen, Germany
| |
Collapse
|
44
|
Hamson EJ, Keane FM, Tholen S, Schilling O, Gorrell MD. Understanding fibroblast activation protein (FAP): Substrates, activities, expression and targeting for cancer therapy. Proteomics Clin Appl 2014; 8:454-63. [DOI: 10.1002/prca.201300095] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 10/16/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Elizabeth J. Hamson
- Molecular Hepatology; Centenary Institute and Sydney Medical School; University of Sydney; Sydney Australia
| | - Fiona M. Keane
- Molecular Hepatology; Centenary Institute and Sydney Medical School; University of Sydney; Sydney Australia
| | - Stefan Tholen
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
- Faculty of Biology; University of Freiburg; Freiburg Germany
| | - Oliver Schilling
- Faculty of Biology; University of Freiburg; Freiburg Germany
- BIOSS Centre for Biological Signaling Studies; University of Freiburg; Freiburg Germany
| | - Mark D. Gorrell
- Molecular Hepatology; Centenary Institute and Sydney Medical School; University of Sydney; Sydney Australia
| |
Collapse
|
45
|
Kwan JC, Liu Y, Ratnayake R, Hatano R, Kuribara A, Morimoto C, Ohnuma K, Paul VJ, Ye T, Luesch H. Grassypeptolides as natural inhibitors of dipeptidyl peptidase 8 and T-cell activation. Chembiochem 2014; 15:799-804. [PMID: 24591193 DOI: 10.1002/cbic.201300762] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Indexed: 01/29/2023]
Abstract
Natural products made by marine cyanobacteria are often highly modified peptides and depsipeptides that have the potential to act as inhibitors for proteases. In the interests of finding new protease inhibition activity and selectivity, grassypeptolide A (1) was screened against a panel of proteases and found to inhibit DPP8 selectively over DPP4. Grassypeptolides were also found to inhibit IL-2 production and proliferation in activated T-cells, consistent with a putative role of DPP8 in the immune system. These effects were also observed in Jurkat cells, and DPP activity in Jurkat cell cytosol was shown to be inhibited by grassypeptolides. In silico docking suggests two possible binding modes of grassypeptolides-at the active site of DPP8 and at one of the entrances to the internal cavity. Collectively these results suggest that grassypeptolides might be useful tool compounds in the study of DPP8 function.
Collapse
Affiliation(s)
- Jason C Kwan
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Drive, Gainesville FL 32610 (USA); Current address: Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison WI 53705 (USA)
| | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Shahinian H, Tholen S, Schilling O. Proteomic identification of protease cleavage sites: cell-biological and biomedical applications. Expert Rev Proteomics 2014; 10:421-33. [DOI: 10.1586/14789450.2013.841547] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
47
|
Gall MG, Chen Y, Vieira de Ribeiro AJ, Zhang H, Bailey CG, Spielman DS, Yu DMT, Gorrell MD. Targeted inactivation of dipeptidyl peptidase 9 enzymatic activity causes mouse neonate lethality. PLoS One 2013; 8:e78378. [PMID: 24223149 PMCID: PMC3819388 DOI: 10.1371/journal.pone.0078378] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/18/2013] [Indexed: 12/15/2022] Open
Abstract
Dipeptidyl Peptidase (DPP) 4 and related dipeptidyl peptidases are emerging as current and potential therapeutic targets. DPP9 is an intracellular protease that is regulated by redox status and by SUMO1. DPP9 can influence antigen processing, epidermal growth factor (EGF)-mediated signaling and tumor biology. We made the first gene knock-in (gki) mouse with a serine to alanine point mutation at the DPP9 active site (S729A). Weaned heterozygote DPP9 (wt/S729A) pups from 110 intercrosses were indistinguishable from wild-type littermates. No homozygote DPP9 (S729A/S729A) weaned mice were detected. DPP9 (S729A/S729A) homozygote embryos, which were morphologically indistinguishable from their wild-type littermate embryos at embryonic day (ED) 12.5 to ED 17.5, were born live but these neonates died within 8 to 24 hours of birth. All neonates suckled and contained milk spots and were of similar body weight. No gender differences were seen. No histological or DPP9 immunostaining pattern differences were seen between genotypes in embryos and neonates. Mouse embryonic fibroblasts (MEFs) from DPP9 (S729A/S729A) ED13.5 embryos and neonate DPP9 (S729A/S729A) mouse livers collected within 6 hours after birth had levels of DPP9 protein and DPP9-related proteases that were similar to wild-type but had less DPP9/DPP8-derived activity. These data confirmed the absence of DPP9 enzymatic activity due to the presence of the serine to alanine mutation and no compensation from related proteases. These novel findings suggest that DPP9 enzymatic activity is essential for early neonatal survival in mice.
Collapse
Affiliation(s)
- Margaret G. Gall
- Centenary Institute, Camperdown and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Yiqian Chen
- Centenary Institute, Camperdown and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Ana Julia Vieira de Ribeiro
- Centenary Institute, Camperdown and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Hui Zhang
- Centenary Institute, Camperdown and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Charles G. Bailey
- Centenary Institute, Camperdown and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Derek S. Spielman
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Denise M. T. Yu
- Centenary Institute, Camperdown and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Mark D. Gorrell
- Centenary Institute, Camperdown and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
48
|
Pilla E, Kilisch M, Lenz C, Urlaub H, Geiss-Friedlander R. The SUMO1-E67 interacting loop peptide is an allosteric inhibitor of the dipeptidyl peptidases 8 and 9. J Biol Chem 2013; 288:32787-32796. [PMID: 24072711 DOI: 10.1074/jbc.m113.489179] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The intracellular peptidases dipeptidyl peptidase (DPP) 8 and DPP9 are involved in multiple cellular pathways including antigen maturation, cellular homeostasis, energy metabolism, and cell viability. Previously we showed that the small ubiquitin-like protein modifier SUMO1 interacts with an armlike structure in DPP9, leading to allosteric activation of the peptidase. Here we demonstrate that the E67-interacting loop (EIL) peptide, which corresponds to the interaction surface of SUMO1 with DPP9, acts as a noncompetitive inhibitor of DPP9. Moreover, by analyzing the sensitivity of DPP9 arm mutants to the EIL peptide, we mapped specific residues in the arm that are important for inhibition by the EIL, suggesting that the peptide acts as an allosteric inhibitor of DPP9. By modifying the EIL peptide, we constructed peptide variants with more than a 1,000-fold selectivity toward DPP8 (147 nM) and DPP9 (170 nM) over DPPIV (200 μM). Furthermore, application of these peptides to cells leads to a clear inhibition of cellular prolyl peptidase activity. Importantly, in line with previous publications, inhibition of DPP9 with these novel allosteric peptide inhibitors leads to an increase in EGF-mediated phosphorylation of Akt. This work highlights the potential use of peptides that mimic interaction surfaces for modulating enzyme activity.
Collapse
Affiliation(s)
- Esther Pilla
- From the Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Goettingen, 37073 Goettingen, Germany
| | - Markus Kilisch
- From the Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Goettingen, 37073 Goettingen, Germany
| | - Christof Lenz
- the Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany; the Institute for Clinical Chemistry, Faculty of Medicine, Georg-August-University of Goettingen, 37075 Goettingen, Germany
| | - Henning Urlaub
- the Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany; the Institute for Clinical Chemistry, Faculty of Medicine, Georg-August-University of Goettingen, 37075 Goettingen, Germany
| | - Ruth Geiss-Friedlander
- From the Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Goettingen, 37073 Goettingen, Germany,.
| |
Collapse
|
49
|
Zhang H, Chen Y, Keane FM, Gorrell MD. Advances in understanding the expression and function of dipeptidyl peptidase 8 and 9. Mol Cancer Res 2013; 11:1487-96. [PMID: 24038034 DOI: 10.1158/1541-7786.mcr-13-0272] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DPP8 and DPP9 are recently identified members of the dipeptidyl peptidase IV (DPPIV) enzyme family, which is characterized by the rare ability to cleave a post-proline bond two residues from the N-terminus of a substrate. DPP8 and DPP9 have unique cellular localization patterns, are ubiquitously expressed in tissues and cell lines, and evidence suggests important contributions to various biological processes including: cell behavior, cancer biology, disease pathogenesis, and immune responses. Importantly, functional differences between these two proteins have emerged, such as DPP8 may be more associated with gut inflammation whereas DPP9 is involved in antigen presentation and intracellular signaling. Similarly, the DPP9 connections with H-Ras and SUMO1, and its role in AKT1 pathway downregulation provide essential insights into the molecular mechanisms of DPP9 action. The recent discovery of novel natural substrates of DPP8 and DPP9 highlights the potential role of these proteases in energy metabolism and homeostasis. This review focuses on the recent progress made with these post-proline dipeptidyl peptidases and underscores their emerging importance.
Collapse
Affiliation(s)
- Hui Zhang
- Molecular Hepatology, Centenary Institute, Locked Bag No. 6, Newtown, NSW 2042, Australia.
| | | | | | | |
Collapse
|
50
|
Butler GS, Overall CM. Matrix metalloproteinase processing of signaling molecules to regulate inflammation. Periodontol 2000 2013; 63:123-48. [DOI: 10.1111/prd.12035] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2013] [Indexed: 12/12/2022]
|