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Ivanov MV, Kopeykina AS, Gorshkov MV. Reanalysis of DIA Data Demonstrates the Capabilities of MS/MS-Free Proteomics to Reveal New Biological Insights in Disease-Related Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1775-1785. [PMID: 38938158 DOI: 10.1021/jasms.4c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Data-independent acquisition (DIA) at the shortened data acquisition time is becoming a method of choice for quantitative proteomic applications requiring high throughput analysis of large cohorts of samples. With the advent of the combination of high resolution mass spectrometry with an asymmetric track lossless analyzer, these DIA capabilities were further extended with the recent demonstration of quantitative analyses at the speed of up to hundreds of samples per day. In particular, the proteomic data for the brain samples related to multiple system atrophy disease were acquired using 7 and 28 min chromatography gradients (Guzman et al., Nat. Biotech. 2024). In this work, we applied the recently introduced DirectMS1 method to reanalysis of these data using only MS1 spectra. Both DirectMS1 and DIA results were matched against long gradient DDA analysis from the earlier study of the same sample cohort. While the quantitation efficiency of DirectMS1 was comparable with DIA on the same data sets, we found an additional five proteins of biological significance relevant to the analyzed tissue samples. Among the findings, DirectMS1 was able to detect decreased caspase activity for Vimentin protein in the multiple system atrophy samples missed by the MS/MS-based quantitation methods. Our study suggests that DirectMS1 can be an efficient MS1-only addition to the analysis of DIA data in high-throughput quantitative proteomic studies.
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Affiliation(s)
- Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna S Kopeykina
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
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2
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Sakthivel D, Brown-Suedel AN, Lopez KE, Salgar S, Coutinho LE, Keane F, Huang S, Sherry KM, Charendoff CI, Dunne KP, Robichaux DJ, Vargas-Hernández A, Le B, Shin CS, Carisey AF, Poreba M, Flanagan JM, Bouchier-Hayes L. Caspase-2 is essential for proliferation and self-renewal of nucleophosmin-mutated acute myeloid leukemia. SCIENCE ADVANCES 2024; 10:eadj3145. [PMID: 39093977 PMCID: PMC11296348 DOI: 10.1126/sciadv.adj3145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/28/2024] [Indexed: 08/04/2024]
Abstract
Mutation in nucleophosmin (NPM1) causes relocalization of this normally nucleolar protein to the cytoplasm (NPM1c+). Despite NPM1 mutation being the most common driver mutation in cytogenetically normal adult acute myeloid leukemia (AML), the mechanisms of NPM1c+-induced leukemogenesis remain unclear. Caspase-2 is a proapoptotic protein activated by NPM1 in the nucleolus. Here, we show that caspase-2 is also activated by NPM1c+ in the cytoplasm and DNA damage-induced apoptosis is caspase-2 dependent in NPM1c+ but not in NPM1wt AML cells. Strikingly, in NPM1c+ cells, caspase-2 loss results in profound cell cycle arrest, differentiation, and down-regulation of stem cell pathways that regulate pluripotency including impairment of the AKT/mTORC1 pathways, and inhibition of Rictor cleavage. In contrast, there were minimal differences in proliferation, differentiation, or the transcriptional profile of NPM1wt cells lacking caspase-2. Our results show that caspase-2 is essential for proliferation and self-renewal of AML cells expressing mutated NPM1. This study demonstrates that caspase-2 is a major effector of NPM1c+ function.
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Affiliation(s)
- Dharaniya Sakthivel
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexandra N. Brown-Suedel
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - Karla E. Lopez
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - Suruchi Salgar
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - Luiza E. Coutinho
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - Francesca Keane
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shixia Huang
- Advanced Technology Cores, Department of Molecular and Cellular Biology, Huffington Department of Education, Innovation & Technology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kenneth Mc Sherry
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chloé I. Charendoff
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin P. Dunne
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dexter J. Robichaux
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander Vargas-Hernández
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - BaoChau Le
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - Crystal S. Shin
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexandre F. Carisey
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Marcin Poreba
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw 50370, Poland
| | - Jonathan M. Flanagan
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - Lisa Bouchier-Hayes
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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3
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Rojo C, Gárate-Rascón M, Recalde M, Álava A, Elizalde M, Azkona M, Aldabe I, Guruceaga E, López-Pascual A, Latasa MU, Sangro B, Fernández-Barrena MG, Ávila MA, Arechederra M, Berasain C. Caspases compromise SLU7 and UPF1 stability and NMD activity during hepatocarcinogenesis. JHEP Rep 2024; 6:101118. [PMID: 39105183 PMCID: PMC11298840 DOI: 10.1016/j.jhepr.2024.101118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 08/07/2024] Open
Abstract
Background & Aims The homeostasis of the cellular transcriptome depends on transcription and splicing mechanisms. Moreover, the fidelity of gene expression, essential to preserve cellular identity and function is secured by different quality control mechanisms including nonsense-mediated RNA decay (NMD). In this context, alternative splicing is coupled to NMD, and several alterations in these mechanisms leading to the accumulation of aberrant gene isoforms are known to be involved in human disease including cancer. Methods RNA sequencing, western blotting, qPCR and co-immunoprecipitation were performed in multiple silenced culture cell lines (replicates n ≥4), primary hepatocytes and samples of animal models (Jo2, APAP, Mdr2 -/- mice, n ≥3). Results Here we show that in animal models of liver injury and in human HCC (TCGA, non-tumoral = 50 vs. HCC = 374), the process of NMD is inhibited. Moreover, we demonstrate that the splicing factor SLU7 interacts with and preserves the levels of the NMD effector UPF1, and that SLU7 is required for correct NMD. Our previous findings demonstrated that SLU7 expression is reduced in the diseased liver, contributing to hepatocellular dedifferentiation and genome instability during disease progression. Here we build on this by providing evidence that caspases activated during liver damage are responsible for the cleavage and degradation of SLU7. Conclusions Here we identify the downregulation of UPF1 and the inhibition of NMD as a new molecular pathway contributing to the malignant reshaping of the liver transcriptome. Moreover, and importantly, we uncover caspase activation as the mechanism responsible for the downregulation of SLU7 expression during liver disease progression, which is a new link between apoptosis and hepatocarcinogenesis. Impact and implications The mechanisms involved in reshaping the hepatocellular transcriptome and thereby driving the progressive loss of cell identity and function in liver disease are not completely understood. In this context, we provide evidence on the impairment of a key mRNA surveillance mechanism known as nonsense-mediated mRNA decay (NMD). Mechanistically, we uncover a novel role for the splicing factor SLU7 in the regulation of NMD, including its ability to interact and preserve the levels of the key NMD factor UPF1. Moreover, we demonstrate that the activation of caspases during liver damage mediates SLU7 and UPF1 protein degradation and NMD inhibition. Our findings identify potential new markers of liver disease progression, and SLU7 as a novel therapeutic target to prevent the functional decay of the chronically injured organ.
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Affiliation(s)
- Carla Rojo
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - María Gárate-Rascón
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Miriam Recalde
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Ane Álava
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - María Elizalde
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - María Azkona
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Iratxe Aldabe
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Elisabet Guruceaga
- Bioinformatics Platform, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, 31008, Spain
- ProteoRed-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Amaya López-Pascual
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - M Ujue Latasa
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Bruno Sangro
- IdiSNA, Navarra Institute for Health Research, Pamplona, 31008, Spain
- Hepatology Unit, Clínica Universidad de Navarra, CCUN, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, 28029, Spain
| | - Maite G. Fernández-Barrena
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, 31008, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, 28029, Spain
| | - Matías A. Ávila
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, 31008, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, 28029, Spain
| | - María Arechederra
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, 31008, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, 28029, Spain
| | - Carmen Berasain
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, 28029, Spain
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Li Z, Wang S, Han J, Shi C, Xi L, Cui Y, Zhang H. Expression of cytokine and Apoptosis-Associated genes in mice bone Marrow-Derived Macrophages stimulated with Brucella recombinant type IV secretion effectors. Cytokine 2024; 182:156711. [PMID: 39094437 DOI: 10.1016/j.cyto.2024.156711] [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: 05/04/2024] [Revised: 06/23/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND Brucellosis is an economically important infectious caused by most commonly by Brucella. Detection of infected animals at the early stage is important for controlling the disease. The diagnostic antigens, usually protein antigens, have attracted much interest. However, the accurate mechanism of immune response is still unknown. The secretory effectors (BPE005, BPE275, and BPE123) of the type IV secretion system (T4SS) were involved in the intracellular circulation process of Brucella and the immune responses of the host. METHODS Genes encoding three B. abortus effector proteins (BPE005, BPE275, and BPE123) of T4SS were cloned and the recombinant proteins were expressed and purified. The purified recombinant proteins were named rBPE005, rBPE275 and rBPE123. Then, the expressions of Th1- and Th2-related cytokine genes were analyzed in mice bone marrow-derived macrophages (BMDMs) after stimulation with rBPE005, rBPE275, and rBPE123. Furthermore, four apoptosis-associated genes (Caspase-3, Caspase-8, Bax, and Bcl-2) were also detected to explore the damage of the proteins to the cells. RESULTS Expressions of all Th1- and Th2-related cytokine genes were induced with three proteins, and different cytokine expression patterns induced by each protein depend on the stimulation time and dose of protein. However, expressions of apoptosis-related genes did not change. CONCLUSION These results showed that the secreted antigens of Brucella induced an immune reaction via the production of Th1- and Th2-type cytokines in BMDMs without exerting any damage on the cells.
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Affiliation(s)
- Zhiqiang Li
- College of Biology and Food, Shangqiu Normal University, Shangqiu 476000, Henan Provence, China; College of Smart Animal Husbandry, Shangqiu Normal University, Shangqiu 476000, Henan Provence, China
| | - Shuli Wang
- College of Biology and Food, Shangqiu Normal University, Shangqiu 476000, Henan Provence, China; College of Smart Animal Husbandry, Shangqiu Normal University, Shangqiu 476000, Henan Provence, China
| | - Jincheng Han
- College of Biology and Food, Shangqiu Normal University, Shangqiu 476000, Henan Provence, China; College of Smart Animal Husbandry, Shangqiu Normal University, Shangqiu 476000, Henan Provence, China
| | - Chuanxin Shi
- College of Biology and Food, Shangqiu Normal University, Shangqiu 476000, Henan Provence, China; College of Smart Animal Husbandry, Shangqiu Normal University, Shangqiu 476000, Henan Provence, China
| | - Li Xi
- College of Biology and Food, Shangqiu Normal University, Shangqiu 476000, Henan Provence, China; College of Smart Animal Husbandry, Shangqiu Normal University, Shangqiu 476000, Henan Provence, China
| | - Yanyan Cui
- College of Biology and Food, Shangqiu Normal University, Shangqiu 476000, Henan Provence, China; College of Smart Animal Husbandry, Shangqiu Normal University, Shangqiu 476000, Henan Provence, China
| | - Hui Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi 832003, Xinjiang Province, China.
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5
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Castellón JO, Ofori S, Burton NR, Julio AR, Turmon AC, Armenta E, Sandoval C, Boatner LM, Takayoshi EE, Faragalla M, Taylor C, Zhou AL, Tran K, Shek J, Yan T, Desai HS, Fregoso OI, Damoiseaux R, Backus KM. Chemoproteomics Identifies State-Dependent and Proteoform-Selective Caspase-2 Inhibitors. J Am Chem Soc 2024; 146:14972-14988. [PMID: 38787738 DOI: 10.1021/jacs.3c12240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Caspases are a highly conserved family of cysteine-aspartyl proteases known for their essential roles in regulating apoptosis, inflammation, cell differentiation, and proliferation. Complementary to genetic approaches, small-molecule probes have emerged as useful tools for modulating caspase activity. However, due to the high sequence and structure homology of all 12 human caspases, achieving selectivity remains a central challenge for caspase-directed small-molecule inhibitor development efforts. Here, using mass spectrometry-based chemoproteomics, we first identify a highly reactive noncatalytic cysteine that is unique to caspase-2. By combining both gel-based activity-based protein profiling (ABPP) and a tobacco etch virus (TEV) protease activation assay, we then identify covalent lead compounds that react preferentially with this cysteine and afford a complete blockade of caspase-2 activity. Inhibitory activity is restricted to the zymogen or precursor form of monomeric caspase-2. Focused analogue synthesis combined with chemoproteomic target engagement analysis in cellular lysates and in cells yielded both pan-caspase-reactive molecules and caspase-2 selective lead compounds together with a structurally matched inactive control. Application of this focused set of tool compounds to stratify the functions of the zymogen and partially processed (p32) forms of caspase-2 provide evidence to support that caspase-2-mediated response to DNA damage is largely driven by the partially processed p32 form of the enzyme. More broadly, our study highlights future opportunities for the development of proteoform-selective caspase inhibitors that target nonconserved and noncatalytic cysteine residues.
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Affiliation(s)
- José O Castellón
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
| | - Samuel Ofori
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
| | - Nikolas R Burton
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Ashley R Julio
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Alexandra C Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Ernest Armenta
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Carina Sandoval
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
| | - Lisa M Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Evan E Takayoshi
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Marina Faragalla
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Cameron Taylor
- California NanoSystems Institute (CNSI), UCLA, Los Angeles, California 90095, United States
| | - Ann L Zhou
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Ky Tran
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Jeremy Shek
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Heta S Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
| | - Oliver I Fregoso
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
| | - Robert Damoiseaux
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, California 90095, United States
- California NanoSystems Institute (CNSI), UCLA, Los Angeles, California 90095, United States
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California 90095, United States
- Department of Bioengineering, Samueli School of Engineering, UCLA, Los Angeles, California 90095, United States
| | - Keriann M Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, California 90095, United States
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6
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Zhra M, Qasem RJ, Aldossari F, Saleem R, Aljada A. A Comprehensive Exploration of Caspase Detection Methods: From Classical Approaches to Cutting-Edge Innovations. Int J Mol Sci 2024; 25:5460. [PMID: 38791499 PMCID: PMC11121653 DOI: 10.3390/ijms25105460] [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: 03/30/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The activation of caspases is a crucial event and an indicator of programmed cell death, also known as apoptosis. These enzymes play a central role in cancer biology and are considered one promising target for current and future advancements in therapeutic interventions. Traditional methods of measuring caspase activity such as antibody-based methods provide fundamental insights into their biological functions, and are considered essential tools in the fields of cell and cancer biology, pharmacology and toxicology, and drug discovery. However, traditional methods, though extensively used, are now recognized as having various shortcomings. In addition, these methods fall short of providing solutions to and matching the needs of the rapid and expansive progress achieved in studying caspases. For these reasons, there has been a continuous improvement in detection methods for caspases and the network of pathways involved in their activation and downstream signaling. Over the past decade, newer methods based on cutting-edge state-of-the-art technologies have been introduced to the biomedical community. These methods enable both the temporal and spatial monitoring of the activity of caspases and their downstream substrates, and with enhanced accuracy and precision. These include fluorescent-labeled inhibitors (FLIs) for live imaging, single-cell live imaging, fluorescence resonance energy transfer (FRET) sensors, and activatable multifunctional probes for in vivo imaging. Recently, the recruitment of mass spectrometry (MS) techniques in the investigation of these enzymes expanded the repertoire of tools available for the identification and quantification of caspase substrates, cleavage products, and post-translational modifications in addition to unveiling the complex regulatory networks implicated. Collectively, these methods are enabling researchers to unravel much of the complex cellular processes involved in apoptosis, and are helping generate a clearer and comprehensive understanding of caspase-mediated proteolysis during apoptosis. Herein, we provide a comprehensive review of various assays and detection methods as they have evolved over the years, so to encourage further exploration of these enzymes, which should have direct implications for the advancement of therapeutics for cancer and other diseases.
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Affiliation(s)
- Mahmoud Zhra
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Rani J. Qasem
- Department of Pharmacology and Pharmacy Practice, College of Pharmacy, Middle East University, Amman 11831, Jordan
| | - Fai Aldossari
- Zoology Department, College of Science, King Saud University, Riyadh 12372, Saudi Arabia
| | - Rimah Saleem
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Ahmad Aljada
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
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7
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Hartley B, Bassiouni W, Roczkowsky A, Fahlman R, Schulz R, Julien O. N-Terminomic Identification of Intracellular MMP-2 Substrates in Cardiac Tissue. J Proteome Res 2024. [PMID: 38647137 DOI: 10.1021/acs.jproteome.3c00755] [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: 04/25/2024]
Abstract
Proteases are enzymes that induce irreversible post-translational modifications by hydrolyzing amide bonds in proteins. One of these proteases is matrix metalloproteinase-2 (MMP-2), which has been shown to modulate extracellular matrix remodeling and intracellular proteolysis during myocardial injury. However, the substrates of MMP-2 in heart tissue are limited, and lesser known are the cleavage sites. Here, we used degradomics to investigate the substrates of intracellular MMP-2 in rat ventricular extracts. First, we designed a novel, constitutively active MMP-2 fusion protein (MMP-2-Fc) that we expressed and purified from mammalian cells. Using this protease, we proteolyzed ventricular extracts and used subtiligase-mediated N-terminomic labeling which identified 95 putative MMP-2-Fc proteolytic cleavage sites using mass spectrometry. The intracellular MMP-2 cleavage sites identified in heart tissue extracts were enriched for proteins primarily involved in metabolism, as well as the breakdown of fatty acids and amino acids. We further characterized the cleavage of three of these MMP-2-Fc substrates based on the gene ontology analysis. We first characterized the cleavage of sarco/endoplasmic reticulum calcium ATPase (SERCA2a), a known MMP-2 substrate in myocardial injury. We then characterized the cleavage of malate dehydrogenase (MDHM) and phosphoglycerate kinase 1 (PGK1), representing new cardiac tissue substrates. Our findings provide insights into the intracellular substrates of MMP-2 in cardiac cells, suggesting that MMP-2 activation plays a role in cardiac metabolism.
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Affiliation(s)
- Bridgette Hartley
- Department of Biochemistry, University of Alberta, Edmonton T6G 2H7, Canada
| | - Wesam Bassiouni
- Department of Pharmacology, University of Alberta, Edmonton T6G 2S2, Canada
| | - Andrej Roczkowsky
- Department of Pharmacology, University of Alberta, Edmonton T6G 2S2, Canada
| | - Richard Fahlman
- Department of Biochemistry, University of Alberta, Edmonton T6G 2H7, Canada
| | - Richard Schulz
- Department of Pharmacology, University of Alberta, Edmonton T6G 2S2, Canada
- Department of Pediatrics, University of Alberta, Edmonton T6G 2S2, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton T6G 2H7, Canada
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8
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Bhardwaj S, Bulluss M, D'Aubeterre A, Derakhshani A, Penner R, Mahajan M, Mahajan VB, Dufour A. Integrating the analysis of human biopsies using post-translational modifications proteomics. Protein Sci 2024; 33:e4979. [PMID: 38533548 DOI: 10.1002/pro.4979] [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: 01/05/2024] [Revised: 03/07/2024] [Accepted: 03/16/2024] [Indexed: 03/28/2024]
Abstract
Proteome diversities and their biological functions are significantly amplified by post-translational modifications (PTMs) of proteins. Shotgun proteomics, which does not typically survey PTMs, provides an incomplete picture of the complexity of human biopsies in health and disease. Recent advances in mass spectrometry-based proteomic techniques that enrich and study PTMs are helping to uncover molecular detail from the cellular level to system-wide functions, including how the microbiome impacts human diseases. Protein heterogeneity and disease complexity are challenging factors that make it difficult to characterize and treat disease. The search for clinical biomarkers to characterize disease mechanisms and complexity related to patient diagnoses and treatment has proven challenging. Knowledge of PTMs is fundamentally lacking. Characterization of complex human samples that clarify the role of PTMs and the microbiome in human diseases will result in new discoveries. This review highlights the key role of proteomic techniques used to characterize unknown biological functions of PTMs derived from complex human biopsies. Through the integration of diverse methods used to profile PTMs, this review explores the genetic regulation of proteoforms, cells of origin expressing specific proteins, and several bioactive PTMs and their subsequent analyses by liquid chromatography and tandem mass spectrometry.
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Affiliation(s)
- Sonali Bhardwaj
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mitchell Bulluss
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ana D'Aubeterre
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Afshin Derakhshani
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Regan Penner
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - MaryAnn Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, USA
| | - Antoine Dufour
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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9
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Nano M, Montell DJ. Apoptotic signaling: Beyond cell death. Semin Cell Dev Biol 2024; 156:22-34. [PMID: 37988794 DOI: 10.1016/j.semcdb.2023.11.002] [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: 06/26/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023]
Abstract
Apoptosis is the best described form of regulated cell death, and was, until relatively recently, considered irreversible once particular biochemical points-of-no-return were activated. In this manuscript, we examine the mechanisms cells use to escape from a self-amplifying death signaling module. We discuss the role of feedback, dynamics, propagation, and noise in apoptotic signaling. We conclude with a revised model for the role of apoptosis in animal development, homeostasis, and disease.
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Affiliation(s)
- Maddalena Nano
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA; Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA.
| | - Denise J Montell
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA; Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA.
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10
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Gomez-Cardona E, Eskandari-Sedighi G, Fahlman R, Westaway D, Julien O. Application of N-Terminal Labeling Methods Provide Novel Insights into Endoproteolysis of the Prion Protein in Vivo. ACS Chem Neurosci 2024; 15:134-146. [PMID: 38095594 PMCID: PMC10768724 DOI: 10.1021/acschemneuro.3c00533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/04/2024] Open
Abstract
Alternative α- and β-cleavage events in the cellular prion protein (PrPC) central region generate fragments with distinct biochemical features that affect prion disease pathogenesis, but the assignment of precise cleavage positions has proven challenging. Exploiting mouse transgenic models expressing wild-type (WT) PrPC and an octarepeat region mutant allele (S3) with increased β-fragmentation, cleavage sites were defined using LC-MS/MS in conjunction with N-terminal enzymatic labeling and chemical in-gel acetylation. Our studies profile the net proteolytic repertoire of the adult brain, as deduced from defining hundreds of proteolytic events in other proteins, and position individual cleavage events in PrPC α- and β-target areas imputed from earlier, lower resolution methods; these latter analyses established site heterogeneity, with six cleavage sites positioned in the β-cleavage region of WT PrPC and nine positions for S3 PrPC. Regarding α-cleavage, aside from reported N-termini at His110 and Val111, we identified a total of five shorter fragments in the brain of both mice lines. We infer that aminopeptidase activity in the brain could contribute to the ragged N-termini observed around PrPC's α- and β-cleavage sites, with this work providing a point of departure for further in vivo studies of brain proteases.
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Affiliation(s)
- Erik Gomez-Cardona
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Ghazaleh Eskandari-Sedighi
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Center
for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2M8, Canada
| | - Richard Fahlman
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - David Westaway
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Center
for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2M8, Canada
- Department
of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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11
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Castellón JO, Ofori S, Armenta E, Burton N, Boatner LM, Takayoshi EE, Faragalla M, Zhou A, Tran K, Shek J, Yan T, Desai HS, Backus KM. Chemoproteomics identifies proteoform-selective caspase-2 inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.563785. [PMID: 37961563 PMCID: PMC10634807 DOI: 10.1101/2023.10.25.563785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Caspases are a highly conserved family of cysteine-aspartyl proteases known for their essential roles in regulating apoptosis, inflammation, cell differentiation, and proliferation. Complementary to genetic approaches, small-molecule probes have emerged as useful tools for modulating caspase activity. However, due to the high sequence and structure homology of all twelve human caspases, achieving selectivity remains a central challenge for caspase-directed small-molecule inhibitor development efforts. Here, using mass spectrometry-based chemoproteomics, we first identify a highly reactive non-catalytic cysteine that is unique to caspase-2. By combining both gel-based activity-based protein profiling (ABPP) and a tobacco etch virus (TEV) protease activation assay, we then identify covalent lead compounds that react preferentially with this cysteine and afford a complete blockade of caspase-2 activity. Inhibitory activity is restricted to the zymogen or precursor form of monomeric caspase-2. Focused analogue synthesis combined with chemoproteomic target engagement analysis in cellular lysates and in cells yielded both pan-caspase reactive molecules and caspase-2 selective lead compounds together with a structurally matched inactive control. Application of this focused set of tool compounds to stratify caspase contributions to initiation of intrinsic apoptosis, supports compensatory caspase-9 activity in the context of caspase-2 inactivation. More broadly, our study highlights future opportunities for the development of proteoform-selective caspase inhibitors that target non-conserved and non-catalytic cysteine residues.
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12
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Sakthivel D, Brown-Suedel AN, Keane F, Huang S, Sherry KM, Charendoff CI, Dunne KP, Robichaux DJ, Le B, Shin CS, Carisey AF, Flanagan JM, Bouchier-Hayes L. Caspase-2 is essential for proliferation and self-renewal of nucleophosmin-mutated acute myeloid leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542723. [PMID: 37398413 PMCID: PMC10312440 DOI: 10.1101/2023.05.29.542723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Mutation in nucleophosmin (NPM1) causes relocalization of this normally nucleolar protein to the cytoplasm ( NPM1c+ ). Despite NPM1 mutation being the most common driver mutation in cytogenetically normal adult acute myeloid leukemia (AML), the mechanisms of NPM1c+-induced leukemogenesis remain unclear. Caspase-2 is a pro-apoptotic protein activated by NPM1 in the nucleolus. Here, we show that caspase-2 is also activated by NPM1c+ in the cytoplasm, and DNA damage-induced apoptosis is caspase-2-dependent in NPM1c+ AML but not in NPM1wt cells. Strikingly, in NPM1c+ cells, loss of caspase-2 results in profound cell cycle arrest, differentiation, and down-regulation of stem cell pathways that regulate pluripotency including impairment in the AKT/mTORC1 and Wnt signaling pathways. In contrast, there were minimal differences in proliferation, differentiation, or the transcriptional profile of NPM1wt cells with and without caspase-2. Together, these results show that caspase-2 is essential for proliferation and self-renewal of AML cells that have mutated NPM1. This study demonstrates that caspase-2 is a major effector of NPM1c+ function and may even be a druggable target to treat NPM1c+ AML and prevent relapse.
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13
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Hanna R, Rozenberg A, Saied L, Ben-Yosef D, Lavy T, Kleifeld O. In-Depth Characterization of Apoptosis N-terminome Reveals a Link Between Caspase-3 Cleavage and Post-Translational N-terminal Acetylation. Mol Cell Proteomics 2023:100584. [PMID: 37236440 PMCID: PMC10362333 DOI: 10.1016/j.mcpro.2023.100584] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 05/28/2023] Open
Abstract
The N-termini of proteins contain information about their biochemical properties and functions. These N-termini can be processed by proteases, and can undergo other co- or post-translational modifications. We have developed LATE (LysN Amino Terminal Enrichment), a method that uses selective chemical derivatization of α-amines to isolate the N-terminal peptides, in order to improve N-terminome identification in conjunction with other enrichment strategies. We applied LATE alongside another N-terminomic method to study caspase-3 mediated proteolysis both in vitro and during apoptosis in cells. This has enabled us to identify many unreported caspase-3 cleavages, some of which cannot be identified by other methods. Moreover, we have found direct evidence that neo-N-termini generated by caspase-3 cleavage can be further modified by Nt-acetylation. Some of these neo-Nt-acetylation events occur in the early phase of the apoptotic process and may have a role in translation inhibition. This has provided a comprehensive overview of the caspase-3 degradome and has uncovered previously unrecognized crosstalk between post-translational Nt-acetylation and caspase proteolytic pathways.
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Affiliation(s)
- Rawad Hanna
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Layla Saied
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Daniel Ben-Yosef
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Tali Lavy
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Oded Kleifeld
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel.
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14
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Pockes S, Walters MA, Ashe KH. Targeting caspase-2 interactions with tau in Alzheimer's disease and related dementias. Transl Res 2023; 254:34-40. [PMID: 36343883 PMCID: PMC9991976 DOI: 10.1016/j.trsl.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022]
Abstract
Targeting amyloid-β plaques and tau tangles has failed to provide effective treatments for Alzheimer's disease and related dementias (ADRD). A more fruitful pathway to ADRD therapeutics may be the development of therapies that target common signaling pathways that disrupt synaptic connections and impede communication between neurons. In this review, we present our characterization of a signaling pathway common to several neurological diseases featuring dementia including Alzheimer's disease, frontotemporal dementia, Lewy body dementia, and Huntington's disease. This signaling pathway features the cleavage of tau by caspase-2 (Casp2) yielding Δtau314 (Casp2/tau/Δtau314). Through a not yet fully delineated mechanism, Δtau314 catalyzes the mislocalization and accumulation of tau to dendritic spines leading to the internalization of AMPA receptors and the concomitant weakening of synaptic transmission. Here, we review the accumulated evidence supporting Casp2 as a druggable target and its importance in ADRD. Additionally, we provide a brief overview of our initial medicinal chemistry explorations aimed at the preparation of novel, brain penetrant Casp2 inhibitors. We anticipate that this review will spark broader interest in Casp2 as a target for restoring synaptic dysfunction in ADRD.
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Affiliation(s)
- Steffen Pockes
- Institute of Pharmacy, University of Regensburg, Regensburg, Germany; Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota; Department of Neurology, University of Minnesota, Minneapolis, Minnesota.
| | - Michael A Walters
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota.
| | - Karen H Ashe
- Department of Neurology, University of Minnesota, Minneapolis, Minnesota.
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15
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Carminati L, Carlessi E, Longhi E, Taraboletti G. Controlled extracellular proteolysis of thrombospondins. Matrix Biol 2023; 119:82-100. [PMID: 37003348 DOI: 10.1016/j.matbio.2023.03.011] [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: 12/22/2022] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023]
Abstract
Limited proteolysis of thrombospondins is a powerful mechanism to ensure dynamic tuning of their activities in the extracellular space. Thrombospondins are multifunctional matricellular proteins composed of multiple domains, each with a specific pattern of interactions with cell receptors, matrix components and soluble factors (growth factors, cytokines and proteases), thus with different effects on cell behavior and responses to changes in the microenvironment. Therefore, the proteolytic degradation of thrombospondins has multiple functional consequences, reflecting the local release of active fragments and isolated domains, exposure or disruption of active sequences, altered protein location, and changes in the composition and function of TSP-based pericellular interaction networks. In this review current data from the literature and databases is employed to provide an overview of cleavage of mammalian thrombospondins by different proteases. The roles of the fragments generated in specific pathological settings, with particular focus on cancer and the tumor microenvironment, are discussed.
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Affiliation(s)
- Laura Carminati
- Laboratory of Tumor Microenvironment, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Elena Carlessi
- Laboratory of Tumor Microenvironment, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Elisa Longhi
- Laboratory of Tumor Microenvironment, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Giulia Taraboletti
- Laboratory of Tumor Microenvironment, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy.
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16
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Wang H, Julien O. CaspSites: A Database and Web Application for Experimentally Observed Human Caspase Substrates Using N-Terminomics. J Proteome Res 2023; 22:454-461. [PMID: 36696595 DOI: 10.1021/acs.jproteome.2c00620] [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: 01/26/2023]
Abstract
CaspSites is a free-to-use database and web application for experimentally observed human caspase substrates using N-terminomics. It can be accessed and used by all users at the web URL www.caspsites.org. CaspSites stores cleavage site information identified for human caspases 1-9 in lysates and apoptotic cells, collected from their corresponding published studies. The database can be queried, viewed, and exported using the search page of the web application. The main parameters offered are protein substrate, cleavage site (P4-P4') residues, and individual caspase data sets, which can be connected using OR, AND, or NOT logical operators for custom user-built queries. CaspSites will be regularly updated with new experimental findings for understudied caspases, providing researchers insight into the distinctive roles human caspases play in cellular processes by identifying their target proteins in relation to each other.
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Affiliation(s)
- Henry Wang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G2H7, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G2H7, Canada
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17
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Panda C, Mahapatra RK. Bi-Directional Relationship Between Autophagy and Inflammasomes in Neurodegenerative Disorders. Cell Mol Neurobiol 2023; 43:115-137. [PMID: 35066716 DOI: 10.1007/s10571-021-01184-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/12/2021] [Indexed: 01/18/2023]
Abstract
The innate immune system, as the first line of cellular defense, triggers a protective response called inflammation when encountered with invading pathogens. Inflammasome is a multi-protein cytosolic signaling complex that induces inflammation and is critical for inflammation-induced pyroptotic cell death. Inflammasome activation has been found associated with neurodegenerative disorders (NDs), inflammatory diseases, and cancer. Autophagy is a crucial intracellular quality control and homeostasis process which removes the dysfunctional organelles, damaged proteins, and pathogens by sequestering the cytosolic components in a double-membrane vesicle, which eventually fuses with lysosome resulting in cargo degradation. Autophagy disruption has been observed in many NDs presented with persistent neuroinflammation and excessive inflammasome activation. An interplay between inflammation activation and the autophagy process has been realized over the last decade. In the case of NDs, autophagy regulates neuroinflammation load and cellular damage either by engulfing the misfolded protein deposits, dysfunctional mitochondria, or the inflammasome complex itself. A healthy two-way regulation between both cellular processes has been realized for cell survival and cell defense during inflammatory conditions. Therefore, clinical interest in the modulation of inflammasome activation by autophagy inducers is rapidly growing. In this review, we discuss the structural basis of inflammasome activation and the mechanistic ideas of the autophagy process in NDs. Along with comments on multiple ways of neuroinflammation regulation by microglial autophagy, we also present a perspective on pharmacological opportunities in this molecular interplay pertaining to NDs.
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Affiliation(s)
- Chinmaya Panda
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha, 751024, India
| | - Rajani Kanta Mahapatra
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha, 751024, India.
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18
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Neurovascular injury associated non-apoptotic endothelial caspase-9 and astroglial caspase-9 mediate inflammation and contrast sensitivity decline. Cell Death Dis 2022; 13:937. [PMID: 36347836 PMCID: PMC9643361 DOI: 10.1038/s41419-022-05387-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022]
Abstract
Retinal neurovascular injuries are a leading cause of vision loss in young adults presenting unmet therapeutic needs. Neurovascular injuries damage homeostatic communication between endothelial, pericyte, glial, and neuronal cells through signaling pathways that remain to be established. To understand the mechanisms that contribute to neuronal death, we use a mouse model of retinal vein occlusion (RVO). Using this model, we previously discovered that after vascular damage, there was non-apoptotic activation of endothelial caspase-9 (EC Casp9); knock-out of EC Casp9 led to a decrease in retinal edema, capillary ischemia, and neuronal death. In this study, we aimed to explore the role of EC Casp9 in vision loss and inflammation. We found that EC Casp9 is implicated in contrast sensitivity decline, induction of inflammatory cytokines, and glial reactivity. One of the noted glial changes was increased levels of astroglial cl-caspase-6, which we found to be activated cell intrinsically by astroglial caspase-9 (Astro Casp9). Lastly, we discovered that Astro Casp9 contributes to capillary ischemia and contrast sensitivity decline after RVO (P-RVO). These findings reveal specific endothelial and astroglial non-apoptotic caspase-9 roles in inflammation and neurovascular injury respectively; and concomitant relevancy to contrast sensitivity decline.
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19
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Effect of mesoporous silica nanoparticles loaded with α-tomatine on HepG2 cancer cells studied in vitro. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.104033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Schaefer K, Lui I, Byrnes JR, Kang E, Zhou J, Weeks AM, Wells JA. Direct Identification of Proteolytic Cleavages on Living Cells Using a Glycan-Tethered Peptide Ligase. ACS CENTRAL SCIENCE 2022; 8:1447-1456. [PMID: 36313159 PMCID: PMC9615116 DOI: 10.1021/acscentsci.2c00899] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 06/16/2023]
Abstract
Proteolytic cleavage of cell surface proteins triggers critical processes including cell-cell interactions, receptor activation, and shedding of signaling proteins. Consequently, dysregulated extracellular proteases contribute to malignant cell phenotypes including most cancers. To understand these effects, methods are needed that identify proteolyzed membrane proteins within diverse cellular contexts. Herein we report a proteomic approach, called cell surface N-terminomics, to broadly identify precise cleavage sites (neo-N-termini) on the surface of living cells. First, we functionalized the engineered peptide ligase, called stabiligase, with an N-terminal nucleophile that enables covalent attachment to naturally occurring glycans. Upon the addition of a biotinylated peptide ester, glycan-tethered stabiligase efficiently tags extracellular neo-N-termini for proteomic analysis. To demonstrate the versatility of this approach, we identified and characterized 1532 extracellular neo-N-termini across a panel of different cell types including primary immune cells. The vast majority of cleavages were not identified by previous proteomic studies. Lastly, we demonstrated that single oncogenes, KRAS(G12V) and HER2, induce extracellular proteolytic remodeling of proteins involved in cancerous cell growth, invasion, and migration. Cell surface N-terminomics is a generalizable platform that can reveal proteolyzed, neoepitopes to target using immunotherapies.
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Affiliation(s)
- Kaitlin Schaefer
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Irene Lui
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James R. Byrnes
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Emily Kang
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Jie Zhou
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Amy M. Weeks
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James A. Wells
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
- Department
of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
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21
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Podvin S, Jiang Z, Boyarko B, Rossitto LA, O’Donoghue A, Rissman RA, Hook V. Dysregulation of Neuropeptide and Tau Peptide Signatures in Human Alzheimer's Disease Brain. ACS Chem Neurosci 2022; 13:1992-2005. [PMID: 35758417 PMCID: PMC9264367 DOI: 10.1021/acschemneuro.2c00222] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Synaptic dysfunction and loss occur in Alzheimer's disease (AD) brains, which results in cognitive deficits and brain neurodegeneration. Neuropeptides comprise the major group of synaptic neurotransmitters in the nervous system. This study evaluated neuropeptide signatures that are hypothesized to differ in human AD brain compared to age-matched controls, achieved by global neuropeptidomics analysis of human brain cortex synaptosomes. Neuropeptidomics demonstrated distinct profiles of neuropeptides in AD compared to controls consisting of neuropeptides derived from chromogranin A (CHGA) and granins, VGF (nerve growth factor inducible), cholecystokinin, and others. The differential neuropeptide signatures indicated differences in proteolytic processing of their proneuropeptides. Analysis of cleavage sites showed that dibasic residues at the N-termini and C-termini of neuropeptides were the main sites for proneuropeptide processing, and data also showed that the AD group displayed differences in preferred residues adjacent to the cleavage sites. Notably, tau peptide signatures differed in the AD compared to age-matched control human brain cortex synaptosomes. Unique tau peptides were derived from the tau protein through proteolysis using similar and differential cleavage sites in the AD brain cortex compared to the control. Protease profiles differed in the AD compared to control, indicated by proteomics data. Overall, these results demonstrate that dysregulation of neuropeptides and tau peptides occurs in AD brain cortex synaptosomes compared to age-matched controls, involving differential cleavage site properties for proteolytic processing of precursor proteins. These dynamic changes in neuropeptides and tau peptide signatures may be associated with the severe cognitive deficits of AD.
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Affiliation(s)
- Sonia Podvin
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Zhenze Jiang
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Ben Boyarko
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Leigh-Ana Rossitto
- Biomedical
Sciences Graduate Program, University of
California, San Diego, La Jolla, California 92093, United States
| | - Anthony O’Donoghue
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Robert A. Rissman
- Department
of Neurosciences, University of California
San Diego, La Jolla, California 92093, United States
- Veterans
Affairs San Diego Health System, La Jolla, California 92093, United States
| | - Vivian Hook
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Biomedical
Sciences Graduate Program, University of
California, San Diego, La Jolla, California 92093, United States
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22
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Bresinsky M, Strasser JM, Hubmann A, Vallaster B, McCue WM, Fuller J, Singh G, Nelson KM, Cuellar ME, Finzel BC, Ashe KH, Walters MA, Pockes S. Characterization of caspase‐2 inhibitors based on specific sites of caspase‐2‐mediated proteolysis. Arch Pharm (Weinheim) 2022; 355:e2200095. [DOI: 10.1002/ardp.202200095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023]
Affiliation(s)
- Merlin Bresinsky
- Institute of Pharmacy University of Regensburg Regensburg Germany
| | - Jessica M. Strasser
- Department of Medicinal Chemistry University of Minnesota Minneapolis Minnesota USA
| | | | | | - William M. McCue
- Department of Medicinal Chemistry University of Minnesota Minneapolis Minnesota USA
| | - Jessica Fuller
- Department of Medicinal Chemistry University of Minnesota Minneapolis Minnesota USA
| | - Gurpreet Singh
- Department of Medicinal Chemistry University of Minnesota Minneapolis Minnesota USA
| | - Kathryn M. Nelson
- Department of Medicinal Chemistry University of Minnesota Minneapolis Minnesota USA
| | - Matthew E. Cuellar
- Department of Medicinal Chemistry University of Minnesota Minneapolis Minnesota USA
| | - Barry C. Finzel
- Department of Medicinal Chemistry University of Minnesota Minneapolis Minnesota USA
| | - Karen H. Ashe
- Department of Neurology University of Minnesota Minneapolis Minnesota USA
- GRECC, Minneapolis VA Hospital Minneapolis Minnesota USA
| | - Michael A. Walters
- Department of Medicinal Chemistry University of Minnesota Minneapolis Minnesota USA
| | - Steffen Pockes
- Institute of Pharmacy University of Regensburg Regensburg Germany
- Department of Medicinal Chemistry University of Minnesota Minneapolis Minnesota USA
- Department of Neurology University of Minnesota Minneapolis Minnesota USA
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23
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Weghorst F, Mirzakhanyan Y, Hernandez KL, Gershon PD, Cramer KS. Non-Apoptotic Caspase Activity Preferentially Targets a Novel Consensus Sequence Associated With Cytoskeletal Proteins in the Developing Auditory Brainstem. Front Cell Dev Biol 2022; 10:844844. [PMID: 35330912 PMCID: PMC8940215 DOI: 10.3389/fcell.2022.844844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/28/2022] [Indexed: 11/24/2022] Open
Abstract
The auditory brainstem relies on precise circuitry to facilitate sound source localization. In the chick, the development of this specialized circuitry requires non-apoptotic activity of caspase-3, for which we previously identified several hundred proteolytic substrates. Here we tested whether the sequence of the caspase cleavage site differentially encodes proteolytic preference in apoptotic and non-apoptotic contexts. We constructed a consensus sequence for caspase activity in the non-apoptotic chick auditory brainstem comprising the four residues N-terminal to the cleavage site: IX(G/R)D↓ where X represents no significant enrichment and ↓ represents the cleavage site. We identified GO terms significantly enriched among caspase substrates containing motifs found in the above consensus sequence. (G/R)D↓ was associated with the term “Structural Constituent of Cytoskeleton” (SCoC), suggesting that SCoC proteins may be specifically targeted by caspase activity during non-apoptotic developmental processes. To ascertain whether this consensus sequence was specific to the non-apoptotic auditory brainstem at embryonic day (E) 10, we used protein mass spectrometry of brainstems harvested at a time when auditory brainstem neurons undergo apoptotic cell death (E13). The apoptotic motif VD was significantly enriched among E13 cleavage sites, indicating that motif preference at the P2 subsite had shifted toward the canonical caspase consensus sequence. Additionally, Monte Carlo simulations revealed that only the GD motif was associated with SCoC substrates in the apoptotic auditory brainstem, indicating that GD encodes specificity for SCoC proteins in both non-apoptotic and apoptotic contexts, despite not being preferred in the latter. Finally, to identify candidate human non-apoptotic consensus sequences, we used Monte Carlo analyses to determine motifs and motif pairs associated with SCoC caspase substrates in the Degrabase, a database of cleavage sites in human apoptotic cell lines. We found 11 motifs significantly associated with SCoC proteolysis, including IXXD and GD. We employed a stepwise method to select motif pairs that optimized SCoC specificity for a given coverage of SCoC cleavage events, yielding 11 motif pairs likely to be preferred in SCoC-directed human non-apoptotic caspase consensus sequences. GD + IXXD was among these motif pairs, suggesting a conservation of non-apoptotic consensus sites among vertebrates.
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Affiliation(s)
- Forrest Weghorst
- Department of Neurobiology and Behavior, UC Irvine, Irvine, CA, United States
| | - Yeva Mirzakhanyan
- Department of Molecular Biology and Biochemistry, UC Irvine, Irvine, CA, United States
| | | | - Paul D Gershon
- Department of Molecular Biology and Biochemistry, UC Irvine, Irvine, CA, United States
| | - Karina S Cramer
- Department of Neurobiology and Behavior, UC Irvine, Irvine, CA, United States
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24
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Dehkordi MH, Munn RGK, Fearnhead HO. Non-Canonical Roles of Apoptotic Caspases in the Nervous System. Front Cell Dev Biol 2022; 10:840023. [PMID: 35281082 PMCID: PMC8904960 DOI: 10.3389/fcell.2022.840023] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Caspases are a family of cysteine proteases that predominantly cleave their substrates after aspartic acid residues. Much of what we know of caspases emerged from investigation a highly conserved form of programmed cell death called apoptosis. This form of cell death is regulated by several caspases, including caspase-2, caspase-3, caspase-7, caspase-8 and caspase-9. However, these “killer” apoptotic caspases have emerged as versatile enzymes that play key roles in a wide range of non-apoptotic processes. Much of what we understand about these non-apoptotic roles is built on work investigating how “killer” caspases control a range of neuronal cell behaviors. This review will attempt to provide an up to date synopsis of these roles.
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Affiliation(s)
- Mahshid H. Dehkordi
- Pharmacology and Therapeutics, National University of Ireland Galway, Galway, Ireland
| | | | - Howard O. Fearnhead
- Pharmacology and Therapeutics, National University of Ireland Galway, Galway, Ireland
- *Correspondence: Howard O. Fearnhead,
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25
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Bahatyrevich-Kharitonik B, Medina-Guzman R, Flores-Cortes A, García-Cruzado M, Kavanagh E, Burguillos MA. Cell Death Related Proteins Beyond Apoptosis in the CNS. Front Cell Dev Biol 2022; 9:825747. [PMID: 35096845 PMCID: PMC8794922 DOI: 10.3389/fcell.2021.825747] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022] Open
Abstract
Cell death related (CDR) proteins are a diverse group of proteins whose original function was ascribed to apoptotic cell death signaling. Recently, descriptions of non-apoptotic functions for CDR proteins have increased. In this minireview, we comment on recent studies of CDR proteins outside the field of apoptosis in the CNS, encompassing areas such as the inflammasome and non-apoptotic cell death, cytoskeleton reorganization, synaptic plasticity, mitophagy, neurodegeneration and calcium signaling among others. Furthermore, we discuss the evolution of proteomic techniques used to predict caspase substrates that could potentially explain their non-apoptotic roles. Finally, we address new concepts in the field of non-apoptotic functions of CDR proteins that require further research such the effect of sexual dimorphism on non-apoptotic CDR protein function and the emergence of zymogen-specific caspase functions.
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Affiliation(s)
- Bazhena Bahatyrevich-Kharitonik
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC, Seville, Spain
| | - Rafael Medina-Guzman
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC, Seville, Spain
| | - Alicia Flores-Cortes
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC, Seville, Spain
| | - Marta García-Cruzado
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC, Seville, Spain
| | - Edel Kavanagh
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC, Seville, Spain
| | - Miguel Angel Burguillos
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC, Seville, Spain
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26
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Araya LE, Soni IV, Hardy JA, Julien O. Deorphanizing Caspase-3 and Caspase-9 Substrates In and Out of Apoptosis with Deep Substrate Profiling. ACS Chem Biol 2021; 16:2280-2296. [PMID: 34553588 DOI: 10.1021/acschembio.1c00456] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Caspases are a family of enzymes that regulate biological processes such as inflammation and programmed cell death, through proteolysis. For example, in the intrinsic pathway of apoptosis, cell death signaling involves cytochrome c release from the mitochondria, which leads to the activation of caspase-9 and eventually the executioners caspase-3 and -7. One key step in our understanding of these proteases is to identify their respective protein substrates. Although hundreds of substrates have been linked to caspase-3, only a small handful of substrates have been reported for caspase-9. Employing deep profiling by subtiligase N-terminomics, we present here an unbiased analysis of caspase-3 and caspase-9 substrates in native cell lysates. We identified 906 putative protein substrates associated with caspase-3 and 124 protein substrates for caspase-9. This is the most comprehensive list of caspase substrates reported for each of these proteases, revealing a pool of new substrates that could not have been discovered using other approaches. Over half of the caspase-9 substrates were also cleaved by caspase-3, but often at unique sites, suggesting an evolved functional redundancy for these two proteases. Correspondingly, nearly half of the caspase-9 cleavage sites were not recognized by caspase-3. Our results suggest that in addition to its important role in activating the executioners, the role of caspase-9 is likely broader and more complex than previously appreciated, which includes proteolysis of key apoptotic substrates other than just caspase-3 and -7 and involvement in non-apoptotic pathways. Our results are well poised to aid the discovery of new biological functions for these two caspases.
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Affiliation(s)
- Luam E. Araya
- Department of Biochemistry, University of Alberta, Edmonton T6G 2H7, Alberta, Canada
| | - Ishankumar V. Soni
- Department of Chemistry, University of Massachusetts, Amherst 01003, Massachusetts, United States
| | - Jeanne A. Hardy
- Department of Chemistry, University of Massachusetts, Amherst 01003, Massachusetts, United States
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton T6G 2H7, Alberta, Canada
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27
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Abstract
Post-translational modifications (PTMs) direct the assembly of protein complexes. In this context, proteolysis is a unique PTM because it is irreversible; the hydrolysis of the peptide backbone generates separate fragments bearing a new N and C terminus. Proteolysis can "re-wire" protein-protein interactions (PPIs) via the recruitment of end-binding proteins to new termini. In this review, we focus on the role of proteolysis in specifically creating complexes by recruiting E3 ubiquitin ligases to new N and C termini. These complexes potentiate proteolytic signaling by "erasing" proteolytic modifications. This activity tunes the duration and magnitude of protease signaling events. Recent work has shown that the stepwise process of proteolysis, end-binding by E3 ubiquitin ligases, and fragment turnover is associated with both the nascent N terminus (i.e., N-degron pathways) and the nascent C terminus (i.e., the C-degron pathways). Here, we discuss how these pathways might harmonize protease signaling with protein homeostasis (i.e., proteostasis).
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Affiliation(s)
- Matthew Ravalin
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Koli Basu
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
- Institute for Neurodegenerative Diseases, University of California at San Francisco, San Francisco, CA, USA
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
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28
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Soni IV, Hardy JA. Caspase-9 Activation of Procaspase-3 but Not Procaspase-6 Is Based on the Local Context of Cleavage Site Motifs and on Sequence. Biochemistry 2021; 60:2824-2835. [PMID: 34472839 DOI: 10.1021/acs.biochem.1c00459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Studying the interactions between a protease and its protein substrates at a molecular level is crucial for identifying the factors facilitating selection of particular proteolytic substrates and not others. These selection criteria include both the sequence and the local context of the substrate cleavage site where the active site of the protease initially binds and then performs proteolytic cleavage. Caspase-9, an initiator of the intrinsic apoptotic pathway, mediates activation of executioner procaspase-3 by cleavage of the intersubunit linker (ISL) at site 172IETD↓S. Although procaspase-6, another executioner, possesses two ISL cleavage sites (site 1, 176DVVD↓N; site 2, 190TEVD↓A), neither is directly cut by caspase-9. Thus, caspase-9 directly activates procaspase-3 but not procaspase-6. To elucidate this selectivity of caspase-9, we engineered constructs of procaspase-3 (e.g., swapping the ISL site, 172IETD↓S, with DVVDN and TEVDA) and procaspase-6 (e.g., swapping site 1, 176DVVD↓N, and site 2, 190TEVD↓A, with IETDS). Using the substrate digestion data of these constructs, we show here that the P4-P1' sequence of procaspase-6 ISL site 1 (DVVDN) can be accessed but not cleaved by caspase-9. We also found that caspase-9 can recognize the P4-P1' sequence of procaspase-6 ISL site 2 (TEVDA); however, the local context of this cleavage site is the critical factor that prevents proteolytic cleavage. Overall, our data have demonstrated that both the sequence and the local context of the ISL cleavage sites play a vital role in preventing the activation of procaspase-6 directly by caspase-9.
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Affiliation(s)
- Ishankumar V Soni
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Jeanne A Hardy
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States.,Models to Medicine Center, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
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29
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Abstract
All living organisms depend on tightly regulated cellular networks to control biological functions. Proteolysis is an important irreversible post-translational modification that regulates most, if not all, cellular processes. Proteases are a large family of enzymes that perform hydrolysis of protein substrates, leading to protein activation or degradation. The 473 known and 90 putative human proteases are divided into 5 main mechanistic groups: metalloproteases, serine proteases, cysteine proteases, threonine proteases, and aspartic acid proteases. Proteases are fundamental to all biological systems, and when dysregulated they profoundly influence disease progression. Inhibiting proteases has led to effective therapies for viral infections, cardiovascular disorders, and blood coagulation just to name a few. Between 5 and 10% of all pharmaceutical targets are proteases, despite limited knowledge about their biological roles. More than 50% of all human proteases have no known substrates. We present here a comprehensive list of all current known human proteases. We also present current and novel biochemical tools to characterize protease functions in vitro, in vivo, and ex vivo. These tools make it achievable to define both beneficial and detrimental activities of proteases in health and disease.
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Affiliation(s)
- Longxiang Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Kimberly Main
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Henry Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
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30
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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.
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31
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Rare CASP6N73T variant associated with hippocampal volume exhibits decreased proteolytic activity, synaptic transmission defect, and neurodegeneration. Sci Rep 2021; 11:12695. [PMID: 34135352 PMCID: PMC8209045 DOI: 10.1038/s41598-021-91367-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/25/2021] [Indexed: 01/22/2023] Open
Abstract
Caspase-6 (Casp6) is implicated in Alzheimer disease (AD) cognitive impairment and pathology. Hippocampal atrophy is associated with cognitive impairment in AD. Here, a rare functional exonic missense CASP6 single nucleotide polymorphism (SNP), causing the substitution of asparagine with threonine at amino acid 73 in Casp6 (Casp6N73T), was associated with hippocampal subfield CA1 volume preservation. Compared to wild type Casp6 (Casp6WT), recombinant Casp6N73T altered Casp6 proteolysis of natural substrates Lamin A/C and α-Tubulin, but did not alter cleavage of the Ac-VEID-AFC Casp6 peptide substrate. Casp6N73T-transfected HEK293T cells showed elevated Casp6 mRNA levels similar to Casp6WT-transfected cells, but, in contrast to Casp6WT, did not accumulate active Casp6 subunits nor show increased Casp6 enzymatic activity. Electrophysiological and morphological assessments showed that Casp6N73T recombinant protein caused less neurofunctional damage and neurodegeneration in hippocampal CA1 pyramidal neurons than Casp6WT. Lastly, CASP6 mRNA levels were increased in several AD brain regions confirming the implication of Casp6 in AD. These studies suggest that the rare Casp6N73T variant may protect against hippocampal atrophy due to its altered catalysis of natural protein substrates and intracellular instability thus leading to less Casp6-mediated damage to neuronal structure and function.
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32
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Wang B, Zhang C, Yu C, Zhu Y, Tang Q, Huang H, Zhao Z. Enterovirus 71 Induces INF2 Cleavage via Activated Caspase-2 in Infected RD Cells. Front Microbiol 2021; 12:684953. [PMID: 34046026 PMCID: PMC8144320 DOI: 10.3389/fmicb.2021.684953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Enterovirus 71 (EV71) is the major causative pathogen of hand, foot, and mouth disease. The lack of understanding of the virus’s pathogenesis hinders the development of anti-virus drugs and the control of EV71 infection. Our previous studies have demonstrated that both mitochondria and endoplasmic reticulum (ER) were altered significantly in EV71 infected cells, but the mechanism is still unclear. In this study, we investigated the effects of EV71 infection on the expression of INF2, a key regulator factor in ER-Mitochondria communication and mitochondrial fission. We found that INF2 was cleaved in EV71 infected RD cells. The INF2 cleavage occurred at Aspartic 1,051 of INF2 and is mediated by activated caspases, predominantly by activated caspase-2. The subcellular localization of INF2 and caspase-2 was significantly altered in infected cells. We speculate that caspase-2-mediated INF2 cleavage is involved in forming viral replication organelles (ROs) and is a positive feedback regulatory mechanism of mitochondrial disorders caused by EV71 infection.
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Affiliation(s)
- Bei Wang
- National Health Commission (NHC) Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Clinical Immunology Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chongyang Zhang
- National Health Commission (NHC) Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Congci Yu
- National Health Commission (NHC) Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Zhu
- National Health Commission (NHC) Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qing Tang
- National Health Commission (NHC) Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - He Huang
- National Health Commission (NHC) Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Clinical Immunology Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhendong Zhao
- National Health Commission (NHC) Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Clinical Immunology Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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33
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Weeks AM, Wells JA. N-Terminal Modification of Proteins with Subtiligase Specificity Variants. ACTA ACUST UNITED AC 2021; 12:e79. [PMID: 32074409 DOI: 10.1002/cpch.79] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Subtiligase is a powerful enzymatic tool for N-terminal modification of proteins and peptides. In a typical subtiligase-catalyzed N-terminal modification reaction, a peptide ester donor substrate is ligated onto the unblocked N terminus of a protein, resulting in the exchange of the ester bond in the donor substrate for an amide bond between the donor substrate and protein N terminus. Using this strategy, new chemical probes and payloads, such as fluorophores, affinity handles, cytotoxic drugs, and reactive functional groups, can be introduced site-specifically into proteins. While the efficiency of this reaction depends on the sequences to be ligated, a panel of mutants was recently developed that expands the scope of substrate sequences that are suitable for subtiligase modification. This article outlines the steps for applying subtiligase or specificity variants for both site-specific bioconjugation of purified proteins and for global modification of cellular N termini to enable their sequencing by tandem mass spectrometry. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Subtiligase-catalyzed site-specific protein bioconjugation Support Protocol 1: Expression and purification of subtiligase-His6 Support Protocol 2: Subtiligase substrate synthesis Basic Protocol 2: Subtiligase N terminomics using a cocktail of subtiligase specificity mutants.
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Affiliation(s)
- Amy M Weeks
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California.,Current address: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
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Adenosine A1 Receptor Agonist (R-PIA) before Pilocarpine Modulates Pro- and Anti-Apoptotic Factors in an Animal Model of Epilepsy. Pharmaceuticals (Basel) 2021; 14:ph14040376. [PMID: 33919533 PMCID: PMC8074097 DOI: 10.3390/ph14040376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 11/26/2022] Open
Abstract
We aimed to characterize the mechanisms involved in neuroprotection by R-PIA administered before pilocarpine-induced seizures. Caspase-1 and caspase-3 activities were assayed using fluorimetry, and cathepsin D, HSP-70, and AKT expression levels were assayed using Western Blot of hippocampal samples. R-PIA was injected before pilocarpine (PILO), and four groups were studied at 1 h 30 min and 7 days following initiation of status epilepticus (SE): PILO, R-PIA+PILO, SALINE, and R-PIA+SALINE. At 1 h 30 min, significantly higher activities of caspase-1 and -3 were observed in the PILO group than in the SALINE group. Caspase-1 and -3 activities were higher in the R-PIA+PILO group than in the PILO group. At 7 days following SE, caspase-1 and -3 activities were higher than in the initial post-seizure phase compared to the SALINE group. The pretreatment of rats receiving PILO significantly reduced caspase activities compared to the PILO group. Expression of HSP-70, AKT, and cathepsin D was significantly higher in the PILO group than in the SALINE. In the R-PIA+PILO group, the expression of AKT and HSP-70 was greater than in rats receiving only PILO, while cathepsin D presented decreased expression. Pretreatment with R-PIA in PILO-injected rats strongly inhibited caspase-1 and caspase-3 activities and cathepsin D expression. It also increased expression levels of the neuroprotective proteins HSP-70 and AKT, suggesting an important role in modulating the cellular survival cascade.
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Özdemir A, İbişoğlu B, Şimay Demir YD, Benhür E, Valipour F, Ark M. A novel proteolytic cleavage of ROCK 1 in cell death: Not only by caspases 3 and 7 but also by caspase 2. Biochem Biophys Res Commun 2021; 547:118-124. [PMID: 33610039 DOI: 10.1016/j.bbrc.2021.02.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/05/2021] [Indexed: 01/05/2023]
Abstract
During apoptosis, myosin light chain phosphorylation induced by ROCK 1, activated by caspase 3-mediated cleavage, results in the formation of membrane blebs. Additionally, actin-myosin-based contraction induced by the activation of ROCK is involved in the apoptotic nuclear disintegration. In previous studies, it was reported that ROCK 1 was only cleaved by caspase 3 in cell death and caspase 7 was involved in truncation of ROCK 1 in in-vitro cell-free conditions. Here we reported that caspase 2 is involved in the truncation of ROCK 1 directly as well as caspase 3 and caspase 7. Utilizing caspase 3-deficient MCF-7, MDA-MB-231 and HeLa cells, we demonstrated that caspase 2 produced an active fragment of approximately 130 kDa of ROCK 1 in cell death. The cleaved active fragment of ROCK 1 is also responsible for the formation of membrane blebbing in cell death. Interestingly, caspase 2-mediated cleavage of ROCK 1 might occur in the region where caspase 3 truncates ROCK 1. Moreover, the presence of an active cleaved form of ROCK 1 in the nuclei implies that this fragment might play a role in the disruption of nuclear integrity. Taken together, it was determined that caspase 2 has a role in the truncation of ROCK 1 in cell death, and a new activation mechanism has been defined for ROCK 1.
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Affiliation(s)
- Aysun Özdemir
- Department of Pharmacology, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey
| | - Burçin İbişoğlu
- Department of Pharmacology, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey
| | | | - Elifnur Benhür
- Department of Pharmacology, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey
| | - Farzaneh Valipour
- Department of Pharmacology, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey
| | - Mustafa Ark
- Department of Pharmacology, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey.
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Brown-Suedel AN, Bouchier-Hayes L. Caspase-2 Substrates: To Apoptosis, Cell Cycle Control, and Beyond. Front Cell Dev Biol 2020; 8:610022. [PMID: 33425918 PMCID: PMC7785872 DOI: 10.3389/fcell.2020.610022] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/03/2020] [Indexed: 01/12/2023] Open
Abstract
Caspase-2 belongs to the caspase family of proteins responsible for essential cellular functions including apoptosis and inflammation. Uniquely, caspase-2 has been identified as a tumor suppressor, but how it regulates this function is still unknown. For many years, caspase-2 has been considered an “orphan” caspase because, although it is able to induce apoptosis, there is an abundance of conflicting evidence that questions its necessity for apoptosis. Recent evidence supports that caspase-2 has non-apoptotic functions in the cell cycle and protection from genomic instability. It is unclear how caspase-2 regulates these opposing functions, which has made the mechanism of tumor suppression by caspase-2 difficult to determine. As a protease, caspase-2 likely exerts its functions by proteolytic cleavage of cellular substrates. This review highlights the known substrates of caspase-2 with a special focus on their functional relevance to caspase-2’s role as a tumor suppressor.
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Affiliation(s)
- Alexandra N Brown-Suedel
- Hematology-Oncology Section, Department of Pediatrics, Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, United States.,William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX, United States
| | - Lisa Bouchier-Hayes
- Hematology-Oncology Section, Department of Pediatrics, Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, United States.,William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX, United States
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Öhlknecht C, Petrov D, Engele P, Kröß C, Sprenger B, Fischer A, Lingg N, Schneider R, Oostenbrink C. Enhancing the promiscuity of a member of the Caspase protease family by rational design. Proteins 2020; 88:1303-1318. [PMID: 32432825 PMCID: PMC7497161 DOI: 10.1002/prot.25950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/19/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
Abstract
The N-terminal cleavage of fusion tags to restore the native N-terminus of recombinant proteins is a challenging task and up to today, protocols need to be optimized for different proteins individually. Within this work, we present a novel protease that was designed in-silico to yield enhanced promiscuity toward different N-terminal amino acids. Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease. These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations. The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results. Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids. We believe that the created mutants constitute an important step toward generalized procedures to restore original N-termini of recombinant fusion proteins.
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Affiliation(s)
- Christoph Öhlknecht
- Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Drazen Petrov
- Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
| | - Petra Engele
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Christina Kröß
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Bernhard Sprenger
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | | | - Nico Lingg
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Rainer Schneider
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
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AND-gate contrast agents for enhanced fluorescence-guided surgery. Nat Biomed Eng 2020; 5:264-277. [PMID: 32989286 PMCID: PMC7969380 DOI: 10.1038/s41551-020-00616-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 08/27/2020] [Indexed: 12/18/2022]
Abstract
The surgical resection of tumours requires the precise location and definition of the margins between lesions and normal tissue. However, this is made difficult by irregular margin borders. Although molecularly targeted optical contrast agents can be used to define tumour margins during surgery in real time, the selectivity of the contrast agents is often limited by the target being expressed in both healthy and tumour tissues. Here, we show that AND-gate optical imaging probes requiring the processing of two substrates by multiple tumour-specific enzymes produce a fluorescent signal with significantly improved specificity and sensitivity to tumour tissue. We evaluated the performance of the probes in mouse models of mammary tumours and of metastatic lung cancer, and during fluorescence-guided robotic surgery. Imaging probes relying on multivariate activation to selectively target complex patterns of enzymatic activity should be useful in disease detection, treatment and monitoring.
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Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries. Proc Natl Acad Sci U S A 2020; 117:25464-25475. [PMID: 32973096 DOI: 10.1073/pnas.2009279117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Proteolysis is a major posttranslational regulator of biology inside and outside of cells. Broad identification of optimal cleavage sites and natural substrates of proteases is critical for drug discovery and to understand protease biology. Here, we present a method that employs two genetically encoded substrate phage display libraries coupled with next generation sequencing (SPD-NGS) that allows up to 10,000-fold deeper sequence coverage of the typical six- to eight-residue protease cleavage sites compared to state-of-the-art synthetic peptide libraries or proteomics. We applied SPD-NGS to two classes of proteases, the intracellular caspases, and the ectodomains of the sheddases, ADAMs 10 and 17. The first library (Lib 10AA) allowed us to identify 104 to 105 unique cleavage sites over a 1,000-fold dynamic range of NGS counts and produced consensus and optimal cleavage motifs based position-specific scoring matrices. A second SPD-NGS library (Lib hP), which displayed virtually the entire human proteome tiled in contiguous 49 amino acid sequences with 25 amino acid overlaps, enabled us to identify candidate human proteome sequences. We identified up to 104 natural linear cut sites, depending on the protease, and captured most of the examples previously identified by proteomics and predicted 10- to 100-fold more. Structural bioinformatics was used to facilitate the identification of candidate natural protein substrates. SPD-NGS is rapid, reproducible, simple to perform and analyze, inexpensive, and renewable, with unprecedented depth of coverage for substrate sequences, and is an important tool for protease biologists interested in protease specificity for specific assays and inhibitors and to facilitate identification of natural protein substrates.
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Abstract
INTRODUCTION The N-terminus of a protein can encode several protein features, including its half-live and its localization. As the proteomics field remains dominated by bottom-up approaches and as N-terminal peptides only account for a fraction of all analyzable peptides, there is a need for their enrichment prior to analysis. COFRADIC, TAILS, and the subtiligase method were among the first N-terminomics methods developed, and several variants and novel methods were introduced that often reduce processing time and/or the amount of material required. AREAS COVERED We present an overview of how the field of N-terminomics developed, including a discussion of the founding methods, several updates made to these and introduce newer methods such as TMPP-labeling, biotin-based methods besides some necessary improvements in data analysis. EXPERT OPINION N-terminomic methods remain being used and improved methods are published however, more efficient use of contemporary mass spectrometers, promising data-independent approaches, and mass spectrometry-free single peptide or protein sequences may threat the N-terminomics field.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
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Chen S, Yim JJ, Bogyo M. Synthetic and biological approaches to map substrate specificities of proteases. Biol Chem 2020; 401:165-182. [PMID: 31639098 DOI: 10.1515/hsz-2019-0332] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023]
Abstract
Proteases are regulators of diverse biological pathways including protein catabolism, antigen processing and inflammation, as well as various disease conditions, such as malignant metastasis, viral infection and parasite invasion. The identification of substrates of a given protease is essential to understand its function and this information can also aid in the design of specific inhibitors and active site probes. However, the diversity of putative protein and peptide substrates makes connecting a protease to its downstream substrates technically difficult and time-consuming. To address this challenge in protease research, a range of methods have been developed to identify natural protein substrates as well as map the overall substrate specificity patterns of proteases. In this review, we highlight recent examples of both synthetic and biological methods that are being used to define the substrate specificity of protease so that new protease-specific tools and therapeutic agents can be developed.
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Affiliation(s)
- Shiyu Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua J Yim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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42
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Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity. Biochem J 2020; 476:3475-3492. [PMID: 31675069 PMCID: PMC6874516 DOI: 10.1042/bcj20190625] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 12/18/2022]
Abstract
Apoptotic caspases evolved with metazoans more than 950 million years ago (MYA), and a series of gene duplications resulted in two subfamilies consisting of initiator and effector caspases. The effector caspase genes (caspases-3, -6, and -7) were subsequently fixed into the Chordata phylum more than 650 MYA when the gene for a common ancestor (CA) duplicated, and the three effector caspases have persisted throughout mammalian evolution. All caspases prefer an aspartate residue at the P1 position of substrates, so each caspase evolved discrete cellular roles through changes in substrate recognition at the P4 position combined with allosteric regulation. We examined the evolution of substrate specificity in caspase-6, which prefers valine at the P4 residue, compared with caspases-3 and -7, which prefer aspartate, by reconstructing the CA of effector caspases (AncCP-Ef1) and the CA of caspase-6 (AncCP-6An). We show that AncCP-Ef1 is a promiscuous enzyme with little distinction between Asp, Val, or Leu at P4. The specificity of caspase-6 was defined early in its evolution, where AncCP-6An demonstrates a preference for Val over Asp at P4. Structures of AncCP-Ef1 and of AncCP-6An show a network of charged amino acids near the S4 pocket that, when combined with repositioning a flexible active site loop, resulted in a more hydrophobic binding pocket in AncCP-6An. The ancestral protein reconstructions show that the caspase-hemoglobinase fold has been conserved for over 650 million years and that only three substitutions in the scaffold are necessary to shift substrate selection toward Val over Asp.
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43
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Frazier CL, Weeks AM. Engineered peptide ligases for cell signaling and bioconjugation. Biochem Soc Trans 2020; 48:1153-1165. [PMID: 32539119 PMCID: PMC8350744 DOI: 10.1042/bst20200001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 11/17/2022]
Abstract
Enzymes that catalyze peptide ligation are powerful tools for site-specific protein bioconjugation and the study of cellular signaling. Peptide ligases can be divided into two classes: proteases that have been engineered to favor peptide ligation, and protease-related enzymes with naturally evolved peptide ligation activity. Here, we provide a review of key natural peptide ligases and proteases engineered to favor peptide ligation activity. We cover the protein engineering approaches used to generate and improve these tools, along with recent biological applications, advantages, and limitations associated with each enzyme. Finally, we address future challenges and opportunities for further development of peptide ligases as tools for biological research.
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Affiliation(s)
- Clara L. Frazier
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amy M. Weeks
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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44
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Chen L, Shan Y, Yang C, Sui Z, Zhang X, Zhang L, Zhang Y. Carboxypeptidase B-Assisted Charge-Based Fractional Diagonal Chromatography for Deep Screening of C-Terminome. Anal Chem 2020; 92:8005-8009. [DOI: 10.1021/acs.analchem.0c00762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lingfan Chen
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Fujian Province New Drug Safety Evaluation Centre, Fujian Medical University, Fuzhou 350108, China
| | - Yichu Shan
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chao Yang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xiaodan Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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45
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Novel Apoptotic Mediators Identified by Conservation of Vertebrate Caspase Targets. Biomolecules 2020; 10:biom10040612. [PMID: 32326640 PMCID: PMC7225963 DOI: 10.3390/biom10040612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/08/2020] [Accepted: 04/13/2020] [Indexed: 12/27/2022] Open
Abstract
Caspases are proteases conserved throughout Metazoans and responsible for initiating and executing the apoptotic program. Currently, there are over 1800 known apoptotic caspase substrates, many of them known regulators of cell proliferation and death, which makes them attractive therapeutic targets. However, most caspase substrates are by-standers, and identifying novel apoptotic mediators amongst all caspase substrates remains an unmet need. Here, we conducted an in silico search for significant apoptotic caspase targets across different species within the Vertebrata subphylum, using different criteria of conservation combined with structural features of cleavage sites. We observed that P1 aspartate is highly conserved while the cleavage sites are extensively variable and found that cleavage sites are located primarily in coiled regions composed of hydrophilic amino acids. Using the combination of these criteria, we determined the final list of the 107 most relevant caspase substrates including 30 novel targets previously unknown for their role in apoptosis and cancer. These newly identified substrates can be potential regulators of apoptosis and candidates for anti-tumor therapy.
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46
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Saavedra E, Del Rosario H, Brouard I, Hernández-Garcés J, García C, Quintana J, Estévez F. The synthetic flavanone 6-methoxy-2-(naphthalen-1-yl)chroman-4-one induces apoptosis and activation of the MAPK pathway in human U-937 leukaemia cells. Bioorg Chem 2019; 94:103450. [PMID: 31785856 DOI: 10.1016/j.bioorg.2019.103450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/19/2019] [Accepted: 11/14/2019] [Indexed: 12/15/2022]
Abstract
Synthetic flavonoids containing a naphthalene ring have attracted attention as potential cytotoxic compounds. Here, we synthesized ten chalcones and their corresponding flavanones and evaluated their antiproliferative activity against the human tumour cell line U-937. This series of chalcone derivatives was characterized by the presence of a naphthalene ring which was kept unaltered- and attached to the β carbon of the 1-phenyl-2-propen-1-one framework. The structure-activity relationship of these chalcone derivatives and their corresponding cyclic compounds was investigated by the introduction of different substituents (methyl, methoxy, benzyloxy, chlorine) or by varying the position of the methoxy or benzyloxy groups on the A ring. The results revealed that both the chalcone containing the methoxy group at 5' position of the A ring as well as its corresponding flavanone [6-methoxy-2-(naphthalen-1-yl)chroman-4-one] were the most cytotoxic compounds, with IC50 values of 2.8 ± 0.2 and 1.3 ± 0.2 μM, respectively, against U-937 cells. This synthetic flavanone was as cytotoxic as the antitumor etoposide in U-937 cells and displayed strong cytotoxicity against additional human leukaemia cell lines, including HL-60, MOLT-3 and NALM-6. Human peripheral blood mononuclear cells were more resistant than leukaemia cells to the cytotoxic effects of the flavanone. Treatment of U-937 cells with this compound induced G2-M cell cycle arrest, an increase in sub-G1 ratio and annexin-V positive cells, mitochondrial cytochrome c release, caspase activation and poly(ADP-ribose)polymerase processing. Apoptosis induction triggered by this flavonoid was blocked by overexpression of the anti-apoptotic protein Bcl-2. This flavanone induces phosphorylation of p38 mitogen-activated protein kinases, extracellular-signal regulated kinases and c-jun N-terminal kinases/stress-activated protein kinases (JNK/SAPK) following different kinetics. Moreover, cell death was attenuated by the inhibition of mitogen-activated extracellular kinases and JNK/SAPK and was independent of reactive oxygen species generation.
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Affiliation(s)
- Ester Saavedra
- Departamento de Bioquímica y Biología Molecular, Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de las Palmas de Gran Canaria, Spain
| | - Henoc Del Rosario
- Departamento de Bioquímica y Biología Molecular, Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de las Palmas de Gran Canaria, Spain
| | - Ignacio Brouard
- Instituto de Productos Naturales y Agrobiología, CSIC, La Laguna, Tenerife, Spain
| | - Judith Hernández-Garcés
- Instituto Universitario de Bio-orgánica AG, Departamento de Química Orgánica, Universidad de La Laguna, Tenerife, Spain
| | - Celina García
- Instituto Universitario de Bio-orgánica AG, Departamento de Química Orgánica, Universidad de La Laguna, Tenerife, Spain
| | - José Quintana
- Departamento de Bioquímica y Biología Molecular, Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de las Palmas de Gran Canaria, Spain
| | - Francisco Estévez
- Departamento de Bioquímica y Biología Molecular, Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de las Palmas de Gran Canaria, Spain.
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47
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Qi E, Wang D, Li Y, Li G, Su Z. Revealing favorable and unfavorable residues in cooperative positions in protease cleavage sites. Biochem Biophys Res Commun 2019; 519:714-720. [PMID: 31543345 DOI: 10.1016/j.bbrc.2019.09.056] [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: 09/02/2019] [Accepted: 09/14/2019] [Indexed: 11/17/2022]
Abstract
Proteases play critical roles in a wide variety of fundamental biological functions, and numerous protease inhibitors have been developed to treat various diseases including cancer. A wide range of experimental and computational methods have been developed to investigate the specificity and catalytic mechanisms of proteases. However, these methods only focused on the preferences of a single position around a cleavage site in a substrate, rarely on the compositionality of the subsites. We present new methods to quantify the specificity of proteases by considering the combinatorial patterns of amino acid residuals of cleavage sites in substrates. By incorporating the preference at positions, we modeled three types of favorable combinations of residues in cleavage sites. Moreover, by constructing a relationship weight matrix of residues between two positions, we can easily identify unfavorable combinations of residues at the positions. Applying these methods to a set of known cleavage sites of proteases, we revealed numerous favorable and unfavorable residues in cooperative positions in the protease cleavage sites. The results can help understand the specificity and catalytic mechanisms of proteases. To our knowledge, this is the first study that quantifies unfavorable combinations of amino acids between two sites. Furthermore, this method is not limited to the study of proteases and cleavage sites, and can be generalized to uncover the relationships of residues at meaningful sites in other proteins.
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Affiliation(s)
- Enfeng Qi
- School of Mathematics, Shandong University, Jinan, 250100, China; School of Mathematics and Statistics, Guangxi Normal University, Guilin, 541000, China
| | - Dongyu Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Yang Li
- School of Mathematics, Shandong University, Jinan, 250100, China
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, 250100, China.
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, 28223, USA.
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48
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Solania A, González-Páez GE, Wolan DW. Selective and Rapid Cell-Permeable Inhibitor of Human Caspase-3. ACS Chem Biol 2019; 14:2463-2470. [PMID: 31334631 DOI: 10.1021/acschembio.9b00564] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Individual roles and overlapping functionalities of 12 human caspases during apoptosis and other cellular processes remain poorly resolved primarily due to a lack of chemical tools. Here we present a new selective caspase-3 inhibitor, termed Ac-ATS010-KE, with rapid and irreversible binding kinetics. Relative to previously designed caspase-3-selective molecules that have tremendously abated inhibitory rates and thus limited use in biological settings, the improved kinetics of Ac-ATS010-KE permits its use in a cell-based capacity. We demonstrate that Ac-ATS010-KE prevents apoptosis with comparable efficacy to the general caspase inhibitor Ac-DEVD-KE and surprisingly does so without side-chain methylation. This observation is in contrast to the well-established peptide modification strategy typically employed for improving cellular permeability. Ac-ATS010-KE protects against extrinsic apoptosis, which demonstrates the utility of a thiophene carboxylate leaving group in biological settings, challenges the requisite neutralization of free carboxylic acids to improve cell permeability, and provides a tool-like compound to interrogate the role of caspase-3 in a variety of cellular processes.
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Affiliation(s)
- Angelo Solania
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gonzalo E. González-Páez
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dennis W. Wolan
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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49
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Abstract
Proteases are key regulators of vital biological processes, such as apoptosis, cell differentiation, viral infection and neurodegeneration. Proteases are tightly regulated, largely because proteolysis is a unique post-translational modification (PTM) that is essentially irreversible. In order to understand the role of proteases in health and disease, the identification of protease substrates is an important step toward our understanding of their biological functions. Classic approaches for the study of proteolysis in complex mixtures employ gel electrophoresis and mass spectrometry. Such approaches typically identify a few protein substrates at a time but often fail to identify specific cleavage site locations. In contrast, modern proteomic methods using enrichment of proteolytic protein fragments can lead to the identification of hundreds of modified peptides with precise cleavage site determination in a single experiment. In this manuscript, we will review recent advances in N-terminomics methods and highlight key studies that have taken advantage of these technologies to advance our understanding of the role of proteases in cellular physiology.
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Affiliation(s)
- Shu Yue Luo
- Department of Biochemistry, University of Alberta, Edmonton, Alberta Canada
| | - Luam Ellen Araya
- Department of Biochemistry, University of Alberta, Edmonton, Alberta Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, Alberta Canada
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50
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Abstract
Subtiligase-catalyzed peptide ligation is a powerful approach for site-specific protein bioconjugation, synthesis and semisynthesis of proteins and peptides, and chemoproteomic analysis of cellular N termini. Here, we provide a comprehensive review of the subtiligase technology, including its development, applications, and impacts on protein science. We highlight key advantages and limitations of the tool and compare it to other peptide ligase enzymes. Finally, we provide a perspective on future applications and challenges and how they may be addressed.
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Affiliation(s)
- Amy M Weeks
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94143, United States
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