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Eichler RAS, Martucci LF, de Castro LM, Ferro ES. Methods for Intracellular Peptidomic Analysis. Methods Mol Biol 2024; 2758:199-212. [PMID: 38549015 DOI: 10.1007/978-1-0716-3646-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Peptides have broad biological significance among different species. Intracellular peptides are considered a particular class of bioactive peptides, whose generation is initiated by proteasomal degradation of cytosolic, nuclear, or mitochondrial proteins. To extract and purify intracellular peptides, which may apply for biological peptides in general, it is important to consider the initial source: tissue, cell, or fluid. First, it is important to proceed fast with inactivation of proteases and/or peptidases commonly present in the biological source of peptides, which might rapidly degrade peptides during the initial process of extraction. The incubation of biological tissues, cells, and fluids at 80 °C for up to 20 min have been sufficient to fully inactivate proteases or peptidases activities. It is particularly important not to acidify the samples at high temperature, because it can lead to nonspecific hydrolysis reactions; particularly, the Asp-Pro peptide bond can be cleaved at acidic environments and elevated temperatures. Unfortunately, not every sample can have proteinases and peptidases denatured by heating the biological source of intracellular peptides. Plasma, for example, when heated at temperatures higher than 55 °C can clot and trap peptides within the fibrin net. Therefore, alternative conditions for inactivating proteinases and peptidases must apply for plasma samples. In this chapter, the most successful methods used in our laboratory to extract intracellular peptides are described.
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Affiliation(s)
- Rosangela A S Eichler
- Department of Pharmacology, Biomedical Sciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Luiz Felipe Martucci
- Department of Pharmacology, Biomedical Sciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Leandro M de Castro
- Biodiversity of Coastal Environments Postgraduate Program, São Paulo State University (UNESP), Bioscience Institute, São Vicente, Brazil
| | - Emer S Ferro
- Department of Pharmacology, Biomedical Sciences Institute, University of São Paulo, São Paulo, SP, Brazil.
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2
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Dow LF, Case AM, Paustian MP, Pinkerton BR, Simeon P, Trippier PC. The evolution of small molecule enzyme activators. RSC Med Chem 2023; 14:2206-2230. [PMID: 37974956 PMCID: PMC10650962 DOI: 10.1039/d3md00399j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023] Open
Abstract
There is a myriad of enzymes within the body responsible for maintaining homeostasis by providing the means to convert substrates to products as and when required. Physiological enzymes are tightly controlled by many signaling pathways and their products subsequently control other pathways. Traditionally, most drug discovery efforts focus on identifying enzyme inhibitors, due to upregulation being prevalent in many diseases and the existence of endogenous substrates that can be modified to afford inhibitor compounds. As enzyme downregulation and reduction of endogenous activators are observed in multiple diseases, the identification of small molecules with the ability to activate enzymes has recently entered the medicinal chemistry toolbox to afford chemical probes and potential therapeutics as an alternative means to intervene in diseases. In this review we highlight the progress made in the identification and advancement of non-kinase enzyme activators and their potential in treating various disease states.
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Affiliation(s)
- Louise F Dow
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Alfie M Case
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Megan P Paustian
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Braeden R Pinkerton
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Princess Simeon
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Paul C Trippier
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center Omaha NE 68106 USA
- UNMC Center for Drug Discovery, University of Nebraska Medical Center Omaha NE 68106 USA
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3
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Cavalcanti DMLP, Teófilo TS, D Rodrigues T, Barbosa TNS, Fontenele-Neto JD. Thimet oligopeptidase (THOP 1) distribution in cane toad (Bufo Marinus, Linnaeus, 1758) brain. J Chem Neuroanat 2023; 133:102345. [PMID: 37778734 DOI: 10.1016/j.jchemneu.2023.102345] [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: 08/03/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/03/2023]
Abstract
Thimet oligopeptides (THOP 1) is a metal-dependent peptidase involved in the metabolism of neuropeptides and the presentation of peptides via MHC-1. It has been shown to play a role in the regulation of protein-protein interactions and the metabolism of intracellular peptides. THOP 1 is associated with important biological processes such as metabolism and neurodegenerative diseases, among others. The objective of this study is to elucidate the distribution of THOP 1 in the Bufo marinus brain. The analysis of THOP 1 amino acid sequences indicates that they have been conserved throughout evolution, with significant homology observed across various phyla. When comparing amphibians with other species, more than 70% identity can be identified. Immunohistochemistry analysis of the toad's brain has demonstrated that the enzyme has a ubiquitous distribution, consistent with previous findings in mammals. THOP 1 can be found in important areas of the brain, such as bulb, thalamic nuclei, striatum, hypothalamus, and among others. Nonetheless, THOP 1 is consistently localized within the nucleus, a pattern also observed in the rat brain. Therefore, based on these results, the toad appears to be an excellent model for studying the general biology of THOP 1, given the substantial homology of this enzyme with mammals and its similarity in distribution within the brain.
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Affiliation(s)
- Diogo M L P Cavalcanti
- Laboratory of Tissue and Development Biology, Medicine College, Department of Health Science, Center for Biological and Health Sciences, Universidade Federal Rural do Semiárido - UFERSA, Brazil.
| | - Tiago S Teófilo
- Laboratory of Tissue and Development Biology, Medicine College, Department of Health Science, Center for Biological and Health Sciences, Universidade Federal Rural do Semiárido - UFERSA, Brazil
| | - Tayline D Rodrigues
- Master's Degree Students, Multicentric Graduate Program in the area of Biochemistry and Molecular Biology (PMBqBM), Universidade do Estado do Rio Grande do Norte - UERN, Brazil
| | - Tayssa N S Barbosa
- Master's Degree Students, Multicentric Graduate Program in the area of Biochemistry and Molecular Biology (PMBqBM), Universidade do Estado do Rio Grande do Norte - UERN, Brazil
| | - José D Fontenele-Neto
- Laboratory of Tissue and Development Biology, Veterinary Medicine College, Department of Animal Science, Center for Biological and Health Sciences, Universidade Federal Rural do Semiárido - UFERSA, Brazil
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4
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Caprioli B, Eichler RAS, Silva RNO, Martucci LF, Reckziegel P, Ferro ES. Neurolysin Knockout Mice in a Diet-Induced Obesity Model. Int J Mol Sci 2023; 24:15190. [PMID: 37894869 PMCID: PMC10607720 DOI: 10.3390/ijms242015190] [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: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Neurolysin oligopeptidase (E.C.3.4.24.16; Nln), a member of the zinc metallopeptidase M3 family, was first identified in rat brain synaptic membranes hydrolyzing neurotensin at the Pro-Tyr peptide bond. The previous development of C57BL6/N mice with suppression of Nln gene expression (Nln-/-), demonstrated the biological relevance of this oligopeptidase for insulin signaling and glucose uptake. Here, several metabolic parameters were investigated in Nln-/- and wild-type C57BL6/N animals (WT; n = 5-8), male and female, fed either a standard (SD) or a hypercaloric diet (HD), for seven weeks. Higher food intake and body mass gain was observed for Nln-/- animals fed HD, compared to both male and female WT control animals fed HD. Leptin gene expression was higher in Nln-/- male and female animals fed HD, compared to WT controls. Both WT and Nln-/- females fed HD showed similar gene expression increase of dipeptidyl peptidase 4 (DPP4), a peptidase related to glucagon-like peptide-1 (GLP-1) metabolism. The present data suggest that Nln participates in the physiological mechanisms related to diet-induced obesity. Further studies will be necessary to better understand the molecular mechanism responsible for the higher body mass gain observed in Nln-/- animals fed HD.
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Affiliation(s)
- Bruna Caprioli
- Pharmacology Department, Biomedical Sciences Institute (ICB), São Paulo 05508-000, SP, Brazil; (B.C.); (R.A.S.E.); (R.N.O.S.); (L.F.M.)
| | - Rosangela A. S. Eichler
- Pharmacology Department, Biomedical Sciences Institute (ICB), São Paulo 05508-000, SP, Brazil; (B.C.); (R.A.S.E.); (R.N.O.S.); (L.F.M.)
| | - Renée N. O. Silva
- Pharmacology Department, Biomedical Sciences Institute (ICB), São Paulo 05508-000, SP, Brazil; (B.C.); (R.A.S.E.); (R.N.O.S.); (L.F.M.)
| | - Luiz Felipe Martucci
- Pharmacology Department, Biomedical Sciences Institute (ICB), São Paulo 05508-000, SP, Brazil; (B.C.); (R.A.S.E.); (R.N.O.S.); (L.F.M.)
| | - Patricia Reckziegel
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences (FCF), University of São Paulo (USP), São Paulo 05508-000, SP, Brazil;
| | - Emer S. Ferro
- Pharmacology Department, Biomedical Sciences Institute (ICB), São Paulo 05508-000, SP, Brazil; (B.C.); (R.A.S.E.); (R.N.O.S.); (L.F.M.)
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5
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Nagano N, Ichihashi Y, Komatsu T, Matsuzaki H, Hata K, Watanabe T, Misawa Y, Suzuki M, Sakamoto S, Kagami Y, Kashiro A, Takeuchi K, Kanemitsu Y, Ochiai H, Watanabe R, Honda K, Urano Y. Development of fluorogenic substrates for colorectal tumor-related neuropeptidases for activity-based diagnosis. Chem Sci 2023; 14:4495-4499. [PMID: 37152255 PMCID: PMC10155908 DOI: 10.1039/d2sc07029d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/29/2023] [Indexed: 05/09/2023] Open
Abstract
The M3 metalloproteases, neurolysin and THOP1, are neuropeptidases that are expressed in various tissues and metabolize neuropeptides, such as neurotensin. The biological roles of these enzymes are not well characterized, partially because the chemical tools to analyse their activities are not well developed. Here, we developed a fluorogenic substrate probe for neurolysin and thimet oligopeptidase 1 (THOP1), which enabled the analysis of enzymatic activity changes in tissue and plasma samples. In particular, the probe was useful for studying enzyme activities in a single-molecule enzyme assay platform, which can detect enzyme activity with high sensitivity. We detected the activity of neurolysin in plasma samples and revealed higher enzyme activity in the blood samples of patients with colorectal tumor. The result indicated that single-molecule neurolysin activity is a promising candidate for a blood biomarker for colorectal cancer diagnosis.
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Affiliation(s)
- Norimichi Nagano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yuki Ichihashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Hiroyuki Matsuzaki
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Keisuke Hata
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toshiaki Watanabe
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yoshihiro Misawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Misa Suzuki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Shingo Sakamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yu Kagami
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Ayumi Kashiro
- Institute for Advanced Medical Sciences, Nippon Medical School 1-1-5 Sendagi Bunkyo-ku Tokyo 113-0033 Japan
| | - Keiko Takeuchi
- Institute for Advanced Medical Sciences, Nippon Medical School 1-1-5 Sendagi Bunkyo-ku Tokyo 113-0033 Japan
| | - Yukihide Kanemitsu
- National Cancer Center Hospital 5-1-1 Tsukiji Chuo-ku Tokyo 104-0045 Japan
| | - Hiroki Ochiai
- National Cancer Center Hospital 5-1-1 Tsukiji Chuo-ku Tokyo 104-0045 Japan
| | - Rikiya Watanabe
- Cluster for Pioneering Research, RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Kazufumi Honda
- Institute for Advanced Medical Sciences, Nippon Medical School 1-1-5 Sendagi Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Medicine, Nippon Medical School 1-1-5 Sendagi Bunkyo-ku Tokyo 113-8602 Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Medicine, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
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6
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Mohammed-Salih HS, Al-lami HA, Saloom HF, Abdulkareem AA, Al-Obaidi JR, Razali N. Detection of orthodontically induced inflammatory root resorption-associated biomarkers from the gingival crevicular fluid by proteomics analysis: a randomized-controlled clinical trial. 3 Biotech 2023; 13:157. [PMID: 37151999 PMCID: PMC10154447 DOI: 10.1007/s13205-023-03572-5] [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: 09/12/2022] [Accepted: 04/19/2023] [Indexed: 05/09/2023] Open
Abstract
Orthodontically induced inflammatory root resorption (OIIRR) is an undesirable complication of orthodontic treatment (OT) with an ambiguous aetiologic mechanism. This study aimed to identify OIIRR-associated biomarkers in the gingival crevicular fluid (GCF) using proteomic analysis. In this randomized clinical trial, the upper first premolars (UFP) were exposed either to light or heavy force. The GCF was collected at 1 h, 1 day, 7 days, 14 days, 21 days, and 28 days following force application. After extraction of UFP, roots were imaged and resorption premolar, was used to deliver either light forcecraters were measured. Proteomic analysis of GCF was performed using 2D gel electrophoresis with MALDI-TOF/TOF MS/MS. Results were further analyzed by bioinformatics analyses showing the biological functions and predicted pathways. The predicted canonical pathways showed that the expression of immunoglobulin kappa (IGKC), neutrophil gelatinase-associated lipocalin (NGAL), neurolysin mitochondrial (NEUL), keratin, type II cytoskeletal 1 (K2C1), S100-A9, and the extracellular calcium-sensing receptor (CASR) were significantly associated with a range of biological and inflammatory processes. In conclusion, up-regulation of S100A9, CASR, and K2C1 suggested a response to force-related inflammation, chemotactic activities, osteoclastogenesis, and epithelial cell breakdown. Meanwhile, the up-regulation of IGKC, NGAL, and K2C1 indicated a response to the inflammatory process, innate immunity activation, and epithelial cell breakdown. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03572-5.
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Affiliation(s)
| | - Hadeel Adel Al-lami
- Department of Orthodontics, College of Dentistry, University of Baghdad, Baghdad, 10011 Iraq
| | - Hayder F. Saloom
- Department of Orthodontics, College of Dentistry, University of Baghdad, Baghdad, 10011 Iraq
| | - Ali Abbas Abdulkareem
- Department of Periodontics, College of Dentistry, University of Baghdad, Baghdad, 10011 Iraq
| | - Jameel R. Al-Obaidi
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900 Tanjong Malim, Perak Malaysia
| | - Nurhanani Razali
- Membranology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1, Tancha, Onna-son, Kunigami-kun, Okinawa, 904-0495 Japan
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7
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Revealing Natural Intracellular Peptides in Gills of Seahorse Hippocampus reidi. Biomolecules 2023; 13:biom13030433. [PMID: 36979368 PMCID: PMC10046794 DOI: 10.3390/biom13030433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 03/03/2023] Open
Abstract
The seahorse is a marine teleost fish member of the Syngnathidae family that displays a complex variety of morphological and reproductive behavior innovations and has been recognized for its medicinal importance. In the Brazilian ichthyofauna, the seahorse Hippocampus reidi is among the three fish species most used by the population in traditional medicine. In this study, a protocol was performed based on fast heat inactivation of proteases plus liquid chromatography coupled to mass spectrometry to identify native peptides in gills of seahorse H. reidi. The MS/MS spectra obtained from gills allowed the identification of 1080 peptides, of which 1013 peptides were present in all samples and 67 peptide sequences were identified in an additional LC-MS/MS run from an alkylated and reduced pool of samples. The majority of peptides were fragments of the internal region of the amino acid sequence of the precursor proteins (67%), and N- and C-terminal represented 18% and 15%, respectively. Many peptide sequences presented ribosomal proteins, histones and hemoglobin as precursor proteins. In addition, peptide fragments from moronecidin-like protein, described with antimicrobial activity, were found in all gill samples of H. reidi. The identified sequences may reveal new bioactive peptides.
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Xiang X, Bao R, Wu Y, Luo Y. Targeting Mitochondrial Proteases for Therapy of Acute Myeloid Leukemia. Br J Pharmacol 2022; 179:3268-3282. [PMID: 35352341 DOI: 10.1111/bph.15844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 02/05/2023] Open
Abstract
Targeting cancer metabolism has emerged as an attractive approach to improve therapeutic regimens in acute myeloid leukemia (AML). Mitochondrial proteases are closely related to cancer metabolism, but their biological functions have not been well characterized in AML. According to different catogory, we comprehensively reviewed the role of mitochondrial proteases in AML. This review highlights some 'powerful' mitochondrial protease targets, including their biological function, chemical modulators, and applicative prospect in AML.
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Affiliation(s)
- Xinrong Xiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Hematology and Hematology Research Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Rui Bao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Wu
- Department of Hematology and Hematology Research Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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9
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Effect of FKBP12-Derived Intracellular Peptides on Rapamycin-Induced FKBP-FRB Interaction and Autophagy. Cells 2022; 11:cells11030385. [PMID: 35159195 PMCID: PMC8834644 DOI: 10.3390/cells11030385] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Intracellular peptides (InPeps) generated by proteasomes were previously suggested as putative natural regulators of protein-protein interactions (PPI). Here, the main aim was to investigate the intracellular effects of intracellular peptide VFDVELL (VFD7) and related peptides on PPI. The internalization of the peptides was achieved using a C-terminus covalently bound cell-penetrating peptide (cpp; YGRKKRRQRRR). The possible inhibition of PPI was investigated using a NanoBiT® luciferase structural complementation reporter system, with a pair of plasmids vectors each encoding, simultaneously, either FK506-binding protein (FKBP) or FKBP-binding domain (FRB) of mechanistic target of rapamycin complex 1 (mTORC1). The interaction of FKBP-FRB within cells occurs under rapamycin induction. Results shown that rapamycin-induced interaction between FKBP-FRB within human embryonic kidney 293 (HEK293) cells was inhibited by VFD7-cpp (10-500 nM) and FDVELLYGRKKRRQRRR (VFD6-cpp; 1-500 nM); additional VFD7-cpp derivatives were either less or not effective in inhibiting FKBP-FRB interaction induced by rapamycin. Molecular dynamics simulations suggested that selected peptides, such as VFD7-cpp, VFD6-cpp, VFAVELLYGRKKKRRQRRR (VFA7-cpp), and VFEVELLYGRKKKRRQRRR (VFA7-cpp), bind to FKBP and to FRB protein surfaces. However, only VFD7-cpp and VFD6-cpp induced changes on FKBP structure, which could help with understanding their mechanism of PPI inhibition. InPeps extracted from HEK293 cells were found mainly associated with macromolecular components (i.e., proteins and/or nucleic acids), contributing to understanding InPeps' intracellular proteolytic stability and mechanism of action-inhibiting PPI within cells. In a model of cell death induced by hypoxia-reoxygenation, VFD6-cpp (1 µM) increased the viability of mouse embryonic fibroblasts cells (MEF) expressing mTORC1-regulated autophagy-related gene 5 (Atg5), but not in autophagy-deficient MEF cells lacking the expression of Atg5. These data suggest that VFD6-cpp could have therapeutic applications reducing undesired side effects of rapamycin long-term treatments. In summary, the present report provides further evidence that InPeps have biological significance and could be valuable tools for the rational design of therapeutic molecules targeting intracellular PPI.
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Silva RNO, Llanos RP, Eichler RAS, Oliveira TB, Gozzo FC, Festuccia WT, Ferro ES. New Intracellular Peptide Derived from Hemoglobin Alpha Chain Induces Glucose Uptake and Reduces Blood Glycemia. Pharmaceutics 2021; 13:pharmaceutics13122175. [PMID: 34959456 PMCID: PMC8708875 DOI: 10.3390/pharmaceutics13122175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
Intracellular peptides were shown to derive from proteasomal degradation of proteins from mammalian and yeast cells, being suggested to play distinctive roles both inside and outside these cells. Here, the role of intracellular peptides previously identified from skeletal muscle and adipose tissues of C57BL6/N wild type (WT) and neurolysin knockout mice were investigated. In differentiated C2C12 mouse skeletal muscle cells, some of these intracellular peptides like insulin activated the expression of several genes related to muscle contraction and gluconeogenesis. One of these peptides, LASVSTVLTSKYR (Ric4; 600 µg/kg), administrated either intraperitoneally or orally in WT mice, decreased glycemia. Neither insulin (10 nM) nor Ric4 (100 µM) induced glucose uptake in adipose tissue explants obtained from conditional knockout mice depleted of insulin receptor. Ric4 (100 µM) similarly to insulin (100 nM) induced Glut4 translocation to the plasma membrane of C2C12 differentiated cells, and increased GLUT4 mRNA levels in epididymal adipose tissue of WT mice. Ric4 (100 µM) increased both Erk and Akt phosphorylation in C2C12, as well as in epididymal adipose tissue from WT mice; Erk, but not Akt phosphorylation was activated by Ric4 in tibial skeletal muscle from WT mice. Ric4 is rapidly degraded in vitro by WT liver and kidney crude extracts, such a response that is largely reduced by structural modifications such as N-terminal acetylation, C-terminal amidation, and substitution of Leu8 for DLeu8 (Ac-LASVSTV[DLeu]TSKYR-NH2; Ric4-16). Ric4-16, among several Ric4 derivatives, efficiently induced glucose uptake in differentiated C2C12 cells. Among six Ric4-derivatives evaluated in vivo, Ac-LASVSTVLTSKYR-NH2 (Ric4-2; 600 µg/kg) and Ac-LASVSTV[DLeu]TSKYR (Ric4-15; 600 µg/kg) administrated orally efficiently reduced glycemia in a glucose tolerance test in WT mice. The potential clinical application of Ric4 and Ric4-derivatives deserves further attention.
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Affiliation(s)
- Renée N. O. Silva
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo 05508-000, SP, Brazil; (R.N.O.S.); (R.P.L.); (R.A.S.E.)
| | - Ricardo P. Llanos
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo 05508-000, SP, Brazil; (R.N.O.S.); (R.P.L.); (R.A.S.E.)
| | - Rosangela A. S. Eichler
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo 05508-000, SP, Brazil; (R.N.O.S.); (R.P.L.); (R.A.S.E.)
| | - Thiago B. Oliveira
- Physiology and Biophysics, Biomedical Science Institute, University of São Paulo, São Paulo 05508-000, SP, Brazil; (T.B.O.); (W.T.F.)
| | - Fábio C. Gozzo
- Institute of Chemistry, State University of Campinas, Campinas 13083-862, SP, Brazil;
| | - William T. Festuccia
- Physiology and Biophysics, Biomedical Science Institute, University of São Paulo, São Paulo 05508-000, SP, Brazil; (T.B.O.); (W.T.F.)
| | - Emer S. Ferro
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo 05508-000, SP, Brazil; (R.N.O.S.); (R.P.L.); (R.A.S.E.)
- Correspondence: ; Tel.: +55-11-3091-7310
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11
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Mirali S, Botham A, Voisin V, Xu C, St-Germain J, Sharon D, Hoff FW, Qiu Y, Hurren R, Gronda M, Jitkova Y, Nachmias B, MacLean N, Wang X, Arruda A, Minden MD, Horton TM, Kornblau SM, Chan SM, Bader GD, Raught B, Schimmer AD. The mitochondrial peptidase, neurolysin, regulates respiratory chain supercomplex formation and is necessary for AML viability. Sci Transl Med 2021; 12:12/538/eaaz8264. [PMID: 32269163 DOI: 10.1126/scitranslmed.aaz8264] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 03/09/2020] [Indexed: 12/18/2022]
Abstract
Neurolysin (NLN) is a zinc metallopeptidase whose mitochondrial function is unclear. We found that NLN was overexpressed in almost half of patients with acute myeloid leukemia (AML), and inhibition of NLN was selectively cytotoxic to AML cells and stem cells while sparing normal hematopoietic cells. Mechanistically, NLN interacted with the mitochondrial respiratory chain. Genetic and chemical inhibition of NLN impaired oxidative metabolism and disrupted the formation of respiratory chain supercomplexes (RCS). Furthermore, NLN interacted with the known RCS regulator, LETM1, and inhibition of NLN disrupted LETM1 complex formation. RCS were increased in patients with AML and positively correlated with NLN expression. These findings demonstrate that inhibiting RCS formation selectively targets AML cells and stem cells and highlights the therapeutic potential of pharmacologically targeting NLN in AML.
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Affiliation(s)
- Sara Mirali
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Institute of Medical Science, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Aaron Botham
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
| | - Veronique Voisin
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Changjiang Xu
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | | | - David Sharon
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Fieke W Hoff
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, Groningen 9700 RB, Netherlands.,Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yihua Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rose Hurren
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Marcela Gronda
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Yulia Jitkova
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Boaz Nachmias
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Neil MacLean
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Xiaoming Wang
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Andrea Arruda
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Institute of Medical Science, University of Toronto, Toronto M5S 1A8, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
| | - Terzah M Horton
- Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX 77030, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Steven M Chan
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
| | - Gary D Bader
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada. .,Institute of Medical Science, University of Toronto, Toronto M5S 1A8, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
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12
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Villar B, Bertran L, Aguilar C, Binetti J, Martínez S, Sabench F, Real M, Riesco D, París M, Del Castillo D, Richart C, Auguet T. Circulating Levels of Pro-Neurotensin and Its Relationship with Nonalcoholic Steatohepatitis and Hepatic Lipid Metabolism. Metabolites 2021; 11:373. [PMID: 34200577 PMCID: PMC8226510 DOI: 10.3390/metabo11060373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 01/03/2023] Open
Abstract
Recent studies suggest a link between pro-neurotensin (pro-NT) and nonalcoholic fatty liver disease (NAFLD), but the published data are conflicting. Thus, we aimed to analyze pro-NT levels in women with morbid obesity (MO) and NAFLD to investigate if this molecule is involved in NAFLD and liver lipid metabolism. Plasma levels of pro-NT were determined in 56 subjects with MO and 18 with normal weight (NW). All patients with MO were subclassified according to their liver histology into the normal liver (NL, n = 20) and NAFLD (n = 36) groups. The NAFLD group had 17 subjects with simple steatosis (SS) and 19 with nonalcoholic steatohepatitis (NASH). We used a chemiluminescence sandwich immunoassay to quantify pro-NT in plasma and RT-qPCR to evaluate the hepatic mRNA levels of several lipid metabolism-related genes. We reported that pro-NT levels were significantly higher in MO with NAFLD than in MO without NAFLD. Additionally, pro-NT levels were higher in NASH patients than in NL. The hepatic expression of lipid metabolism-related genes was found to be altered in NAFLD, as previously reported. Additionally, although pro-NT levels correlated with LDL, there was no association with the main lipid metabolism-related genes. These findings suggest that pro-NT could be related to NAFLD progression.
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Affiliation(s)
- Beatriz Villar
- Servei Medicina Interna, Hospital Universitari Joan XXIII, Universitat Rovira i Virgili, 4, 43007 Tarragona, Spain; (B.V.); (J.B.); (M.R.); (D.R.)
| | - Laia Bertran
- Grup d’Estudi de Malalties Metabòliques associades a Insulino Resistència (GEMMAIR)–AGAUR, Departament de Medicina i Cirurgia, Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 4, 43007 Tarragona, Spain; (L.B.); (C.A.); (C.R.)
| | - Carmen Aguilar
- Grup d’Estudi de Malalties Metabòliques associades a Insulino Resistència (GEMMAIR)–AGAUR, Departament de Medicina i Cirurgia, Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 4, 43007 Tarragona, Spain; (L.B.); (C.A.); (C.R.)
| | - Jessica Binetti
- Servei Medicina Interna, Hospital Universitari Joan XXIII, Universitat Rovira i Virgili, 4, 43007 Tarragona, Spain; (B.V.); (J.B.); (M.R.); (D.R.)
| | - Salomé Martínez
- Servei Anatomia Patològica, Hospital Universitari Joan XXIII Tarragona, 4, 43007 Tarragona, Spain;
| | - Fàtima Sabench
- Servei de Cirurgia, Hospital Sant Joan de Reus, Institut d’Investigació Sanitària Pere Virgili. Avinguda, Departament de Medicina i Cirurgia, Universitat Rovira i Virgili, 2, 43204 Reus, Spain; (F.S.); (M.P.); (D.D.C.)
| | - Monica Real
- Servei Medicina Interna, Hospital Universitari Joan XXIII, Universitat Rovira i Virgili, 4, 43007 Tarragona, Spain; (B.V.); (J.B.); (M.R.); (D.R.)
| | - David Riesco
- Servei Medicina Interna, Hospital Universitari Joan XXIII, Universitat Rovira i Virgili, 4, 43007 Tarragona, Spain; (B.V.); (J.B.); (M.R.); (D.R.)
| | - Marta París
- Servei de Cirurgia, Hospital Sant Joan de Reus, Institut d’Investigació Sanitària Pere Virgili. Avinguda, Departament de Medicina i Cirurgia, Universitat Rovira i Virgili, 2, 43204 Reus, Spain; (F.S.); (M.P.); (D.D.C.)
| | - Daniel Del Castillo
- Servei de Cirurgia, Hospital Sant Joan de Reus, Institut d’Investigació Sanitària Pere Virgili. Avinguda, Departament de Medicina i Cirurgia, Universitat Rovira i Virgili, 2, 43204 Reus, Spain; (F.S.); (M.P.); (D.D.C.)
| | - Cristóbal Richart
- Grup d’Estudi de Malalties Metabòliques associades a Insulino Resistència (GEMMAIR)–AGAUR, Departament de Medicina i Cirurgia, Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 4, 43007 Tarragona, Spain; (L.B.); (C.A.); (C.R.)
| | - Teresa Auguet
- Servei Medicina Interna, Hospital Universitari Joan XXIII, Universitat Rovira i Virgili, 4, 43007 Tarragona, Spain; (B.V.); (J.B.); (M.R.); (D.R.)
- Grup d’Estudi de Malalties Metabòliques associades a Insulino Resistència (GEMMAIR)–AGAUR, Departament de Medicina i Cirurgia, Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 4, 43007 Tarragona, Spain; (L.B.); (C.A.); (C.R.)
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13
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Wang F, Zhang L, Xu Y, Xie Y, Li S. Comprehensive Analysis and Identification of Key Driver Genes for Distinguishing Between Esophageal Adenocarcinoma and Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:676156. [PMID: 34124063 PMCID: PMC8194272 DOI: 10.3389/fcell.2021.676156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/09/2021] [Indexed: 01/01/2023] Open
Abstract
Background: Esophageal cancer (EC) is one of the deadliest cancers in the world. However, the mechanism that drives the evolution of EC is still unclear. On this basis, we identified the key genes and molecular pathways that may be related to the progression of esophageal adenocarcinoma and squamous cell carcinoma to find potential markers or therapeutic targets. Methods: GSE26886 were obtained from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) among normal samples, EA, and squamous cell carcinoma were determined using R software. Then, potential functions of DEGs were determined using the Database for Annotation, Visualization and Integrated Discovery (DAVID). The STRING software was used to identify the most important modules in the protein-protein interaction (PPI) network. The expression levels of hub genes were confirmed using UALCAN database. Kaplan-Meier plotters were used to confirm the correlation between hub genes and outcomes in EC. Results: In this study, we identified 1,098 genes induced in esophageal adenocarcinoma (EA) and esophageal squamous cell carcinoma (ESCC), and 669 genes were reduced in EA and ESCC, suggesting that these genes may play an important role in the occurrence and development of EC tumors. Bioinformatics analysis showed that these genes were involved in cell cycle regulation and p53 and phosphoinositide 3-kinase (PI3K)/Akt signaling pathway. In addition, we identified 147 induced genes and 130 reduced genes differentially expressed in EA and ESCC. The expression of ESCC in the EA group was different from that in the control group. By PPI network analysis, we identified 10 hub genes, including GNAQ, RGS5, MAPK1, ATP1B1, HADHA, HSDL2, SLC25A20, ACOX1, SCP2, and NLN. TCGA validation showed that these genes were present in the dysfunctional samples between EC and normal samples and between EA and ESCC. Kaplan-Meier analysis showed that MAPK1, ACOX1, SCP2, and NLN were associated with overall survival in patients with ESCC and EA. Conclusions: In this study, we identified a series of DEGs between EC and normal samples and between EA and ESCC samples. We also identified 10 key genes involved in the EC process. We believe that this study may provide a new biomarker for the prognosis of EA and ESCC.
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Affiliation(s)
- Feng Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lan Zhang
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yue Xu
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yilin Xie
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Shenglei Li
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
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14
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Peptidomic profiling of cerebrospinal fluid from patients with intracranial saccular aneurysms. J Proteomics 2021; 240:104188. [PMID: 33781962 DOI: 10.1016/j.jprot.2021.104188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 01/05/2023]
Abstract
Intracranial saccular aneurysms (ISA) represent 90%-95% of all intracranial aneurysm cases, characterizing abnormal pockets at arterial branch points. Ruptures lead to subarachnoid hemorrhages (SAH) and poor prognoses. We applied mass spectrometry-based peptidomics to investigate the peptidome of twelve cerebrospinal fluid (CSF) samples collected from eleven patients diagnosed with ISA. For peptide profile analyses, participants were classified into: 1) ruptured intracranial saccular aneurysms (RIA), 2) unruptured intracranial saccular aneurysms (UIA), and late-ruptured intracranial saccular aneurysms (LRIA). Altogether, a total of 2199 peptides were detected by both Mascot and Peaks software, from which 484 (22.0%) were unique peptides. All unique peptides presented conserved chains, domains, regions of protein modulation and/or post-translational modification sites related to human diseases. Gene Ontology (GO) analyses of peptide precursor proteins showed that 42% are involved in binding, 56% in cellular anatomical entities, and 39% in intercellular signaling molecules. Unique peptides identified in patients diagnosed with RIA have a larger molecular weight and a distinctive developmental process compared to UIA and LRIA (P ≤ 0.05). Continued investigations will allow the characterization of the biological and clinical significance of the peptides identified in the present study, as well as identify prototypes for peptide-based pharmacological therapies to treat ISA. SIGNIFICANCE.
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15
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Thimet Oligopeptidase Biochemical and Biological Significances: Past, Present, and Future Directions. Biomolecules 2020; 10:biom10091229. [PMID: 32847123 PMCID: PMC7565970 DOI: 10.3390/biom10091229] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/15/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
Thimet oligopeptidase (EC 3.4.24.15; EP24.15, THOP1) is a metallopeptidase ubiquitously distributed in mammalian tissues. Beyond its previously well characterized role in major histocompatibility class I (MHC-I) antigen presentation, the recent characterization of the THOP1 C57BL6/N null mice (THOP1−/−) phenotype suggests new key functions for THOP1 in hyperlipidic diet-induced obesity, insulin resistance and non-alcoholic liver steatosis. Distinctive levels of specific intracellular peptides (InPeps), genes and microRNAs were observed when comparing wild type C57BL6/N to THOP1−/− fed either standard or hyperlipidic diets. A possible novel mechanism of action was suggested for InPeps processed by THOP1, which could be modulating protein-protein interactions and microRNA processing, thus affecting the phenotype. Together, research into the biochemical and biomedical significance of THOP1 suggests that degradation by the proteasome is a step in the processing of various proteins, not merely for ending their existence. This allows many functional peptides to be generated by proteasomal degradation in order to, for example, control mRNA translation and the formation of protein complexes.
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16
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Mirali S, Schimmer AD. The role of mitochondrial proteases in leukemic cells and leukemic stem cells. Stem Cells Transl Med 2020; 9:1481-1487. [PMID: 32761807 PMCID: PMC7695628 DOI: 10.1002/sctm.20-0142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/18/2020] [Accepted: 05/30/2020] [Indexed: 12/13/2022] Open
Abstract
The biological function of most mitochondrial proteases has not been well characterized. Moreover, most of the available information on the normal function of these proteases has been derived from studies in model organisms. Recently, the mitochondrial proteases caseinolytic protease P (CLPP) and neurolysin (NLN) have been identified as therapeutic targets in acute myeloid leukemia (AML). Both proteases are overexpressed in approximately 40% of AML patients. Mechanistically, CLPP and NLN maintain the integrity of the mitochondrial respiratory chain: CLPP cleaves defective respiratory chain proteins, while NLN promotes the formation of respiratory chain supercomplexes. In this review, we highlight the functional consequences of inhibiting and activating mitochondrial proteases and discuss their potential as therapeutic targets in AML.
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Affiliation(s)
- Sara Mirali
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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17
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Abstract
We recently identified the mitochondrial peptidase, neurolysin (NLN), as a top hit in an acute myeloid leukemia (AML) viability screen. Using chemical and genetic approaches, we demonstrated that loss of NLN disrupted respiratory chain supercomplex assembly and impaired oxidative metabolism in AML. Moreover, inhibition of NLN in vitro and in vivo reduced the growth of AML cells.
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Affiliation(s)
- Sara Mirali
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medicine, Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Aaron D Schimmer
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medicine, Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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18
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The Relevance of Thimet Oligopeptidase in the Regulation of Energy Metabolism and Diet-Induced Obesity. Biomolecules 2020; 10:biom10020321. [PMID: 32079362 PMCID: PMC7072564 DOI: 10.3390/biom10020321] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
Thimet oligopeptidase (EC 3.4.24.15; EP24.15; THOP1) is a potential therapeutic target, as it plays key biological functions in processing biologically functional peptides. The structural conformation of THOP1 provides a unique restriction regarding substrate size, in that it only hydrolyzes peptides (optimally, those ranging from eight to 12 amino acids) and not proteins. The proteasome activity of hydrolyzing proteins releases a large number of intracellular peptides, providing THOP1 substrates within cells. The present study aimed to investigate the possible function of THOP1 in the development of diet-induced obesity (DIO) and insulin resistance by utilizing a murine model of hyperlipidic DIO with both C57BL6 wild-type (WT) and THOP1 null (THOP1−/−) mice. After 24 weeks of being fed a hyperlipidic diet (HD), THOP1−/− and WT mice ingested similar chow and calories; however, the THOP1−/− mice gained 75% less body weight and showed neither insulin resistance nor non-alcoholic fatty liver steatosis when compared to WT mice. THOP1−/− mice had increased adrenergic-stimulated adipose tissue lipolysis as well as a balanced level of expression of genes and microRNAs associated with energy metabolism, adipogenesis, or inflammation. Altogether, these differences converge to a healthy phenotype of THOP1−/− fed a HD. The molecular mechanism that links THOP1 to energy metabolism is suggested herein to involve intracellular peptides, of which the relative levels were identified to change in the adipose tissue of WT and THOP1−/− mice. Intracellular peptides were observed by molecular modeling to interact with both pre-miR-143 and pre-miR-222, suggesting a possible novel regulatory mechanism for gene expression. Therefore, we successfully demonstrated the previously anticipated relevance of THOP1 in energy metabolism regulation. It was suggested that intracellular peptides were responsible for mediating the phenotypic differences that are described herein by a yet unknown mechanism of action.
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19
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Jia C, Li C, Fu D, Chu M, Zan L, Wang H, Liang C, Yan P. Identification of genetic loci associated with growth traits at weaning in yak through a genome-wide association study. Anim Genet 2019; 51:300-305. [PMID: 31877578 DOI: 10.1111/age.12897] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2019] [Indexed: 12/18/2022]
Abstract
A multilocus GWAS was performed to explore the genetic architecture of four growth traits in yak. In total, 354 female yaks for which measurements of body weight (BW), withers height (WH), body length (BL) and chest girth (CG) at weaning were available underwent genotyping with the Illumina BovineHD BeadChip (770K). After quality control, we retained 98 688 SNPs and 354 animals for GWAS analysis. We identified seven, 18, seven and nine SNPs (corresponding to seven, 17, seven and eight candidate genes) associated with BW, WH, BL and CG at weaning respectively. Interestingly, most of these candidate genes were reported to be involved in growth-related processes such as muscle formation, lipid deposition, feed efficiency, carcass composition and development of the central and peripheral nervous system. Our results offer novel insight into the molecular architecture underpinning yak growth traits. Further functional analyses are thus warranted to explore the molecular mechanisms whereby these genes affect these traits of interest.
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Affiliation(s)
- C Jia
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - C Li
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - D Fu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - M Chu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - L Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - H Wang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - C Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - P Yan
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
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20
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Thimet Oligopeptidase (EC 3.4.24.15) Key Functions Suggested by Knockout Mice Phenotype Characterization. Biomolecules 2019; 9:biom9080382. [PMID: 31431000 PMCID: PMC6722639 DOI: 10.3390/biom9080382] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 12/14/2022] Open
Abstract
Thimet oligopeptidase (THOP1) is thought to be involved in neuropeptide metabolism, antigen presentation, neurodegeneration, and cancer. Herein, the generation of THOP1 C57BL/6 knockout mice (THOP1−/−) is described showing that they are viable, have estrus cycle, fertility, and a number of puppies per litter similar to C57BL/6 wild type mice (WT). In specific brain regions, THOP1-/- exhibit altered mRNA expression of proteasome beta5, serotonin 5HT2a receptor and dopamine D2 receptor, but not of neurolysin (NLN). Peptidomic analysis identifies differences in intracellular peptide ratios between THOP1-/- and WT mice, which may affect normal cellular functioning. In an experimental model of multiple sclerosis THOP1-/- mice present worse clinical behavior scores compared to WT mice, corroborating its possible involvement in neurodegenerative diseases. THOP1-/- mice also exhibit better survival and improved behavior in a sepsis model, but also a greater peripheral pain sensitivity measured in the hot plate test after bradykinin administration in the paw. THOP1-/- mice show depressive-like behavior, as well as attention and memory retention deficits. Altogether, these results reveal a role of THOP1 on specific behaviors, immune-stimulated neurodegeneration, and infection-induced inflammation.
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21
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de Araujo CB, Heimann AS, Remer RA, Russo LC, Colquhoun A, Forti FL, Ferro ES. Intracellular Peptides in Cell Biology and Pharmacology. Biomolecules 2019; 9:biom9040150. [PMID: 30995799 PMCID: PMC6523763 DOI: 10.3390/biom9040150] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/02/2019] [Accepted: 04/12/2019] [Indexed: 12/11/2022] Open
Abstract
Intracellular peptides are produced by proteasomes following degradation of nuclear, cytosolic, and mitochondrial proteins, and can be further processed by additional peptidases generating a larger pool of peptides within cells. Thousands of intracellular peptides have been sequenced in plants, yeast, zebrafish, rodents, and in human cells and tissues. Relative levels of intracellular peptides undergo changes in human diseases and also when cells are stimulated, corroborating their biological function. However, only a few intracellular peptides have been pharmacologically characterized and their biological significance and mechanism of action remains elusive. Here, some historical and general aspects on intracellular peptides' biology and pharmacology are presented. Hemopressin and Pep19 are examples of intracellular peptides pharmacologically characterized as inverse agonists to cannabinoid type 1 G-protein coupled receptors (CB1R), and hemopressin fragment NFKF is shown herein to attenuate the symptoms of pilocarpine-induced epileptic seizures. Intracellular peptides EL28 (derived from proteasome 26S protease regulatory subunit 4; Rpt2), PepH (derived from Histone H2B type 1-H), and Pep5 (derived from G1/S-specific cyclin D2) are examples of peptides that function intracellularly. Intracellular peptides are suggested as biological functional molecules, and are also promising prototypes for new drug development.
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Affiliation(s)
- Christiane B de Araujo
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Butantan Institute, São Paulo SP 05503-900, Brazil.
| | | | | | - Lilian C Russo
- Department of Biochemistry, Chemistry Institute, University of São Paulo 1111, São Paulo 05508-000, Brazil.
| | - Alison Colquhoun
- Department of Cell and Developmental Biology, University of São Paulo (USP), São Paulo 05508-000, Brazil.
| | - Fábio L Forti
- Department of Biochemistry, Chemistry Institute, University of São Paulo 1111, São Paulo 05508-000, Brazil.
| | - Emer S Ferro
- Department of Pharmacology, Biomedical Sciences Institute, University of São Paulo (USP), São Paulo 05508-000, Brazil.
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22
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Jeong H, Moye LS, Southey BR, Hernandez AG, Dripps I, Romanova EV, Rubakhin SS, Sweedler JV, Pradhan AA, Rodriguez-Zas SL. Gene Network Dysregulation in the Trigeminal Ganglia and Nucleus Accumbens of a Model of Chronic Migraine-Associated Hyperalgesia. Front Syst Neurosci 2018; 12:63. [PMID: 30618656 PMCID: PMC6305622 DOI: 10.3389/fnsys.2018.00063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/03/2018] [Indexed: 12/28/2022] Open
Abstract
The pharmacological agent nitroglycerin (NTG) elicits hyperalgesia and allodynia in mice. This model has been used to study the neurological disorder of trigeminovascular pain or migraine, a debilitating form of hyperalgesia. The present study validates hyperalgesia in an established mouse model of chronic migraine triggered by NTG and advances the understanding of the associated molecular mechanisms. The RNA-seq profiles of two nervous system regions associated with pain, the trigeminal ganglia (TG) and the nucleus accumbens (NAc), were compared in mice receiving chronic NTG treatment relative to control (CON) mice. Among the 109 genes that exhibited an NTG treatment-by-region interaction, solute carrier family 32 (GABA vesicular transporter) member 1 (Slc32a1) and preproenkephalin (Penk) exhibited reversal of expression patterns between the NTG and CON groups. Erb-b2 receptor tyrosine kinase 4 (Erbb4) and solute carrier family 1 (glial high affinity glutamate transporter) member 2 (Slc1a2) exhibited consistent differential expression between treatments across regions albeit at different magnitude. Period circadian clock 1 (Per1) was among the 165 genes that exhibited significant NTG treatment effect. Biological processes disrupted by NTG in a region-specific manner included adaptive and innate immune responses; whereas glutamatergic and dopaminergic synapses and rhythmic process were disrupted in both regions. Regulatory network reconstruction highlighted the widespread role of several transcription factors (including Snrnp70, Smad1, Pax6, Cebpa, and Smpx) among the NTG-disrupted target genes. These results advance the understanding of the molecular mechanisms of hyperalgesia that can be applied to therapies to ameliorate chronic pain and migraine.
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Affiliation(s)
- Hyeonsoo Jeong
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Laura S. Moye
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States
| | - Bruce R. Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Alvaro G. Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Isaac Dripps
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States
| | - Elena V. Romanova
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Stanislav S. Rubakhin
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Amynah A. Pradhan
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States
| | - Sandra L. Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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23
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Gonzales NM, Seo J, Hernandez Cordero AI, St Pierre CL, Gregory JS, Distler MG, Abney M, Canzar S, Lionikas A, Palmer AA. Genome wide association analysis in a mouse advanced intercross line. Nat Commun 2018; 9:5162. [PMID: 30514929 PMCID: PMC6279738 DOI: 10.1038/s41467-018-07642-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022] Open
Abstract
The LG/J x SM/J advanced intercross line of mice (LG x SM AIL) is a multigenerational outbred population. High minor allele frequencies, a simple genetic background, and the fully sequenced LG and SM genomes make it a powerful population for genome-wide association studies. Here we use 1,063 AIL mice to identify 126 significant associations for 50 traits relevant to human health and disease. We also identify thousands of cis- and trans-eQTLs in the hippocampus, striatum, and prefrontal cortex of ~200 mice. We replicate an association between locomotor activity and Csmd1, which we identified in an earlier generation of this AIL, and show that Csmd1 mutant mice recapitulate the locomotor phenotype. Our results demonstrate the utility of the LG x SM AIL as a mapping population, identify numerous novel associations, and shed light on the genetic architecture of mammalian behavior.
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Affiliation(s)
- Natalia M Gonzales
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Jungkyun Seo
- Center for Genomic & Computational Biology, Duke University, Durham, NC, 27708, USA
- Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, 27708, USA
| | - Ana I Hernandez Cordero
- School of Medicine, Medical Sciences and Nutrition, College of Life Sciences and Medicine, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Celine L St Pierre
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Jennifer S Gregory
- School of Medicine, Medical Sciences and Nutrition, College of Life Sciences and Medicine, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Margaret G Distler
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Mark Abney
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Stefan Canzar
- Gene Center, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Arimantas Lionikas
- School of Medicine, Medical Sciences and Nutrition, College of Life Sciences and Medicine, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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24
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Giant tortoise genomes provide insights into longevity and age-related disease. Nat Ecol Evol 2018; 3:87-95. [PMID: 30510174 PMCID: PMC6314442 DOI: 10.1038/s41559-018-0733-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 10/25/2018] [Indexed: 12/21/2022]
Abstract
Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George-the iconic last member of Chelonoidis abingdonii-and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations.
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25
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Neurolysin: From Initial Detection to Latest Advances. Neurochem Res 2018; 43:2017-2024. [DOI: 10.1007/s11064-018-2624-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/22/2018] [Accepted: 08/27/2018] [Indexed: 01/20/2023]
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26
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Nakashima Y, Miyagi-Shiohira C, Kobayashi N, Saitoh I, Watanabe M, Noguchi H. A proteome analysis of pig pancreatic islets and exocrine tissue by liquid chromatography with tandem mass spectrometry. Islets 2017; 9:159-176. [PMID: 29099648 PMCID: PMC5710700 DOI: 10.1080/19382014.2017.1389826] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liquid chromatography with tandem mass spectrometry (LC-MS/MS) is a proteome analysis method, and the shotgun analysis by LC-MS/MS comprehensively identifies proteins from tissues and cells with high resolving power. In this study, we analyzed the protein expression in pancreatic tissue by LC-MS/MS. Islets isolated from porcine pancreata (purity ≥95%) and exocrine tissue (purity ≥99%) were used in this study. LC-MS/MS showed that 13 proteins were expressed in pancreatic islets only (Group I), 43 proteins were expressed in both islets and exocrine tissue (Group I&E), and 102 proteins were expressed in exocrine tissue only (Group E). Proteins involved in islet differentiation and cell proliferation were identified in Group I (e.g. CLUS, CMGA, MIF). In addition, various functional proteins (e.g. SCG2, TBA1A) were identified in islet by using the new method of 'principal component analysis (PCA)'. However, the function of such proteins on islets remains unclear. EPCAM was identified in Group E. Group E was found to include proteins involved in clinical inflammatory diseases such as pancreatitis (e.g. CBPA1, CGL, CYTB, ISK1 and PA21B). Many of these identified proteins were reported less frequently in previous studies, and HS71B, NEC2, PRAF3 and SCG1 were newly detected in Group I while CPNS1, DPEP1, GANAB, GDIB, GGT1, HSPB1, ICTL, VILI, MUTA, NDKB, PTGR1, UCHL3, VAPB and VINC were newly detected in Group E. These results show that comprehensive expression analysis of proteins by LC-MS/MS is useful as a method to investigate new factors constructing cellular component, biological process, and molecular function.
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Affiliation(s)
- Yoshiki Nakashima
- Department of Regenerative Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Chika Miyagi-Shiohira
- Department of Regenerative Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | | | - Issei Saitoh
- Division of Pediatric Dentistry, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Masami Watanabe
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hirofumi Noguchi
- Department of Regenerative Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
- CONTACT Hirofumi Noguchi Department of Regenerative Medicine, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan
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27
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Onagi J, Komatsu T, Ichihashi Y, Kuriki Y, Kamiya M, Terai T, Ueno T, Hanaoka K, Matsuzaki H, Hata K, Watanabe T, Nagano T, Urano Y. Discovery of Cell-Type-Specific and Disease-Related Enzymatic Activity Changes via Global Evaluation of Peptide Metabolism. J Am Chem Soc 2017; 139:3465-3472. [PMID: 28191944 DOI: 10.1021/jacs.6b11376] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cellular homeostasis is maintained by a complex network of reactions catalyzed by enormous numbers of enzymatic activities (the enzymome), which serve to determine the phenotypes of cells. Here, we focused on the enzymomics of proteases and peptidases because these enzymes are an important class of disease-related proteins. We describe a system that (A) simultaneously evaluates metabolic activities of peptides using a series of exogenous peptide substrates and (B) identifies the enzymes that metabolize the specified peptide substrate with high throughput. We confirmed that the developed system was able to discover cell-type-specific and disease-related exo- and endopeptidase activities and identify the responsible enzymes. For example, we found that the activity of the endopeptidase neurolysin is highly elevated in human colorectal tumor tissue samples. This simple but powerful enzymomics platform should be widely applicable to uncover cell-type-specific reactions and altered enzymatic functions with potential value as biomarkers or drug targets in various disease states and to investigate the mechanisms of the underlying pathologies.
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Affiliation(s)
| | - Toru Komatsu
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | | | | | - Mako Kamiya
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | | | | | | | | | | | | | | | - Yasuteru Urano
- Core Research for Evolutional Science and Technology (CREST) Investigator, Japan Agency for Medical Research and Development (AMED) , 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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28
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Monte ER, Rossato C, Llanos RP, Russo LC, de Castro LM, Gozzo FC, de Araujo CB, Peron JPS, Sant'Anna OA, Ferro ES, Rioli V. Interferon-gamma activity is potentiated by an intracellular peptide derived from the human 19S ATPase regulatory subunit 4 of the proteasome. J Proteomics 2017; 151:74-82. [DOI: 10.1016/j.jprot.2016.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/20/2016] [Accepted: 08/04/2016] [Indexed: 11/24/2022]
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29
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Preparation and preliminary characterization of recombinant neurolysin for in vivo studies. J Biotechnol 2016; 234:105-115. [PMID: 27496565 DOI: 10.1016/j.jbiotec.2016.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/05/2016] [Accepted: 07/11/2016] [Indexed: 11/23/2022]
Abstract
The goal of this study was to produce milligram quantities of pure, catalytically active, endotoxin-free recombinant neurolysin (rNln) in standard laboratory conditions for use as a research tool. To this end, we transformed E. coli cells with a plasmid construct for polyhistidine-tagged rNln, selected a high-expressing clone and determined the optimal time-point for translation of rNln. rNln was purified to homogeneity from the soluble pool of the cell lysate using Ni-NTA affinity and size-exclusion chromatography, followed by removal of endotoxins. Using this protocol ∼3mg pure, catalytically active and nearly endotoxin-free (≈0.003EU/μg protein) rNln was reproducibly obtained from 1l of culture. Lack of cytotoxicity of rNln preparation was documented in cultured mouse cells, whereas stability in whole mouse blood. Intraperitonealy administered rNln in mice reached the systemic circulation in intact and enzymatically active form with Tmax of 1h and T1/2 of ∼30min. Administration of rNln (2 and 10mg/kg) did not alter arterial blood pressure, heart rate, body temperature and blood glucose levels in mice. These studies demonstrate that the rNln preparation is suitable for cell culture and in vivo studies and can serve as a research tool to investigate the (patho)physiological function of this peptidase.
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30
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Holder JL, Cheung SW. Refinement of the postnatal growth restriction locus of chromosome 5q12-13 deletion syndrome. Am J Med Genet A 2015; 167A:2737-41. [PMID: 26138022 DOI: 10.1002/ajmg.a.37228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 06/11/2015] [Indexed: 11/05/2022]
Abstract
Individuals with deletions of chromosome 5q12-13 have rarely been reported and have a range of phenotypes including postnatal growth restriction, intellectual disability, hyperactivity, and ocular abnormalities. Most individuals reported have large deletions or complex rearrangements which have made identifying genes responsible for these phenotypes challenging. Here we report an individual with a chromosome 5q12-13 deletion with intellectual disability, hyperactivity and restricted linear growth. Based on the location of our patient's deletion in relation to the previously reported deletions, we have narrowed the locus for postnatal growth restriction to less than 1 megabase. Further refinement of this locus with reports of additional individuals with deletions of this region will allow for better understanding of the gene(s) responsible for this phenotype.
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Affiliation(s)
- J Lloyd Holder
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Sau-Wai Cheung
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
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31
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Mousel MR, Reynolds JO, White SN. Genome-Wide Association Identifies SLC2A9 and NLN Gene Regions as Associated with Entropion in Domestic Sheep. PLoS One 2015; 10:e0128909. [PMID: 26098909 PMCID: PMC4476619 DOI: 10.1371/journal.pone.0128909] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 05/01/2015] [Indexed: 12/22/2022] Open
Abstract
Entropion is an inward rolling of the eyelid allowing contact between the eyelashes and cornea that may lead to blindness if not corrected. Although many mammalian species, including humans and dogs, are afflicted by congenital entropion, no specific genes or gene regions related to development of entropion have been reported in any mammalian species to date. Entropion in domestic sheep is known to have a genetic component therefore, we used domestic sheep as a model system to identify genomic regions containing genes associated with entropion. A genome-wide association was conducted with congenital entropion in 998 Columbia, Polypay, and Rambouillet sheep genotyped with 50,000 SNP markers. Prevalence of entropion was 6.01%, with all breeds represented. Logistic regression was performed in PLINK with additive allelic, recessive, dominant, and genotypic inheritance models. Two genome-wide significant (empirical P<0.05) SNP were identified, specifically markers in SLC2A9 (empirical P = 0.007; genotypic model) and near NLN (empirical P = 0.026; dominance model). Six additional genome-wide suggestive SNP (nominal P<1x10-5) were identified including markers in or near PIK3CB (P = 2.22x10-6; additive model), KCNB1 (P = 2.93x10-6; dominance model), ZC3H12C (P = 3.25x10-6; genotypic model), JPH1 (P = 4.68x20-6; genotypic model), and MYO3B (P = 5.74x10-6; recessive model). This is the first report of specific gene regions associated with congenital entropion in any mammalian species, to our knowledge. Further, none of these genes have previously been associated with any eyelid traits. These results represent the first genome-wide analysis of gene regions associated with entropion and provide target regions for the development of sheep genetic markers for marker-assisted selection.
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Affiliation(s)
- Michelle R. Mousel
- Range Sheep Production Efficiency Research Unit, Agricultural Research Service, Department of Agriculture, Dubois, ID, United States of America
- * E-mail:
| | - James O. Reynolds
- Animal Disease Research Unit, Agricultural Research Service, Department of Agriculture, Pullman, WA, United States of America
| | - Stephen N. White
- Animal Disease Research Unit, Agricultural Research Service, Department of Agriculture, Pullman, WA, United States of America
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States of America
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32
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Nikolskiy I, Conrad DF, Chun S, Fay JC, Cheverud JM, Lawson HA. Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides. BMC Genomics 2015; 16:415. [PMID: 26016481 PMCID: PMC4445795 DOI: 10.1186/s12864-015-1592-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 04/28/2015] [Indexed: 12/04/2022] Open
Abstract
Background The laboratory mouse is the most commonly used model for studying variation in complex traits relevant to human disease. Here we present the whole-genome sequences of two inbred strains, LG/J and SM/J, which are frequently used to study variation in complex traits as diverse as aging, bone-growth, adiposity, maternal behavior, and methamphetamine sensitivity. Results We identified small nucleotide variants (SNVs) and structural variants (SVs) in the LG/J and SM/J strains relative to the reference genome and discovered novel variants in these two strains by comparing their sequences to other mouse genomes. We find that 39% of the LG/J and SM/J genomes are identical-by-descent (IBD). We characterized amino-acid changing mutations using three algorithms: LRT, PolyPhen-2 and SIFT. We also identified polymorphisms between LG/J and SM/J that fall in regulatory regions and highly informative transcription factor binding sites (TFBS). We intersected these functional predictions with quantitative trait loci (QTL) mapped in advanced intercrosses of these two strains. We find that QTL are both over-represented in non-IBD regions and highly enriched for variants predicted to have a functional impact. Variants in QTL associated with metabolic (231 QTL identified in an F16 generation) and developmental (41 QTL identified in an F34 generation) traits were interrogated and we highlight candidate quantitative trait genes (QTG) and nucleotides (QTN) in a QTL on chr13 associated with variation in basal glucose levels and in a QTL on chr6 associated with variation in tibia length. Conclusions We show how integrating genomic sequence with QTL reduces the QTL search space and helps researchers prioritize candidate genes and nucleotides for experimental follow-up. Additionally, given the LG/J and SM/J phylogenetic context among inbred strains, these data contribute important information to the genomic landscape of the laboratory mouse. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1592-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Igor Nikolskiy
- Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.
| | - Donald F Conrad
- Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.
| | - Sung Chun
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Justin C Fay
- Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.
| | | | - Heather A Lawson
- Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.
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Abstract
Recent advances in mitochondrial biology have revealed the high diversity and complexity of proteolytic enzymes that regulate mitochondrial function. We have classified mitochondrial proteases, or mitoproteases, on the basis of their function and location, and defined the human mitochondrial degradome as the complete set of mitoproteases that are encoded by the human genome. In addition to their nonspecific degradative functions, mitoproteases perform highly regulated proteolytic reactions that are important in mitochondrial function, integrity and homeostasis. These include protein synthesis, quality control, mitochondrial biogenesis and dynamics, mitophagy and apoptosis. Impaired or dysregulated function of mitoproteases is associated with ageing and with many pathological conditions such as neurodegenerative disorders, metabolic syndromes and cancer. A better understanding of the mitochondrial proteolytic landscape and its modulation may contribute to improving human lifespan and 'healthspan'.
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34
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Speth RC, Carrera EJ, Bretón C, Linares A, Gonzalez-Reiley L, Swindle JD, Santos KL, Schadock I, Bader M, Karamyan VT. Distribution of non-AT1, non-AT2 binding of 125I-sarcosine1, isoleucine8 angiotensin II in neurolysin knockout mouse brains. PLoS One 2014; 9:e105762. [PMID: 25147932 PMCID: PMC4141804 DOI: 10.1371/journal.pone.0105762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/13/2014] [Indexed: 11/18/2022] Open
Abstract
The recent identification of a novel binding site for angiotensin (Ang) II as the peptidase neurolysin (E.C. 3.4.24.16) has implications for the renin-angiotensin system (RAS). This report describes the distribution of specific binding of 125I-Sarcosine1, Isoleucine8 Ang II (125I-SI Ang II) in neurolysin knockout mouse brains compared to wild-type mouse brains using quantitative receptor autoradiography. In the presence of p-chloromercuribenzoic acid (PCMB), which unmasks the novel binding site, widespread distribution of specific (3 µM Ang II displaceable) 125I-SI Ang II binding in 32 mouse brain regions was observed. Highest levels of binding >700 fmol/g initial wet weight were seen in hypothalamic, thalamic and septal regions, while the lowest level of binding <300 fmol/g initial wet weight was in the mediolateral medulla. 125I-SI Ang II binding was substantially higher by an average of 85% in wild-type mouse brains compared to neurolysin knockout brains, suggesting the presence of an additional non-AT1, non-AT2, non-neurolysin Ang II binding site in the mouse brain. Binding of 125I-SI Ang II to neurolysin in the presence of PCMB was highest in hypothalamic and ventral cortical brain regions, but broadly distributed across all regions surveyed. Non-AT1, non-AT2, non-neurolysin binding was also highest in the hypothalamus but had a different distribution than neurolysin. There was a significant reduction in AT2 receptor binding in the neurolysin knockout brain and a trend towards decreased AT1 receptor binding. In the neurolysin knockout brains, the size of the lateral ventricles was increased by 56% and the size of the mid forebrain (−2.72 to +1.48 relative to Bregma) was increased by 12%. These results confirm the identity of neurolysin as a novel Ang II binding site, suggesting that neurolysin may play a significant role in opposing the pathophysiological actions of the brain RAS and influencing brain morphology.
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Affiliation(s)
- Robert C. Speth
- Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Eduardo J. Carrera
- Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
- Farquhar College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
| | - Catalina Bretón
- Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
- Farquhar College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
| | - Andrea Linares
- Farquhar College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
| | - Luz Gonzalez-Reiley
- Farquhar College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
| | - Jamala D. Swindle
- Farquhar College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
| | - Kira L. Santos
- Farquhar College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
- College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Ines Schadock
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Michael Bader
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Vardan T. Karamyan
- Department of Pharmaceutical Sciences, Texas Tech University Health Sciences Center, Amarillo, Texas, United States of America
- Center for Blood-Brain Barrier Research, Texas Tech University Health Sciences Center, Amarillo, Texas, United States of America
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