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Mailhot B, Christin M, Tessandier N, Sotoudeh C, Bretheau F, Turmel R, Pellerin È, Wang F, Bories C, Joly-Beauparlant C, De Koninck Y, Droit A, Cicchetti F, Scherrer G, Boilard E, Sharif-Naeini R, Lacroix S. Neuronal interleukin-1 receptors mediate pain in chronic inflammatory diseases. J Exp Med 2021; 217:151879. [PMID: 32573694 PMCID: PMC7478735 DOI: 10.1084/jem.20191430] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 03/03/2020] [Accepted: 05/13/2020] [Indexed: 12/20/2022] Open
Abstract
Chronic pain is a major comorbidity of chronic inflammatory diseases. Here, we report that the cytokine IL-1β, which is abundantly produced during multiple sclerosis (MS), arthritis (RA), and osteoarthritis (OA) both in humans and in animal models, drives pain associated with these diseases. We found that the type 1 IL-1 receptor (IL-1R1) is highly expressed in the mouse and human by a subpopulation of TRPV1+ dorsal root ganglion neurons specialized in detecting painful stimuli, termed nociceptors. Strikingly, deletion of the Il1r1 gene specifically in TRPV1+ nociceptors prevented the development of mechanical allodynia without affecting clinical signs and disease progression in mice with experimental autoimmune encephalomyelitis and K/BxN serum transfer–induced RA. Conditional restoration of IL-1R1 expression in nociceptors of IL-1R1–knockout mice induced pain behavior but did not affect joint damage in monosodium iodoacetate–induced OA. Collectively, these data reveal that neuronal IL-1R1 signaling mediates pain, uncovering the potential benefit of anti–IL-1 therapies for pain management in patients with chronic inflammatory diseases.
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Affiliation(s)
- Benoit Mailhot
- Axe Neurosciences du Centre de recherche du CHU de Québec-Université Laval et Département de médecine moléculaire de l'Université Laval, Québec, Canada
| | - Marine Christin
- Department of Physiology and Cell Information Systems Group, McGill University, Montreal, Canada
| | - Nicolas Tessandier
- Axe Maladies infectieuses et immunitaires du Centre de recherche du CHU de Québec-Université Laval et Département de microbiologie-infectiologie et d'immunologie de l'Université Laval, Québec, Canada
| | - Chaudy Sotoudeh
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Palo Alto, CA
| | - Floriane Bretheau
- Axe Neurosciences du Centre de recherche du CHU de Québec-Université Laval et Département de médecine moléculaire de l'Université Laval, Québec, Canada
| | - Roxanne Turmel
- Axe Neurosciences du Centre de recherche du CHU de Québec-Université Laval et Département de médecine moléculaire de l'Université Laval, Québec, Canada
| | - Ève Pellerin
- Axe Neurosciences du Centre de recherche du CHU de Québec-Université Laval et Département de médecine moléculaire de l'Université Laval, Québec, Canada
| | - Feng Wang
- Centre de recherche CERVO, Québec, Canada
| | | | - Charles Joly-Beauparlant
- Axe Endocrinologie-néphrologie du Centre de recherche du CHU de Québec-Université Laval et Département de médecine moléculaire de l'Université Laval, Québec, Canada
| | | | - Arnaud Droit
- Axe Endocrinologie-néphrologie du Centre de recherche du CHU de Québec-Université Laval et Département de médecine moléculaire de l'Université Laval, Québec, Canada
| | - Francesca Cicchetti
- Axe Neurosciences du Centre de recherche du CHU de Québec-Université Laval et Département de psychiatrie et de neurosciences de l'Université Laval, Québec, Canada
| | - Grégory Scherrer
- Department of Cell Biology and Physiology, University of North Carolina Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC.,New York Stem Cell Foundation - Robertson Investigator, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Eric Boilard
- Axe Maladies infectieuses et immunitaires du Centre de recherche du CHU de Québec-Université Laval et Département de microbiologie-infectiologie et d'immunologie de l'Université Laval, Québec, Canada
| | - Reza Sharif-Naeini
- Department of Physiology and Cell Information Systems Group, McGill University, Montreal, Canada
| | - Steve Lacroix
- Axe Neurosciences du Centre de recherche du CHU de Québec-Université Laval et Département de médecine moléculaire de l'Université Laval, Québec, Canada
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52
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Torres MDT, Cao J, Franco OL, Lu TK, de la Fuente-Nunez C. Synthetic Biology and Computer-Based Frameworks for Antimicrobial Peptide Discovery. ACS NANO 2021; 15:2143-2164. [PMID: 33538585 PMCID: PMC8734659 DOI: 10.1021/acsnano.0c09509] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Antibiotic resistance is one of the greatest challenges of our time. This global health problem originated from a paucity of truly effective antibiotic classes and an increased incidence of multi-drug-resistant bacterial isolates in hospitals worldwide. Indeed, it has been recently estimated that 10 million people will die annually from drug-resistant infections by the year 2050. Therefore, the need to develop out-of-the-box strategies to combat antibiotic resistance is urgent. The biological world has provided natural templates, called antimicrobial peptides (AMPs), which exhibit multiple intrinsic medical properties including the targeting of bacteria. AMPs can be used as scaffolds and, via engineering, can be reconfigured for optimized potency and targetability toward drug-resistant pathogens. Here, we review the recent development of tools for the discovery, design, and production of AMPs and propose that the future of peptide drug discovery will involve the convergence of computational and synthetic biology principles.
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Affiliation(s)
- Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jicong Cao
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Octavio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, DF 70790160, Brazil
- S-inova Biotech, Universidade Católica Dom Bosco, Campo Grande, MS 79117010, Brazil
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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53
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DeLaney K, Hu M, Hellenbrand T, Dickinson PS, Nusbaum MP, Li L. Mass Spectrometry Quantification, Localization, and Discovery of Feeding-Related Neuropeptides in Cancer borealis. ACS Chem Neurosci 2021; 12:782-798. [PMID: 33522802 DOI: 10.1021/acschemneuro.1c00007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The crab Cancer borealis nervous system is an important model for understanding neural circuit dynamics and modulation, but the identity of neuromodulatory substances and their influence on circuit dynamics in this system remains incomplete, particularly with respect to behavioral state-dependent modulation. Therefore, we used a multifaceted mass spectrometry (MS) method to identify neuropeptides that differentiate the unfed and fed states. Duplex stable isotope labeling revealed that the abundance of 80 of 278 identified neuropeptides was distinct in ganglia and/or neurohemal tissue from fed vs unfed animals. MS imaging revealed that an additional 7 and 11 neuropeptides exhibited altered spatial distributions in the brain and the neuroendocrine pericardial organs (POs), respectively, during these two feeding states. Furthermore, de novo sequencing yielded 69 newly identified putative neuropeptides that may influence feeding state-related neuromodulation. Two of these latter neuropeptides were determined to be upregulated in PO tissue from fed crabs, and one of these two peptides influenced heartbeat in ex vivo preparations. Overall, the results presented here identify a cohort of neuropeptides that are poised to influence feeding-related behaviors, providing valuable opportunities for future functional studies.
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Affiliation(s)
- Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Mengzhou Hu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, United States
| | - Tessa Hellenbrand
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Patsy S. Dickinson
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, Maine 04011, United States
| | - Michael P. Nusbaum
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, 211 Clinical Research Building, 415 Curie Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, United States
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54
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Molecular characterization of the stress network in individuals at risk for schizophrenia. Neurobiol Stress 2021; 14:100307. [PMID: 33644266 PMCID: PMC7893486 DOI: 10.1016/j.ynstr.2021.100307] [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: 07/09/2020] [Revised: 01/14/2021] [Accepted: 02/03/2021] [Indexed: 01/24/2023] Open
Abstract
The biological mechanisms underlying inter-individual differences in human stress reactivity remain poorly understood. We aimed to identify the molecular underpinning of aberrant neural stress sensitivity in individuals at risk for schizophrenia. Linking mRNA expression data from the Allen Human Brain Atlas to task-based fMRI revealed 201 differentially expressed genes in cortex-specific brain regions differentially activated by stress in individuals with low (healthy siblings of schizophrenia patients) or high (healthy controls) stress sensitivity. These genes are associated with stress-related psychiatric disorders (e.g. schizophrenia and anxiety) and include markers for specific neuronal populations (e.g. ADCYAP1, GABRB1, SSTR1, and TNFRSF12A), neurotransmitter receptors (e.g. GRIN3A, SSTR1, GABRB1, and HTR1E), and signaling factors that interact with the corticosteroid receptor and hypothalamic-pituitary-adrenal axis (e.g. ADCYAP1, IGSF11, and PKIA). Overall, the identified genes potentially underlie altered stress reactivity in individuals at risk for schizophrenia and other psychiatric disorders and play a role in mounting an adaptive stress response in at-risk individuals, making them potentially druggable targets for stress-related diseases.
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55
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Lee EY, Chan LC, Wang H, Lieng J, Hung M, Srinivasan Y, Wang J, Waschek JA, Ferguson AL, Lee KF, Yount NY, Yeaman MR, Wong GCL. PACAP is a pathogen-inducible resident antimicrobial neuropeptide affording rapid and contextual molecular host defense of the brain. Proc Natl Acad Sci U S A 2021; 118:e1917623117. [PMID: 33372152 PMCID: PMC7817161 DOI: 10.1073/pnas.1917623117] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Defense of the central nervous system (CNS) against infection must be accomplished without generation of potentially injurious immune cell-mediated or off-target inflammation which could impair key functions. As the CNS is an immune-privileged compartment, inducible innate defense mechanisms endogenous to the CNS likely play an essential role in this regard. Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide known to regulate neurodevelopment, emotion, and certain stress responses. While PACAP is known to interact with the immune system, its significance in direct defense of brain or other tissues is not established. Here, we show that our machine-learning classifier can screen for immune activity in neuropeptides, and correctly identified PACAP as an antimicrobial neuropeptide in agreement with previous experimental work. Furthermore, synchrotron X-ray scattering, antimicrobial assays, and mechanistic fingerprinting provided precise insights into how PACAP exerts antimicrobial activities vs. pathogens via multiple and synergistic mechanisms, including dysregulation of membrane integrity and energetics and activation of cell death pathways. Importantly, resident PACAP is selectively induced up to 50-fold in the brain in mouse models of Staphylococcus aureus or Candida albicans infection in vivo, without inducing immune cell infiltration. We show differential PACAP induction even in various tissues outside the CNS, and how these observed patterns of induction are consistent with the antimicrobial efficacy of PACAP measured in conditions simulating specific physiologic contexts of those tissues. Phylogenetic analysis of PACAP revealed close conservation of predicted antimicrobial properties spanning primitive invertebrates to modern mammals. Together, these findings substantiate our hypothesis that PACAP is an ancient neuro-endocrine-immune effector that defends the CNS against infection while minimizing potentially injurious neuroinflammation.
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Affiliation(s)
- Ernest Y Lee
- Department of Bioengineering, University of California, Los Angeles, CA 90095
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095
| | - Liana C Chan
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA 90509
- Division of Molecular Medicine, Los Angeles County, Harbor-UCLA Medical Center, Torrance, CA 90509
- Division of Infectious Diseases, Los Angeles County, Harbor-UCLA Medical Center, Torrance, CA 90509
| | - Huiyuan Wang
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA 90509
- Division of Molecular Medicine, Los Angeles County, Harbor-UCLA Medical Center, Torrance, CA 90509
| | - Juelline Lieng
- Department of Bioengineering, University of California, Los Angeles, CA 90095
| | - Mandy Hung
- Department of Bioengineering, University of California, Los Angeles, CA 90095
| | - Yashes Srinivasan
- Department of Bioengineering, University of California, Los Angeles, CA 90095
| | - Jennifer Wang
- Department of Bioengineering, University of California, Los Angeles, CA 90095
| | - James A Waschek
- Semel Institute for Neuroscience and Human Behavior, Intellectual Development and Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637
| | - Kuo-Fen Lee
- Peptide Biology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Nannette Y Yount
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA 90509
- Division of Molecular Medicine, Los Angeles County, Harbor-UCLA Medical Center, Torrance, CA 90509
| | - Michael R Yeaman
- Division of Molecular Medicine, Los Angeles County, Harbor-UCLA Medical Center, Torrance, CA 90509;
- Division of Infectious Diseases, Los Angeles County, Harbor-UCLA Medical Center, Torrance, CA 90509
- Semel Institute for Neuroscience and Human Behavior, Intellectual Development and Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, CA 90095;
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
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56
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Serafin EK, Paranjpe A, Brewer CL, Baccei ML. Single-nucleus characterization of adult mouse spinal dynorphin-lineage cells and identification of persistent transcriptional effects of neonatal hindpaw incision. Pain 2021; 162:203-218. [PMID: 33045156 PMCID: PMC7744314 DOI: 10.1097/j.pain.0000000000002007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Neonatal tissue damage can have long-lasting effects on nociceptive processing in the central nervous system, which may reflect persistent injury-evoked alterations to the normal balance between synaptic inhibition and excitation in the spinal dorsal horn. Spinal dynorphin-lineage (pDyn) neurons are part of an inhibitory circuit which limits the flow of nociceptive input to the brain and is disrupted by neonatal tissue damage. To identify the potential molecular underpinnings of this disruption, an unbiased single-nucleus RNAseq analysis of adult mouse spinal pDyn cells characterized this population in depth and then identified changes in gene expression evoked by neonatal hindpaw incision. The analysis revealed 11 transcriptionally distinct subpopulations (ie, clusters) of dynorphin-lineage cells, including both inhibitory and excitatory neurons. Investigation of injury-evoked differential gene expression identified 15 genes that were significantly upregulated or downregulated in adult pDyn neurons from neonatally incised mice compared with naive littermate controls, with both cluster-specific and pan-neuronal transcriptional changes observed. Several of the identified genes, such as Oxr1 and Fth1 (encoding ferritin), were related to the cellular stress response. However, the relatively low number of injury-evoked differentially expressed genes also suggests that posttranscriptional regulation within pDyn neurons may play a key role in the priming of developing nociceptive circuits by early-life injury. Overall, the findings reveal novel insights into the molecular heterogeneity of a key population of dorsal horn interneurons that has previously been implicated in the suppression of mechanical pain and itch.
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Affiliation(s)
- Elizabeth K Serafin
- Department of Anesthesiology, Pain Research Center, University of Cincinnati Medical Center, Cincinnati, OH, United States . Dr. Brewer is now with the Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, United States
| | - Aditi Paranjpe
- Division of Biomedical Informatics, Bioinformatics Collaborative Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Chelsie L Brewer
- Department of Anesthesiology, Pain Research Center, University of Cincinnati Medical Center, Cincinnati, OH, United States . Dr. Brewer is now with the Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, United States
- Neuroscience Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Mark L Baccei
- Department of Anesthesiology, Pain Research Center, University of Cincinnati Medical Center, Cincinnati, OH, United States . Dr. Brewer is now with the Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, United States
- Neuroscience Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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57
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Barati M, Javanmardi F, Mousavi Jazayeri SMH, Jabbari M, Rahmani J, Barati F, Nickho H, Davoodi SH, Roshanravan N, Mousavi Khaneghah A. Techniques, perspectives, and challenges of bioactive peptide generation: A comprehensive systematic review. Compr Rev Food Sci Food Saf 2020; 19:1488-1520. [PMID: 33337080 DOI: 10.1111/1541-4337.12578] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 04/03/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022]
Abstract
Due to the digestible refractory and absorbable structures of bioactive peptides (BPs), they could induce notable biological impacts on the living organism. In this regard, the current study was devoted to providing an overview regarding the available methods for BPs generation by the aid of a systematic review conducted on the published articles up to April 2019. In this context, the PubMed and Scopus databases were screened to retrieve the related publications. According to the results, although the characterization of BPs mainly has been performed using enzymatic and microbial in-vitro methods, they cannot be considered as suitable techniques for further stimulation of digestion in the gastrointestinal tract. Therefore, new approaches for both in-vivo and in-silico methods for BPs identification should be developed to overcome the obstacles that belonged to the current methods. The purpose of this review was to compile the recent analytical methods applied for studying various aspects of food-derived biopeptides, and emphasizing generation at in vitro, in vivo, and in silico.
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Affiliation(s)
- Meisam Barati
- Student Research Committee, Department of Cellular and Molecular Nutrition, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fardin Javanmardi
- Department of Food Science and Technology, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Masoumeh Jabbari
- Department of Community Nutrition, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamal Rahmani
- Department of Community Nutrition, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzaneh Barati
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Hamid Nickho
- Immunology Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sayed Hossein Davoodi
- Department of Clinical Nutrition and Dietetic, National Institute and Faculty of Nutrition and Food Technology; Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Neda Roshanravan
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amin Mousavi Khaneghah
- Department of Food Science, Faculty of Food Engineering, University of Campinas (UNICAMP), São Paulo, Brazil
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58
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Cardon T, Fournier I, Salzet M. Shedding Light on the Ghost Proteome. Trends Biochem Sci 2020; 46:239-250. [PMID: 33246829 DOI: 10.1016/j.tibs.2020.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 01/19/2023]
Abstract
Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics has led to the identification of proteins translated from alternative open reading frames (AltORFs) in mRNAs. AltORFs are found in addition to predicted reference ORFs and noncoding RNA. Alternative proteins are not represented in the conventional protein databases, and this 'Ghost proteome' was not considered until recently. Some of these proteins are functional, and there is growing evidence that they are involved in central functions in physiological and physiopathological contexts. Here, we review how this Ghost proteome fills the gap in our understanding of signaling pathways, establishes new markers of pathologies, and highlights therapeutic targets.
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Affiliation(s)
- Tristan Cardon
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France.
| | - Isabelle Fournier
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France; Institut Universitaire de France, Paris, France.
| | - Michel Salzet
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France; Institut Universitaire de France, Paris, France.
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59
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Mendel HC, Kaas Q, Muttenthaler M. Neuropeptide signalling systems - An underexplored target for venom drug discovery. Biochem Pharmacol 2020; 181:114129. [PMID: 32619425 PMCID: PMC7116218 DOI: 10.1016/j.bcp.2020.114129] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 01/06/2023]
Abstract
Neuropeptides are signalling molecules mainly secreted from neurons that act as neurotransmitters or peptide hormones to affect physiological processes and modulate behaviours. In humans, neuropeptides are implicated in numerous diseases and understanding their role in physiological processes and pathologies is important for therapeutic development. Teasing apart the (patho)physiology of neuropeptides remains difficult due to ligand and receptor promiscuity and the complexity of the signalling pathways. The current approach relies on a pharmacological toolbox of agonists and antagonists displaying high selectivity for independent receptor subtypes, with the caveat that only few selective ligands have been discovered or developed. Animal venoms represent an underexplored source for novel receptor subtype-selective ligands that could aid in dissecting human neuropeptide signalling systems. Multiple endogenous-like neuropeptides as well as peptides acting on neuropeptide receptors are present in venoms. In this review, we summarise current knowledge on neuropeptides and discuss venoms as a source for ligands targeting neuropeptide signalling systems.
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Affiliation(s)
- Helen C Mendel
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Markus Muttenthaler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Vienna, Austria.
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60
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Transcriptional profile of spinal dynorphin-lineage interneurons in the developing mouse. Pain 2020; 160:2380-2397. [PMID: 31166300 DOI: 10.1097/j.pain.0000000000001636] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mounting evidence suggests that the spinal dorsal horn (SDH) contains multiple subpopulations of inhibitory interneurons that play distinct roles in somatosensory processing, as exemplified by the importance of spinal dynorphin-expressing neurons for the suppression of mechanical pain and chemical itch. Although it is clear that GABAergic transmission in the SDH undergoes significant alterations during early postnatal development, little is known about the maturation of discrete inhibitory "microcircuits" within the region. As a result, the goal of this study was to elucidate the gene expression profile of spinal dynorphin (pDyn)-lineage neurons throughout life. We isolated nuclear RNA specifically from pDyn-lineage SDH interneurons at postnatal days 7, 21, and 80 using the Isolation of Nuclei Tagged in Specific Cell Types (INTACT) technique, followed by RNA-seq analysis. Over 650 genes were ≥2-fold enriched in adult pDyn nuclei compared with non-pDyn spinal cord nuclei, including targets with known relevance to pain such as galanin (Gal), prepronociceptin (Pnoc), and nitric oxide synthase 1 (Nos1). In addition, the gene encoding a membrane-bound guanylate cyclase, Gucy2d, was identified as a novel and highly selective marker of the pDyn population within the SDH. Differential gene expression analysis comparing pDyn nuclei across the 3 ages revealed sets of genes that were significantly upregulated (such as Cartpt, encoding cocaine- and amphetamine-regulated transcript peptide) or downregulated (including Npbwr1, encoding the receptor for neuropeptides B/W) during postnatal development. Collectively, these results provide new insight into the potential molecular mechanisms underlying the known age-dependent changes in spinal nociceptive processing and pain sensitivity.
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61
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Madsen TD, Hansen LH, Hintze J, Ye Z, Jebari S, Andersen DB, Joshi HJ, Ju T, Goetze JP, Martin C, Rosenkilde MM, Holst JJ, Kuhre RE, Goth CK, Vakhrushev SY, Schjoldager KT. An atlas of O-linked glycosylation on peptide hormones reveals diverse biological roles. Nat Commun 2020; 11:4033. [PMID: 32820167 PMCID: PMC7441158 DOI: 10.1038/s41467-020-17473-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
Peptide hormones and neuropeptides encompass a large class of bioactive peptides that regulate physiological processes like anxiety, blood glucose, appetite, inflammation and blood pressure. Here, we execute a focused discovery strategy to provide an extensive map of O-glycans on peptide hormones. We find that almost one third of the 279 classified peptide hormones carry O-glycans. Many of the identified O-glycosites are conserved and are predicted to serve roles in proprotein processing, receptor interaction, biodistribution and biostability. We demonstrate that O-glycans positioned within the receptor binding motifs of members of the neuropeptide Y and glucagon families modulate receptor activation properties and substantially extend peptide half-lives. Our study highlights the importance of O-glycosylation in the biology of peptide hormones, and our map of O-glycosites in this large class of biomolecules serves as a discovery platform for an important class of molecules with potential opportunities for drug designs.
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Affiliation(s)
- Thomas D Madsen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Lasse H Hansen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.,Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100, Copenhagen O, Denmark
| | - John Hintze
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Shifa Jebari
- Biofisika Institute (UPV/EHU, CSIC), Departamento de Bioquímica, Universidad del País Vasco, Bilbao, 48080, Spain
| | - Daniel B Andersen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Tongzhong Ju
- Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Jens P Goetze
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100, Copenhagen O, Denmark.,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Cesar Martin
- Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Mette M Rosenkilde
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Jens J Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Rune E Kuhre
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Christoffer K Goth
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.
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Bin Y, Zhang W, Tang W, Dai R, Li M, Zhu Q, Xia J. Prediction of Neuropeptides from Sequence Information Using Ensemble Classifier and Hybrid Features. J Proteome Res 2020; 19:3732-3740. [DOI: 10.1021/acs.jproteome.0c00276] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yannan Bin
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
- School of Computer Science and Technology, Anhui University, Hefei, Anhui 230601, China
| | - Wei Zhang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Wending Tang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Ruyu Dai
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Menglu Li
- School of Computer Science and Technology, Anhui University, Hefei, Anhui 230601, China
| | - Qizhi Zhu
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Junfeng Xia
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
- School of Computer Science and Technology, Anhui University, Hefei, Anhui 230601, China
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Aguilera-Mendoza L, Marrero-Ponce Y, Beltran JA, Tellez Ibarra R, Guillen-Ramirez HA, Brizuela CA. Graph-based data integration from bioactive peptide databases of pharmaceutical interest: toward an organized collection enabling visual network analysis. Bioinformatics 2020; 35:4739-4747. [PMID: 30994884 DOI: 10.1093/bioinformatics/btz260] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/30/2019] [Accepted: 04/10/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Bioactive peptides have gained great attention in the academy and pharmaceutical industry since they play an important role in human health. However, the increasing number of bioactive peptide databases is causing the problem of data redundancy and duplicated efforts. Even worse is the fact that the available data is non-standardized and often dirty with data entry errors. Therefore, there is a need for a unified view that enables a more comprehensive analysis of the information on this topic residing at different sites. RESULTS After collecting web pages from a large variety of bioactive peptide databases, we organized the web content into an integrated graph database (starPepDB) that holds a total of 71 310 nodes and 348 505 relationships. In this graph structure, there are 45 120 nodes representing peptides, and the rest of the nodes are connected to peptides for describing metadata. Additionally, to facilitate a better understanding of the integrated data, a software tool (starPep toolbox) has been developed for supporting visual network analysis in a user-friendly way; providing several functionalities such as peptide retrieval and filtering, network construction and visualization, interactive exploration and exporting data options. AVAILABILITY AND IMPLEMENTATION Both starPepDB and starPep toolbox are freely available at http://mobiosd-hub.com/starpep/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Longendri Aguilera-Mendoza
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Mexico.,Grupo de Investigación de Bioinformática, Universidad de las Ciencias Informáticas (UCI), CP 17100, La Habana, Cuba
| | - Yovani Marrero-Ponce
- Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Translacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades Médicas, CP 170901, Quito, Pichincha, Ecuador.,Grupo de Investigación Ambiental (GIA), Programas Ambientales, Facultad de Ingenierías, Fundacion Universitaria Tecnologico Comfenalco - Cartagena, Cr 44 D N° 30A - 91, CP 130015, Cartagena, Bolívar, Colombia
| | - Jesus A Beltran
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Mexico
| | - Roberto Tellez Ibarra
- Grupo de Investigación de Bioinformática, Universidad de las Ciencias Informáticas (UCI), CP 17100, La Habana, Cuba
| | - Hugo A Guillen-Ramirez
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Mexico
| | - Carlos A Brizuela
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Mexico
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DeLaney K, Cao W, Ma Y, Ma M, Zhang Y, Li L. PRESnovo: Prescreening Prior to de novo Sequencing to Improve Accuracy and Sensitivity of Neuropeptide Identification. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1358-1371. [PMID: 32266812 PMCID: PMC7332408 DOI: 10.1021/jasms.0c00013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Identification of peptides in species lacking fully sequenced genomes is challenging due to the lack of prior knowledge. De novo sequencing is the method of choice, but its performance is less than satisfactory due to algorithmic bias and interference in complex MS/MS spectra. The task becomes even more challenging for endogenous peptides that do not involve an enzymatic digestion step, such as neuropeptides. However, many neuropeptides possess common sequence motifs that are conserved across members of the same family. Taking advantage of this feature to improve de novo sequencing of neuropeptides, we have developed a method named PRESnovo (prescreening precursors prior to de novo sequencing) to predict the motif from a MS/MS spectrum. A neuropeptide sequence is broken into a motif with conserved amino acid residues and the remaining partial sequence. By searching against a predefined motif database constructed from known homologous sequences, PRESnovo assigns the most probable motif to each precursor via a sophisticated scoring function. Performance analysis was conducted with 15 neuropeptide standards, and 11 neuropeptides were correctly identified with PRESnovo compared to 1 identification by PEAKS only. We applied PRESnovo to assign motifs to peptide sequences in conjunction with PEAKS for assigning the rest of the peptide sequence in order to discover neuropeptides in tissue samples of green crab, C. maenas, and Jonah crab, C. borealis. Collectively, a large number of neuropeptides were identified, including 13 putative neuropeptides identified in green crab brain, 77 in Jonah crab brain, and 47 in Jonah crab sinus glands for the first time. This PRESnovo strategy greatly simplifies de novo sequencing and enhances the accuracy and sensitivity of neuropeptide identification when common motifs are present.
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Schredelseker T, Veit F, Dorsky RI, Driever W. Bsx Is Essential for Differentiation of Multiple Neuromodulatory Cell Populations in the Secondary Prosencephalon. Front Neurosci 2020; 14:525. [PMID: 32581684 PMCID: PMC7290237 DOI: 10.3389/fnins.2020.00525] [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: 11/29/2019] [Accepted: 04/28/2020] [Indexed: 01/17/2023] Open
Abstract
The hypothalamus is characterized by great neuronal diversity, with many neuropeptides and other neuromodulators being expressed within its multiple anatomical domains. The regulatory networks directing hypothalamic development have been studied in detail, but, for many neuron types, control of differentiation is still not understood. The highly conserved Brain-specific homeobox (Bsx) transcription factor has previously been described in regulating Agrp and Npy expression in the hypothalamic arcuate nucleus (ARC) in mice. While Bsx is expressed in many more subregions of both tuberal and mamillary hypothalamus, the functions therein are not known. Using genetic analyses in zebrafish, we show that most bsx expression domains are dependent on Nkx2.1 and Nkx2.4 homeodomain transcription factors, while a subset depends on Otp. We show that the anatomical pattern of the ventral forebrain appears normal in bsx mutants, but that Bsx is necessary for the expression of many neuropeptide encoding genes, including agrp, penka, vip, trh, npb, and nts, in distinct hypothalamic anatomical domains. We also found Bsx to be critical for normal expression of two Crh family members, crhb and uts1, as well as crhbp, in the hypothalamus and the telencephalic septal region. Furthermore, we demonstrate a crucial role for Bsx in serotonergic, histaminergic and nitrergic neuron development in the hypothalamus. We conclude that Bsx is critical for the terminal differentiation of multiple neuromodulatory cell types in the forebrain.
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Affiliation(s)
- Theresa Schredelseker
- Developmental Biology, Institute Biology 1, Faculty of Biology, Albert Ludwig University of Freiburg, Freiburg im Breisgau, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, Germany.,CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Florian Veit
- Developmental Biology, Institute Biology 1, Faculty of Biology, Albert Ludwig University of Freiburg, Freiburg im Breisgau, Germany
| | - Richard I Dorsky
- Department of Neurobiology & Anatomy, University of Utah, Salt Lake City, UT, United States
| | - Wolfgang Driever
- Developmental Biology, Institute Biology 1, Faculty of Biology, Albert Ludwig University of Freiburg, Freiburg im Breisgau, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, Germany.,CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, Germany
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66
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Tai KY, Wong K, Aghakhanian F, Parhar IS, Dhaliwal J, Ayub Q. Selected neuropeptide genes show genetic differentiation between Africans and non-Africans. BMC Genet 2020; 21:31. [PMID: 32171244 PMCID: PMC7071772 DOI: 10.1186/s12863-020-0835-8] [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: 09/24/2019] [Accepted: 02/28/2020] [Indexed: 11/10/2022] Open
Abstract
Background Publicly available genome data provides valuable information on the genetic variation patterns across different modern human populations. Neuropeptide genes are crucial to the nervous, immune, endocrine system, and physiological homeostasis as they play an essential role in communicating information in neuronal functions. It remains unclear how evolutionary forces, such as natural selection and random genetic drift, have affected neuropeptide genes among human populations. To date, there are over 100 known human neuropeptides from the over 1000 predicted peptides encoded in the genome. The purpose of this study is to analyze and explore the genetic variation in continental human populations across all known neuropeptide genes by examining highly differentiated SNPs between African and non-African populations. Results We identified a total of 644,225 SNPs in 131 neuropeptide genes in 6 worldwide population groups from a public database. Of these, 5163 SNPs that had ΔDAF |(African - non-African)| ≥ 0.20 were identified and fully annotated. A total of 20 outlier SNPs that included 19 missense SNPs with a moderate impact and one stop lost SNP with high impact, were identified in 16 neuropeptide genes. Our results indicate that an overall strong population differentiation was observed in the non-African populations that had a higher derived allele frequency for 15/20 of those SNPs. Highly differentiated SNPs in four genes were particularly striking: NPPA (rs5065) with high impact stop lost variant; CHGB (rs6085324, rs236150, rs236152, rs742710 and rs742711) with multiple moderate impact missense variants; IGF2 (rs10770125) and INS (rs3842753) with moderate impact missense variants that are in linkage disequilibrium. Phenotype and disease associations of these differentiated SNPs indicated their association with hypertension and diabetes and highlighted the pleiotropic effects of these neuropeptides and their role in maintaining physiological homeostasis in humans. Conclusions We compiled a list of 131 human neuropeptide genes from multiple databases and literature survey. We detect significant population differentiation in the derived allele frequencies of variants in several neuropeptide genes in African and non-African populations. The results highlights SNPs in these genes that may also contribute to population disparities in prevalence of diseases such as hypertension and diabetes.
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Affiliation(s)
- Kah Yee Tai
- School of Information Technology, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - KokSheik Wong
- School of Information Technology, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Farhang Aghakhanian
- Monash University Malaysia Genomics Facility, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Ishwar S Parhar
- Jeffrey Cheah School of Medicine and Health Sciences, Brain Research Institute, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Jasbir Dhaliwal
- School of Information Technology, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - Qasim Ayub
- Monash University Malaysia Genomics Facility, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
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67
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Fleites LA, Johnson R, Kruse AR, Nachman RJ, Hall DG, MacCoss M, Heck ML. Peptidomics Approaches for the Identification of Bioactive Molecules from Diaphorina citri. J Proteome Res 2020; 19:1392-1408. [PMID: 32037832 DOI: 10.1021/acs.jproteome.9b00509] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Huanglongbing (HLB), a deadly citrus disease, is primarily associated with Candidatus Liberibacter asiaticus (CLas) and spread by the hemipteran insect Diaphorina citri. Control strategies to combat HLB are urgently needed. In this work, we developed and compared workflows for the extraction of the D. citri peptidome, a dynamic set of polypeptides produced by proteolysis and other cellular processes. High-resolution mass spectrometry revealed bias among methods reflecting the physiochemical properties of the peptides: while TCA/acetone-based methods resulted in enrichment of C-terminally amidated peptides, a modification characteristic of bioactive peptides, larger peptides were overrepresented in the aqueous phase of chloroform/methanol extracts, possibly indicative of reduced co-analytical degradation during sample preparation. Parallel reaction monitoring (PRM) was used to validate the structure and upregulation of peptides derived from hemocyanin, a D. citri immune system protein, in insects reared on healthy and CLas-infected trees. Mining of the data sets also revealed 122 candidate neuropeptides, including PK/PBAN family neuropeptides and kinins, biostable analogs of which have known insecticidal properties. Taken together, this information yields new, in-depth insights into peptidomics methodology. Additionally, the putative neuropeptides identified may lead to psyllid mortality if applied to or expressed in citrus, consequently blocking the spread of HLB disease in citrus groves.
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Affiliation(s)
- Laura A Fleites
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States.,USDA Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, 14853-2901, United States.,Department of Plant Pathology and Plant Microbe Biology, Cornell University, Ithaca, New York 14850-5905, United States
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Angela R Kruse
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States.,Department of Plant Pathology and Plant Microbe Biology, Cornell University, Ithaca, New York 14850-5905, United States
| | - Ronald J Nachman
- USDA Agricultural Research Service, Insect Control and Cotton Disease Research Unit, College Station, Texas 77845, United States
| | - David G Hall
- USDA Agricultural Research Service, US Horticulture Research Laboratory, Fort Pierce, Florida 34945, United States
| | - Michael MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Michelle L Heck
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States.,USDA Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, 14853-2901, United States.,Department of Plant Pathology and Plant Microbe Biology, Cornell University, Ithaca, New York 14850-5905, United States
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68
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BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities. Int J Mol Sci 2019; 20:ijms20235978. [PMID: 31783634 PMCID: PMC6928608 DOI: 10.3390/ijms20235978] [Citation(s) in RCA: 384] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/21/2019] [Accepted: 11/25/2019] [Indexed: 12/11/2022] Open
Abstract
The BIOPEP-UWM™ database of bioactive peptides (formerly BIOPEP) has recently become a popular tool in the research on bioactive peptides, especially on these derived from foods and being constituents of diets that prevent development of chronic diseases. The database is continuously updated and modified. The addition of new peptides and the introduction of new information about the existing ones (e.g., chemical codes and references to other databases) is in progress. New opportunities include the possibility of annotating peptides containing D-enantiomers of amino acids, batch processing option, converting amino acid sequences into SMILES code, new quantitative parameters characterizing the presence of bioactive fragments in protein sequences, and finding proteinases that release particular peptides.
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69
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Smith SJ, Sümbül U, Graybuck LT, Collman F, Seshamani S, Gala R, Gliko O, Elabbady L, Miller JA, Bakken TE, Rossier J, Yao Z, Lein E, Zeng H, Tasic B, Hawrylycz M. Single-cell transcriptomic evidence for dense intracortical neuropeptide networks. eLife 2019; 8:47889. [PMID: 31710287 PMCID: PMC6881117 DOI: 10.7554/elife.47889] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/10/2019] [Indexed: 12/19/2022] Open
Abstract
Seeking new insights into the homeostasis, modulation and plasticity of cortical synaptic networks, we have analyzed results from a single-cell RNA-seq study of 22,439 mouse neocortical neurons. Our analysis exposes transcriptomic evidence for dozens of molecularly distinct neuropeptidergic modulatory networks that directly interconnect all cortical neurons. This evidence begins with a discovery that transcripts of one or more neuropeptide precursor (NPP) and one or more neuropeptide-selective G-protein-coupled receptor (NP-GPCR) genes are highly abundant in all, or very nearly all, cortical neurons. Individual neurons express diverse subsets of NP signaling genes from palettes encoding 18 NPPs and 29 NP-GPCRs. These 47 genes comprise 37 cognate NPP/NP-GPCR pairs, implying the likelihood of local neuropeptide signaling. Here, we use neuron-type-specific patterns of NP gene expression to offer specific, testable predictions regarding 37 peptidergic neuromodulatory networks that may play prominent roles in cortical homeostasis and plasticity.
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Affiliation(s)
| | - Uygar Sümbül
- Allen Institute for Brain Science, Seattle, United States
| | | | | | | | - Rohan Gala
- Allen Institute for Brain Science, Seattle, United States
| | - Olga Gliko
- Allen Institute for Brain Science, Seattle, United States
| | - Leila Elabbady
- Allen Institute for Brain Science, Seattle, United States
| | | | | | - Jean Rossier
- Neuroscience Paris Seine, Sorbonne Université, Paris, France
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, United States
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, United States
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, United States
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, United States
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Abstract
Metabolomics uses advanced analytical chemistry techniques to enable the high-throughput characterization of metabolites from cells, organs, tissues, or biofluids. The rapid growth in metabolomics is leading to a renewed interest in metabolism and the role that small molecule metabolites play in many biological processes. As a result, traditional views of metabolites as being simply the "bricks and mortar" of cells or just the fuel for cellular energetics are being upended. Indeed, metabolites appear to have much more varied and far more important roles as signaling molecules, immune modulators, endogenous toxins, and environmental sensors. This review explores how metabolomics is yielding important new insights into a number of important biological and physiological processes. In particular, a major focus is on illustrating how metabolomics and discoveries made through metabolomics are improving our understanding of both normal physiology and the pathophysiology of many diseases. These discoveries are yielding new insights into how metabolites influence organ function, immune function, nutrient sensing, and gut physiology. Collectively, this work is leading to a much more unified and system-wide perspective of biology wherein metabolites, proteins, and genes are understood to interact synergistically to modify the actions and functions of organelles, organs, and organisms.
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Affiliation(s)
- David S Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, Canada
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71
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Iwaniak A, Darewicz M, Mogut D, Minkiewicz P. Elucidation of the role of in silico methodologies in approaches to studying bioactive peptides derived from foods. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.103486] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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72
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Torres MD, Sothiselvam S, Lu TK, de la Fuente-Nunez C. Peptide Design Principles for Antimicrobial Applications. J Mol Biol 2019; 431:3547-3567. [DOI: 10.1016/j.jmb.2018.12.015] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 02/08/2023]
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73
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DeLaney K, Li L. Data Independent Acquisition Mass Spectrometry Method for Improved Neuropeptidomic Coverage in Crustacean Neural Tissue Extracts. Anal Chem 2019; 91:5150-5158. [PMID: 30888792 PMCID: PMC6481171 DOI: 10.1021/acs.analchem.8b05734] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Neuropeptides are an important class of signaling molecules in the nervous and neuroendocrine system, but they are challenging to study due to their low concentration in vivo in the presence of numerous interfering artifacts. Often the limitation of mass spectrometry analyses of neuropeptides in complex tissue extracts is not due to neuropeptides being below the detection limit but due to ions not being selected for tandem mass spectrometry during the liquid chromatography elution time and therefore not being identified. In this study, a data independent acquisition (DIA) method was developed to improve the coverage of neuropeptides in neural tissue from the model organism C. borealis. The optimal mass-to-charge ratio range and isolation window were determined and subsequently used to detect more neuropeptides in extracts from the brain and pericardial organs than the conventional data dependent acquisition method. The DIA method led to the detection of almost twice as many neuropeptides in the brain and approximately 1.5-fold more neuropeptides in the pericardial organs. The technical and biological reproducibility were also explored and found to be improved over the original method, with 56% of neuropeptides detected in 3 out of 3 replicate injections and 62% in 3 out of 3 biological replicates. Furthermore, 68 putative novel neuropeptides were detected and identified with de novo sequencing. The quantitative accuracy of the method was also explored. The developed method is anticipated to be useful for gaining a deeper profiling of neuropeptides, especially those in low abundance, in a variety of sample types.
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Affiliation(s)
- Kellen DeLaney
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
- School of Pharmacy, University of Wisconsin–Madison, 5125 Rennebohm Hall, 777 Highland Avenue, Madison, Wisconsin 53705-2222, United States
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74
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Llopis-Giménez A, Han Y, Kim Y, Ros VID, Herrero S. Identification and expression analysis of the Spodoptera exigua neuropeptidome under different physiological conditions. INSECT MOLECULAR BIOLOGY 2019; 28:161-175. [PMID: 30171635 DOI: 10.1111/imb.12535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Neuropeptides are small signalling molecules acting as neurohormones, neurotransmitters and neuromodulators. Being part of the chemical communication system between cells within an organism, they are involved in the regulation of different aspects of animal physiology and behaviour such as feeding, reproduction, development and locomotion. Transcriptomic data from larval and adult tissues have been obtained and mined to generate a comprehensive neuropeptidome for the polyphagous insect pest Spodoptera exigua. Sixty-three neuropeptides have been identified and described based on their tissue specificity and their regulation in response to different abiotic perturbations. Expression analyses have identified those neuropeptides involved in ingestive and digestive behaviour of S. exigua larvae and revealed a general pattern of upregulation in the midgut during larval starvation. Our results represent a comprehensive neuropeptidome of a lepidopteran species that will be highly relevant to future studies and provide novel information of the insect's perception of its environment.
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Affiliation(s)
- A Llopis-Giménez
- Department of Genetics and Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI-BIOTECMED), Universitat de València, Burjassot (Valencia), Spain
| | - Y Han
- Laboratory of Virology, Wageningen University & Research, Wageningen, Netherlands
| | - Y Kim
- Department of Bio-Sciences, Andong National University, Andong, Republic of Korea
| | - V I D Ros
- Laboratory of Virology, Wageningen University & Research, Wageningen, Netherlands
| | - S Herrero
- Department of Genetics and Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI-BIOTECMED), Universitat de València, Burjassot (Valencia), Spain
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75
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NeuroPIpred: a tool to predict, design and scan insect neuropeptides. Sci Rep 2019; 9:5129. [PMID: 30914676 PMCID: PMC6435694 DOI: 10.1038/s41598-019-41538-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/05/2019] [Indexed: 12/15/2022] Open
Abstract
Insect neuropeptides and their associated receptors have been one of the potential targets for the pest control. The present study describes in silico models developed using natural and modified insect neuropeptides for predicting and designing new neuropeptides. Amino acid composition analysis revealed the preference of residues C, D, E, F, G, N, S, and Y in insect neuropeptides The positional residue preference analysis show that in natural neuropeptides residues like A, N, F, D, P, S, and I are preferred at N terminus and residues like L, R, P, F, N, and G are preferred at C terminus. Prediction models were developed using input features like amino acid and dipeptide composition, binary profiles and implementing different machine learning techniques. Dipeptide composition based SVM model performed best among all the models. In case of NeuroPIpred_DS1, model achieved an accuracy of 86.50% accuracy and 0.73 MCC on training dataset and 83.71% accuracy and 0.67 MCC on validation dataset whereas in case of NeuroPIpred_DS2, model achieved 97.47% accuracy and 0.95 MCC on training dataset and 97.93% accuracy and 0.96 MCC on validation dataset. In order to assist researchers, we created standalone and user friendly web server NeuroPIpred, available at (https://webs.iiitd.edu.in/raghava/neuropipred.)
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76
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Vyvers A, Schmidt A, Wiemuth D, Gründer S. Screening of 109 neuropeptides on ASICs reveals no direct agonists and dynorphin A, YFMRFamide and endomorphin-1 as modulators. Sci Rep 2018; 8:18000. [PMID: 30573735 PMCID: PMC6301962 DOI: 10.1038/s41598-018-36125-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/14/2018] [Indexed: 01/01/2023] Open
Abstract
Acid-sensing ion channels (ASICs) belong to the DEG/ENaC gene family. While ASIC1a, ASIC1b and ASIC3 are activated by extracellular protons, ASIC4 and the closely related bile acid-sensitive ion channel (BASIC or ASIC5) are orphan receptors. Neuropeptides are important modulators of ASICs. Moreover, related DEG/ENaCs are directly activated by neuropeptides, rendering neuropeptides interesting ligands of ASICs. Here, we performed an unbiased screen of 109 short neuropeptides (<20 amino acids) on five homomeric ASICs: ASIC1a, ASIC1b, ASIC3, ASIC4 and BASIC. This screen revealed no direct agonist of any ASIC but three modulators. First, dynorphin A as a modulator of ASIC1a, which increased currents of partially desensitized channels; second, YFMRFamide as a modulator of ASIC1b and ASIC3, which decreased currents of ASIC1b and slowed desensitization of ASIC1b and ASIC3; and, third, endomorphin-1 as a modulator of ASIC3, which also slowed desensitization. With the exception of YFMRFamide, which, however, is not a mammalian neuropeptide, we identified no new modulator of ASICs. In summary, our screen confirmed some known peptide modulators of ASICs but identified no new peptide ligands of ASICs, suggesting that most short peptides acting as ligands of ASICs are already known.
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Affiliation(s)
- Anna Vyvers
- Institute of Physiology, RWTH Aachen University, Pauwelsstrasse 30, D-52074, Aachen, Germany
| | - Axel Schmidt
- Institute of Physiology, RWTH Aachen University, Pauwelsstrasse 30, D-52074, Aachen, Germany.
| | - Dominik Wiemuth
- Institute of Physiology, RWTH Aachen University, Pauwelsstrasse 30, D-52074, Aachen, Germany
| | - Stefan Gründer
- Institute of Physiology, RWTH Aachen University, Pauwelsstrasse 30, D-52074, Aachen, Germany.
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77
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Abstract
The brain hosts a vast and diverse repertoire of neuropeptides, a class of signalling molecules often described as neurotransmitters. Here I argue that this description entails a catalogue of misperceptions, misperceptions that feed into a narrative in which information processing in the brain can be understood only through mapping neuronal connectivity and by studying the transmission of electrically conducted signals through chemical synapses. I argue that neuropeptide signalling in the brain involves primarily autocrine, paracrine and neurohormonal mechanisms that do not depend on synaptic connectivity and that it is not solely dependent on electrical activity but on mechanisms analogous to secretion from classical endocrine cells. As in classical endocrine systems, to understand the role of neuropeptides in the brain, we must understand not only how their release is regulated, but also how their synthesis is regulated and how the sensitivity of their targets is regulated. We must also understand the full diversity of effects of neuropeptides on those targets, including their effects on gene expression.
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Affiliation(s)
- Gareth Leng
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
- Correspondence should be addressed to G Leng:
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78
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Lee MW, Lee EY, Ferguson AL, Wong GCL. Machine learning antimicrobial peptide sequences: Some surprising variations on the theme of amphiphilic assembly. Curr Opin Colloid Interface Sci 2018; 38:204-213. [PMID: 31093008 DOI: 10.1016/j.cocis.2018.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Antimicrobial peptides (AMPs) collectively constitute a key component of the host innate immune system. They span a diverse space of sequences and can be α-helical, β-sheet, or unfolded in structure. Despite a wealth of knowledge about them from decades of experiments, it remains difficult to articulate general principles governing such peptides. How are they different from other molecules that are also cationic and amphiphilic? What other functions, in immunity and otherwise, are enabled by these simple sequences? In this short review, we present some recent work that engages these questions using methods not usually applied to AMP studies, such as machine learning. We find that not only do AMP-like sequences confer membrane remodeling activity to an unexpectedly broad range of protein classes, their cationic and amphiphilic signature also allows them to act as meta-antigens and self-assemble with immune ligands into nanocrystalline complexes for multivalent presentation to Toll-like receptors.
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Affiliation(s)
- Michelle W Lee
- Department of Bioengineering, Department of Chemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States
| | - Ernest Y Lee
- Department of Bioengineering, Department of Chemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States
| | - Andrew L Ferguson
- Institute for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, United States
| | - Gerard C L Wong
- Department of Bioengineering, Department of Chemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States
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79
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Wang J, Yin T, Xiao X, He D, Xue Z, Jiang X, Wang Y. StraPep: a structure database of bioactive peptides. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4974332. [PMID: 29688386 PMCID: PMC5905355 DOI: 10.1093/database/bay038] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 03/21/2018] [Indexed: 12/03/2022]
Abstract
Bioactive peptides, with a variety of biological activities and wide distribution in nature, have attracted great research interest in biological and medical fields, especially in pharmaceutical industry. The structural information of bioactive peptide is important for the development of peptide-based drugs. Many databases have been developed cataloguing bioactive peptides. However, to our knowledge, database dedicated to collect all the bioactive peptides with known structure is not available yet. Thus, we developed StraPep, a structure database of bioactive peptides. StraPep holds 3791 bioactive peptide structures, which belong to 1312 unique bioactive peptide sequences. About 905 out of 1312 (68%) bioactive peptides in StraPep contain disulfide bonds, which is significantly higher than that (21%) of PDB. Interestingly, 150 out of 616 (24%) bioactive peptides with three or more disulfide bonds form a structural motif known as cystine knot, which confers considerable structural stability on proteins and is an attractive scaffold for drug design. Detailed information of each peptide, including the experimental structure, the location of disulfide bonds, secondary structure, classification, post-translational modification and so on, has been provided. A wide range of user-friendly tools, such as browsing, sequence and structure-based searching and so on, has been incorporated into StraPep. We hope that this database will be helpful for the research community. Database URL: http://isyslab.info/StraPep
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Affiliation(s)
- Jian Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tailang Yin
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Xuwen Xiao
- School of Software Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dan He
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Zhidong Xue
- School of Software Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xinnong Jiang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yan Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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80
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Imaging neuropeptide effects on human brain function. Cell Tissue Res 2018; 375:279-286. [PMID: 30069597 DOI: 10.1007/s00441-018-2899-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/20/2018] [Indexed: 10/28/2022]
Abstract
The discovery of prosocial effects of oxytocin (OT) opened new directions for studying neuropeptide effects on the human brain. However, despite obvious effects of OT on neural responses as reported in numerous studies, other peptides have received less attention. Therefore, we will only briefly summarize evidence of OT effects on human functional magnetic resonance imaging (fMRI) and primarily focus on OT's sister neuropeptide arginine-vasopressin by presenting our own coordinated-based activation likelihood estimation meta-analysis. In addition, we will recapitulate rather limited data on few other neuropeptides, including pharmacological and genetic fMRI studies. Finally, we will review experiments with external neuropeptide administration to patients afflicted with mental disorders, such as autism or schizophrenia. In conclusion, despite remaining uncertainty regarding the penetrance of exogenous neuropeptides through the blood-brain barrier, it is evident that neuropeptides simultaneously influence the activity of limbic and cortical areas, indicating that these systems have a good potential for therapeutic drug development. Hence, this calls for further systematic studies of a wide spectrum of known and less known neuropeptides to understand their normal function in the brain and, subsequently, to tackle their potential contribution for pathophysiological mechanisms of mental disorders.
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81
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Yang N, Anapindi KDB, Rubakhin SS, Wei P, Yu Q, Li L, Kenny PJ, Sweedler JV. Neuropeptidomics of the Rat Habenular Nuclei. J Proteome Res 2018. [PMID: 29518334 DOI: 10.1021/acs.jproteome.7b00811] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Conserved across vertebrates, the habenular nuclei are a pair of small symmetrical structures in the epithalamus. The nuclei functionally link the forebrain and midbrain by receiving input from and projecting to several brain regions. Each habenular nucleus comprises two major asymmetrical subnuclei, the medial and lateral habenula. These subnuclei are associated with different physiological processes and disorders, such as depression, nicotine addiction, and encoding aversive stimuli or omitting expected rewarding stimuli. Elucidating the functions of the habenular nuclei at the molecular level requires knowledge of their neuropeptide complement. In this work, three mass spectrometry (MS) techniques-liquid chromatography (LC) coupled to Orbitrap tandem MS (MS/MS), LC coupled to Fourier transform (FT)-ion cyclotron resonance (ICR) MS/MS, and matrix-assisted laser desorption/ionization (MALDI) FT-ICR MS-were used to uncover the neuropeptide profiles of the rodent medial and lateral habenula. With the assistance of tissue stabilization and bioinformatics, a total of 262 and 177 neuropeptides produced from 27 and 20 prohormones were detected and identified from the medial and lateral habenula regions, respectively. Among these neuropeptides, 136 were exclusively found in the medial habenula, and 51 were exclusively expressed in the lateral habenula. Additionally, novel sites of sulfation, a rare post-translational modification, on the secretogranin I prohormone are identified. The results demonstrate that these two small brain nuclei have a rich and differentiated peptide repertoire, with this information enabling a range of follow-up studies.
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Affiliation(s)
- Ning Yang
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Krishna D B Anapindi
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Stanislav S Rubakhin
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Pingli Wei
- Chemistry Department , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Qing Yu
- School of Pharmacy , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Lingjun Li
- Chemistry Department , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,School of Pharmacy , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Paul J Kenny
- Department of Pharmacology & Systems Therapeutics , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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82
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Usmani SS, Kumar R, Bhalla S, Kumar V, Raghava GPS. In Silico Tools and Databases for Designing Peptide-Based Vaccine and Drugs. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 112:221-263. [PMID: 29680238 DOI: 10.1016/bs.apcsb.2018.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The prolonged conventional approaches of drug screening and vaccine designing prerequisite patience, vigorous effort, outrageous cost as well as additional manpower. Screening and experimentally validating thousands of molecules for a specific therapeutic property never proved to be an easy task. Similarly, traditional way of vaccination includes administration of either whole or attenuated pathogen, which raises toxicity and safety issues. Emergence of sequencing and recombinant DNA technology led to the epitope-based advanced vaccination concept, i.e., small peptides (epitope) can stimulate specific immune response. Advent of bioinformatics proved to be an adjunct in vaccine and drug designing. Genomic study of pathogens aid to identify and analyze the protective epitope. A number of in silico tools have been developed to design immunotherapy as well as peptide-based drugs in the last two decades. These tools proved to be a catalyst in drug and vaccine designing. This review solicits therapeutic peptide databases as well as in silico tools developed for designing peptide-based vaccine and drugs.
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Affiliation(s)
- Salman Sadullah Usmani
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India; Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Rajesh Kumar
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India; Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sherry Bhalla
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Vinod Kumar
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India; Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Gajendra P S Raghava
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India; Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India.
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83
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Russo AF. Overview of Neuropeptides: Awakening the Senses? Headache 2018; 57 Suppl 2:37-46. [PMID: 28485842 DOI: 10.1111/head.13084] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 03/10/2017] [Accepted: 03/10/2017] [Indexed: 12/27/2022]
Abstract
Humans have a diverse collection of neuropeptides that can influence a multitude of activities. There are now over 100 known neuropeptides and probably many more yet to be identified from the over 1000 predicted peptides encoded in the genome. While diverse, peptides generally share three common characteristics: (1) post-translational processing and release from vesicles, (2) activation of cell-surface receptors over a relatively large distance, and (3) modulation of target cells that are often in the brain and periphery. Within the brain, neuropeptides can modulate the activity of co-released neurotransmitters to either increase or decrease the strength of synaptic signaling. Within the periphery, neuropeptides can function similar to peptide hormones and modulate nearly all bodily functions. Given the clear involvement of the neuropeptide CGRP in migraine and the emerging evidence for other peptides, it seems likely that neuropeptides may help "awaken" the senses and contribute to the heightened sensory state of migraine.
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Affiliation(s)
- Andrew F Russo
- Department of Molecular Physiology and Biophysics, Department of Neurology, University of Iowa, Iowa City, IA, 52242, USA.,Veterans Affairs Medical Center, Iowa City, IA, 52246, USA
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84
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DeLaney K, Buchberger AR, Atkinson L, Gründer S, Mousley A, Li L. New techniques, applications and perspectives in neuropeptide research. ACTA ACUST UNITED AC 2018; 221:221/3/jeb151167. [PMID: 29439063 DOI: 10.1242/jeb.151167] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Neuropeptides are one of the most diverse classes of signaling molecules and have attracted great interest over the years owing to their roles in regulation of a wide range of physiological processes. However, there are unique challenges associated with neuropeptide studies stemming from the highly variable molecular sizes of the peptides, low in vivo concentrations, high degree of structural diversity and large number of isoforms. As a result, much effort has been focused on developing new techniques for studying neuropeptides, as well as novel applications directed towards learning more about these endogenous peptides. The areas of importance for neuropeptide studies include structure, localization within tissues, interaction with their receptors, including ion channels, and physiological function. Here, we discuss these aspects and the associated techniques, focusing on technologies that have demonstrated potential in advancing the field in recent years. Most identification and structural information has been gained by mass spectrometry, either alone or with confirmations from other techniques, such as nuclear magnetic resonance spectroscopy and other spectroscopic tools. While mass spectrometry and bioinformatic tools have proven to be the most powerful for large-scale analyses, they still rely heavily on complementary methods for confirmation. Localization within tissues, for example, can be probed by mass spectrometry imaging, immunohistochemistry and radioimmunoassays. Functional information has been gained primarily from behavioral studies coupled with tissue-specific assays, electrophysiology, mass spectrometry and optogenetic tools. Concerning the receptors for neuropeptides, the discovery of ion channels that are directly gated by neuropeptides opens up the possibility of developing a new generation of tools for neuroscience, which could be used to monitor neuropeptide release or to specifically change the membrane potential of neurons. It is expected that future neuropeptide research will involve the integration of complementary bioanalytical technologies and functional assays.
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Affiliation(s)
- Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Amanda R Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Louise Atkinson
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Stefan Gründer
- Institute of Physiology, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Angela Mousley
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA .,School of Pharmacy, University of Wisconsin-Madison, 1450 Linden Drive, Madison, WI 53706, USA
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85
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Abstract
In this final chapter I project my personal perspective on the future of peptidomics. A bird's eye view is shed on the discipline and a bid is made to frame it in the broader arena of the life sciences of tomorrow. Inferring from its present state-of-the-art and from the general direction of some evolutionary trends which are to be discerned, a case is made that peptidomics enjoys full ripeness as a young branch of science today, from which a bright future for the discipline can be predicted.
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Affiliation(s)
- Peter D E M Verhaert
- University of Maastricht Multimodal Molecular Imaging Institute (M4i), Faculty of Health, Medicine & Life Sciences, 50 Universiteitssingel, Maastricht, 6229ER, Netherlands.
- ProteoFormiX, 30 Turnhoutseweg, Beerse, 2340, Belgium.
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86
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Yu Q, Canales A, Glover MS, Das R, Shi X, Liu Y, Keller MP, Attie AD, Li L. Targeted Mass Spectrometry Approach Enabled Discovery of O-Glycosylated Insulin and Related Signaling Peptides in Mouse and Human Pancreatic Islets. Anal Chem 2017; 89:9184-9191. [PMID: 28726377 PMCID: PMC6314835 DOI: 10.1021/acs.analchem.7b01926] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
O-Linked glycosylation often involves the covalent attachment of sugar moieties to the hydroxyl group of serine or threonine on proteins/peptides. Despite growing interest in glycoproteins, little attention has been directed to glycosylated signaling peptides, largely due to lack of enabling analytical tools. Here we explore the occurrence of naturally O-linked glycosylation on the signaling peptides extracted from mouse and human pancreatic islets using mass spectrometry (MS). A novel targeted MS-based method is developed to increase the likelihood of capturing these modified signaling peptides and to provide improved sequence coverage and accurate glycosite localization, enabling the first large-scale discovery of O-glycosylation on signaling peptides. Several glycosylated signaling peptides with multiple glycoforms are identified, including the first report of glycosylated insulin-B chain and insulin-C peptide and BigLEN. This discovery may reveal potential novel functions as glycosylation could influence their conformation and biostability. Given the importance of insulin and its related peptide hormones and previous studies of glycosylated insulin analogues, this natural glycosylation may provide important insights into diabetes research and therapeutic treatments.
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Affiliation(s)
- Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Alejandra Canales
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Matthew S. Glover
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Rahul Das
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Xudong Shi
- Department of Surgery, Wisconsin Institute for Medical Research, Madison, Wisconsin 53705, United States
| | - Yang Liu
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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87
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Copy number alteration of neuropeptides and receptors in multiple cancers. Sci Rep 2017; 7:4598. [PMID: 28676692 PMCID: PMC5496884 DOI: 10.1038/s41598-017-04832-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/22/2017] [Indexed: 11/29/2022] Open
Abstract
Neuropeptides are peptide hormones used as chemical signals by the neuroendocrine system to communicate between cells. Recently, neuropeptides have been recognized for their ability to act as potent cellular growth factors on many cell types, including cancer cells. However, the molecular mechanism for how this occurs is unknown. To clarify the relationship between neuropeptides and cancer, we manually curated a total of 127 human neuropeptide genes by integrating information from the literature, homologous sequences, and database searches. Using human ligand-receptor interaction data, we first identified an interactome of 226 interaction pairs between 93 neuropeptides and 133 G-protein coupled receptors. We further identified four neuropeptide-receptor functional modules with ten or more genes, all of which were highly mutated in multiple cancers. We have identified a number of neuropeptide signaling systems with both oncogenic and tumour-suppressing roles for cancer progression, such as the insulin-like growth factors. By focusing on the neuroendocrine prostate cancer mutational data, we found prevalent amplification of neuropeptide and receptors in about 72% of samples. In summary, we report the first observation of abundant copy number variations on neuropeptides and receptors, which will be valuable for the design of peptide-based cancer prognosis, diagnosis and treatment.
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88
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Wang T, Zhao M, Liang D, Bose U, Kaur S, McManus DP, Cummins SF. Changes in the neuropeptide content of Biomphalaria ganglia nervous system following Schistosoma infection. Parasit Vectors 2017; 10:275. [PMID: 28578678 PMCID: PMC5455113 DOI: 10.1186/s13071-017-2218-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molluscs, including snails, are prone to parasite infection, which can lead to massive physiological and behavioural changes, yet many of the molecular components involved remain unresolved. Central to this point is the neural system that in snails consists of several ganglia that regulate the animals' physiology and behaviour patterns. The availability of a genomic resource for the freshwater snail Biomphalaria glabrata provides a mean towards the high throughput analysis of changes in the central nervous system (CNS) following infection with Schistosoma miracidia. RESULTS In this study, we performed a proteomic analysis of the B. glabrata CNS at pre-patent infection, providing a list of proteins that were further used within a protein-protein interaction (PPI) framework against S. mansoni proteins. A hub with most connections for both non-infected and infected Biomphalaria includes leucine aminopeptidase 2 (LAP2), which interacts with numerous miracidia proteins that together belong to the immunoglobulin family of cell adhesion related molecules. We additionally reveal the presence of at least 165 neuropeptides derived from the precursors of buccalin, enterin, FMRF, FVRI, pedal peptide 1, 2, 3 and 4, RYamide, RFamide, pleurin and others. Many of these were present at significantly reduced levels in the snail's CNS post-infection, such as the egg laying hormone, a neuropeptide required to initiate egg laying in gastropod molluscs. CONCLUSIONS Our analysis demonstrates that LAP2 may be a key component that regulates parasite infection physiology, as well as establishing that parasite-induced reproductive castration may be facilitated by significant reductions in reproduction-associated neuropeptides. This work helps in our understanding of molluscan neuropeptides and further stimulates advances in parasite-host interactions.
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Affiliation(s)
- Tianfang Wang
- Genecology Research Centre, Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore DC, Queensland 4558 Australia
| | - Min Zhao
- Genecology Research Centre, Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore DC, Queensland 4558 Australia
| | - Di Liang
- Genecology Research Centre, Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore DC, Queensland 4558 Australia
| | - Utpal Bose
- Genecology Research Centre, Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore DC, Queensland 4558 Australia
| | - Satwant Kaur
- Institute of Environment, Health and Societies, Brunel University London, Kingston Lane, London, UB8 3PH UK
| | - Donald P. McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006 Australia
| | - Scott F. Cummins
- Genecology Research Centre, Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore DC, Queensland 4558 Australia
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89
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Nederpelt I, Bunnik J, IJzerman AP, Heitman LH. Kinetic Profile of Neuropeptide–Receptor Interactions. Trends Neurosci 2016; 39:830-839. [DOI: 10.1016/j.tins.2016.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 01/18/2023]
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90
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Brandes N, Ofer D, Linial M. ASAP: a machine learning framework for local protein properties. Database (Oxford) 2016; 2016:baw133. [PMID: 27694209 PMCID: PMC5045867 DOI: 10.1093/database/baw133] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/08/2016] [Accepted: 08/28/2016] [Indexed: 11/14/2022]
Abstract
Determining residue-level protein properties, such as sites of post-translational modifications (PTMs), is vital to understanding protein function. Experimental methods are costly and time-consuming, while traditional rule-based computational methods fail to annotate sites lacking substantial similarity. Machine Learning (ML) methods are becoming fundamental in annotating unknown proteins and their heterogeneous properties. We present ASAP (Amino-acid Sequence Annotation Prediction), a universal ML framework for predicting residue-level properties. ASAP extracts numerous features from raw sequences, and supports easy integration of external features such as secondary structure, solvent accessibility, intrinsically disorder or PSSM profiles. Features are then used to train ML classifiers. ASAP can create new classifiers within minutes for a variety of tasks, including PTM prediction (e.g. cleavage sites by convertase, phosphoserine modification). We present a detailed case study for ASAP: CleavePred, an ASAP-based model to predict protein precursor cleavage sites, with state-of-the-art results. Protein cleavage is a PTM shared by a wide variety of proteins sharing minimal sequence similarity. Current rule-based methods suffer from high false positive rates, making them suboptimal. The high performance of CleavePred makes it suitable for analyzing new proteomes at a genomic scale. The tool is attractive to protein design, mass spectrometry search engines and the discovery of new bioactive peptides from precursors. ASAP functions as a baseline approach for residue-level protein sequence prediction. CleavePred is freely accessible as a web-based application. Both ASAP and CleavePred are open-source with a flexible Python API.Database URL: ASAP's and CleavePred source code, webtool and tutorials are available at: https://github.com/ddofer/asap; http://protonet.cs.huji.ac.il/cleavepred.
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Affiliation(s)
- Nadav Brandes
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Dan Ofer
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
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91
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Secher A, Kelstrup CD, Conde-Frieboes KW, Pyke C, Raun K, Wulff BS, Olsen JV. Analytic framework for peptidomics applied to large-scale neuropeptide identification. Nat Commun 2016; 7:11436. [PMID: 27142507 PMCID: PMC4857386 DOI: 10.1038/ncomms11436] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 03/24/2016] [Indexed: 01/03/2023] Open
Abstract
Large-scale mass spectrometry-based peptidomics for drug discovery is relatively unexplored because of challenges in peptide degradation and identification following tissue extraction. Here we present a streamlined analytical pipeline for large-scale peptidomics. We developed an optimized sample preparation protocol to achieve fast, reproducible and effective extraction of endogenous peptides from sub-dissected organs such as the brain, while diminishing unspecific protease activity. Each peptidome sample was analysed by high-resolution tandem mass spectrometry and the resulting data set was integrated with publically available databases. We developed and applied an algorithm that reduces the peptide complexity for identification of biologically relevant peptides. The developed pipeline was applied to rat hypothalamus and identifies thousands of neuropeptides and their post-translational modifications, which is combined in a resource format for visualization, qualitative and quantitative analyses. Neuropeptide research is challenged by technical difficulties in identifying new bioactive peptides. Here the authors present an analytical pipeline for large-scale peptidomics applied to the rat hypothalamus, identifying thousands of endogenous neuropeptides and their post-translational modifications.
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Affiliation(s)
- Anna Secher
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark.,Histology and Imaging, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Maaloev, Denmark
| | - Christian D Kelstrup
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | | | - Charles Pyke
- Histology and Imaging, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Maaloev, Denmark
| | - Kirsten Raun
- Incretin &Obesity Pharmacology, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Maaloev, Denmark
| | - Birgitte S Wulff
- Incretin &Obesity Research, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Maaloev, Denmark
| | - Jesper V Olsen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
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92
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Derst C, Dircksen H, Meusemann K, Zhou X, Liu S, Predel R. Evolution of neuropeptides in non-pterygote hexapods. BMC Evol Biol 2016; 16:51. [PMID: 26923142 PMCID: PMC4770511 DOI: 10.1186/s12862-016-0621-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/15/2016] [Indexed: 01/29/2023] Open
Abstract
Background Neuropeptides are key players in information transfer and act as important regulators of development, growth, metabolism, and reproduction within multi-cellular animal organisms (Metazoa). These short protein-like substances show a high degree of structural variability and are recognized as the most diverse group of messenger molecules. We used transcriptome sequences from the 1KITE (1K Insect Transcriptome Evolution) project to search for neuropeptide coding sequences in 24 species from the non-pterygote hexapod lineages Protura (coneheads), Collembola (springtails), Diplura (two-pronged bristletails), Archaeognatha (jumping bristletails), and Zygentoma (silverfish and firebrats), which are often referred to as “basal” hexapods. Phylogenetically, Protura, Collembola, Diplura, and Archaeognatha are currently placed between Remipedia and Pterygota (winged insects); Zygentoma is the sistergroup of Pterygota. The Remipedia are assumed to be among the closest relatives of all hexapods and belong to the crustaceans. Results We identified neuropeptide precursor sequences within whole-body transcriptome data from these five hexapod groups and complemented this dataset with homologous sequences from three crustaceans (including Daphnia pulex), three myriapods, and the fruit fly Drosophila melanogaster. Our results indicate that the reported loss of several neuropeptide genes in a number of winged insects, particularly holometabolous insects, is a trend that has occurred within Pterygota. The neuropeptide precursor sequences of the non-pterygote hexapods show numerous amino acid substitutions, gene duplications, variants following alternative splicing, and numbers of paracopies. Nevertheless, most of these features fall within the range of variation known from pterygote insects. However, the capa/pyrokinin genes of non-pterygote hexapods provide an interesting example of rapid evolution, including duplication of a neuropeptide gene encoding different ligands. Conclusions Our findings delineate a basic pattern of neuropeptide sequences that existed before lineage-specific developments occurred during the evolution of pterygote insects. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0621-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christian Derst
- Institute for Zoology, Functional Peptidomics Group, University of Cologne, D-50674, Cologne, Germany.
| | - Heinrich Dircksen
- Department of Zoology, Stockholm University, S-10691, Stockholm, Sweden.
| | - Karen Meusemann
- Center for Molecular Biodiversity Research, Zoological Research Museum A. Koenig, D-53113, Bonn, Germany. .,Australian National Insect Collection, CSIRO National Research Collections Australia, Acton, ACT, 2601, Canberra, Australia.
| | - Xin Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.
| | - Shanlin Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.
| | - Reinhard Predel
- Institute for Zoology, Functional Peptidomics Group, University of Cologne, D-50674, Cologne, Germany.
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93
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The Role of Hypothalamic Neuropeptides in Neurogenesis and Neuritogenesis. Neural Plast 2016; 2016:3276383. [PMID: 26881105 PMCID: PMC4737468 DOI: 10.1155/2016/3276383] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/18/2015] [Accepted: 11/22/2015] [Indexed: 01/23/2023] Open
Abstract
The hypothalamus is a source of neural progenitor cells which give rise to different populations of specialized and differentiated cells during brain development. Newly formed neurons in the hypothalamus can synthesize and release various neuropeptides. Although term neuropeptide recently undergoes redefinition, small-size hypothalamic neuropeptides remain major signaling molecules mediating short- and long-term effects on brain development. They represent important factors in neurite growth and formation of neural circuits. There is evidence suggesting that the newly generated hypothalamic neurons may be involved in regulation of metabolism, energy balance, body weight, and social behavior as well. Here we review recent data on the role of hypothalamic neuropeptides in adult neurogenesis and neuritogenesis with special emphasis on the development of food intake and social behavior related brain circuits.
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94
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Hook V, Bandeira N. Neuropeptidomics Mass Spectrometry Reveals Signaling Networks Generated by Distinct Protease Pathways in Human Systems. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1970-80. [PMID: 26483184 PMCID: PMC4749436 DOI: 10.1007/s13361-015-1251-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/30/2015] [Accepted: 08/05/2015] [Indexed: 05/23/2023]
Abstract
Neuropeptides regulate intercellular signaling as neurotransmitters of the central and peripheral nervous systems, and as peptide hormones in the endocrine system. Diverse neuropeptides of distinct primary sequences of various lengths, often with post-translational modifications, coordinate and integrate regulation of physiological functions. Mass spectrometry-based analysis of the diverse neuropeptide structures in neuropeptidomics research is necessary to define the full complement of neuropeptide signaling molecules. Human neuropeptidomics has notable importance in defining normal and dysfunctional neuropeptide signaling in human health and disease. Neuropeptidomics has great potential for expansion in translational research opportunities for defining neuropeptide mechanisms of human diseases, providing novel neuropeptide drug targets for drug discovery, and monitoring neuropeptides as biomarkers of drug responses. In consideration of the high impact of human neuropeptidomics for health, an observed gap in this discipline is the few published articles in human neuropeptidomics compared with, for example, human proteomics and related mass spectrometry disciplines. Focus on human neuropeptidomics will advance new knowledge of the complex neuropeptide signaling networks participating in the fine control of neuroendocrine systems. This commentary review article discusses several human neuropeptidomics accomplishments that illustrate the rapidly expanding diversity of neuropeptides generated by protease processing of pro-neuropeptide precursors occurring within the secretory vesicle proteome. Of particular interest is the finding that human-specific cathepsin V participates in producing enkephalin and likely other neuropeptides, indicating unique proteolytic mechanisms for generating human neuropeptides. The field of human neuropeptidomics has great promise to solve new mechanisms in disease conditions, leading to new drug targets and therapeutic agents for human diseases. Graphical Abstract ᅟ.
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Affiliation(s)
- Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0719, USA.
- School of Medicine, Department of Neurosciences and Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093-0719, USA.
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0719, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, 92093-0719, USA
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95
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Ye H, Wang J, Zhang Z, Jia C, Schmerberg C, Catherman AD, Thomas PM, Kelleher NL, Li L. Defining the Neuropeptidome of the Spiny Lobster Panulirus interruptus Brain Using a Multidimensional Mass Spectrometry-Based Platform. J Proteome Res 2015; 14:4776-91. [PMID: 26390183 DOI: 10.1021/acs.jproteome.5b00627] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Decapod crustaceans are important animal models for neurobiologists due to their relatively simple nervous systems with well-defined neural circuits and extensive neuromodulation by a diverse set of signaling peptides. However, biochemical characterization of these endogenous neuropeptides is often challenging due to limited sequence information about these neuropeptide genes and the encoded preprohormones. By taking advantage of sequence homology in neuropeptides observed in related species using a home-built crustacean neuropeptide database, we developed a semi-automated sequencing strategy to characterize the neuropeptidome of Panulirus interruptus, an important aquaculture species, with few known neuropeptide preprohormone sequences. Our streamlined process searched the high mass accuracy and high-resolution data acquired on a LTQ-Orbitrap with a flexible algorithm in ProSight that allows for sequence discrepancy from reported sequences in our database, resulting in the detection of 32 neuropeptides, including 19 novel ones. We further improved the overall coverage to 51 neuropeptides with our multidimensional platform that employed multiple analytical techniques including dimethylation-assisted fragmentation, de novo sequencing using nanoliquid chromatography-electrospray ionization-quadrupole-time-of-flight (nanoLC-ESI-Q-TOF), direct tissue analysis, and mass spectrometry imaging on matrix-assisted laser desorption/ionization (MALDI)-TOF/TOF. The high discovery rate from this unsequenced model organism demonstrated the utility of our neuropeptide discovery pipeline and highlighted the advantage of utilizing multiple sequencing strategies. Collectively, our study expands the catalog of crustacean neuropeptides and more importantly presents an approach that can be adapted to exploring neuropeptidome from species that possess limited sequence information.
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Affiliation(s)
- Hui Ye
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University , Nanjing 210009, China.,School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | | | - Zichuan Zhang
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Chenxi Jia
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Claire Schmerberg
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Adam D Catherman
- Departments of Chemistry and Molecular Biosciences, Proteomics Center of Excellence and Chemistry of Life Processes Institute, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Paul M Thomas
- Departments of Chemistry and Molecular Biosciences, Proteomics Center of Excellence and Chemistry of Life Processes Institute, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, Proteomics Center of Excellence and Chemistry of Life Processes Institute, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,School of Life Sciences, Tianjin University , No. 92 Weijin Road, Nankai District, Tianjin 300072, China
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96
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Chandrashekar G, Alisafaei F, Han CS. Length scale dependent deformation in natural rubber. J Appl Polym Sci 2015. [DOI: 10.1002/app.42683] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gurudutt Chandrashekar
- Department of Mechanical Engineering; University of Wyoming, 1000 E. University Ave; Laramie Wyoming 82071
| | - Farid Alisafaei
- Department of Mechanical Engineering; University of Wyoming, 1000 E. University Ave; Laramie Wyoming 82071
| | - Chung-Souk Han
- Department of Mechanical Engineering; University of Wyoming, 1000 E. University Ave; Laramie Wyoming 82071
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