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Madsen CT, Refsgaard JC, Teufel FG, Kjærulff SK, Wang Z, Meng G, Jessen C, Heljo P, Jiang Q, Zhao X, Wu B, Zhou X, Tang Y, Jeppesen JF, Kelstrup CD, Buckley ST, Tullin S, Nygaard-Jensen J, Chen X, Zhang F, Olsen JV, Han D, Grønborg M, de Lichtenberg U. Combining mass spectrometry and machine learning to discover bioactive peptides. Nat Commun 2022; 13:6235. [PMID: 36266275 PMCID: PMC9584923 DOI: 10.1038/s41467-022-34031-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 10/10/2022] [Indexed: 12/25/2022] Open
Abstract
Peptides play important roles in regulating biological processes and form the basis of a multiplicity of therapeutic drugs. To date, only about 300 peptides in human have confirmed bioactivity, although tens of thousands have been reported in the literature. The majority of these are inactive degradation products of endogenous proteins and peptides, presenting a needle-in-a-haystack problem of identifying the most promising candidate peptides from large-scale peptidomics experiments to test for bioactivity. To address this challenge, we conducted a comprehensive analysis of the mammalian peptidome across seven tissues in four different mouse strains and used the data to train a machine learning model that predicts hundreds of peptide candidates based on patterns in the mass spectrometry data. We provide in silico validation examples and experimental confirmation of bioactivity for two peptides, demonstrating the utility of this resource for discovering lead peptides for further characterization and therapeutic development.
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Affiliation(s)
- Christian T. Madsen
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark
| | - Jan C. Refsgaard
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark ,Intomics, Kongens Lyngby, Denmark
| | - Felix G. Teufel
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark
| | - Sonny K. Kjærulff
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark ,Intomics, Kongens Lyngby, Denmark
| | - Zhe Wang
- Novo Nordisk Research Centre China, Beijing, China
| | - Guangjun Meng
- Novo Nordisk Research Centre China, Beijing, China ,Pulmongene LTD. Rm 502, Building 2, No. 9, Yike Road, Zhongguancun Life Science Park, Changping District, Beijing, China
| | - Carsten Jessen
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark
| | - Petteri Heljo
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark
| | - Qunfeng Jiang
- Novo Nordisk Research Centre China, Beijing, China ,Innovent Biologics, Inc. DongPing Jie 168, Suzhou, China
| | - Xin Zhao
- Novo Nordisk Research Centre China, Beijing, China
| | - Bo Wu
- Novo Nordisk Research Centre China, Beijing, China ,QL Biopharmaceutical, Rm 101, Building 7, 20 Life Science Park Road, Beijing, China
| | - Xueping Zhou
- Novo Nordisk Research Centre China, Beijing, China ,grid.421648.d0000 0004 5997 3165Crinetics pharmaceuticals, 10222 Barnes Canyon Rd Building 2, San Diego, CA 92121 USA
| | - Yang Tang
- Novo Nordisk Research Centre China, Beijing, China ,Roche R&D Center (China) Ltd, Building 5, 371 Lishizhen Road, 201203 Pudong, Shanghai China
| | - Jacob F. Jeppesen
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark
| | - Christian D. Kelstrup
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark
| | - Stephen T. Buckley
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark
| | - Søren Tullin
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark ,grid.420061.10000 0001 2171 7500Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach, Germany
| | - Jan Nygaard-Jensen
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark ,grid.420061.10000 0001 2171 7500Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach, Germany
| | - Xiaoli Chen
- Novo Nordisk Research Centre China, Beijing, China
| | - Fang Zhang
- Novo Nordisk Research Centre China, Beijing, China ,Structure Therapeutics. 701 Gateway Blvd., South San Francisco, CA 94080 USA
| | - Jesper V. Olsen
- grid.5254.60000 0001 0674 042XDepartment of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Dan Han
- Novo Nordisk Research Centre China, Beijing, China
| | - Mads Grønborg
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark
| | - Ulrik de Lichtenberg
- grid.425956.90000 0004 0391 2646Global Research Technologies, Novo Nordisk A/S, Maaloev, Denmark ,grid.487026.f0000 0000 9922 7627The Novo Nordisk Foundation, Tuborg Havnevej 19, 2900 Hellerup, Denmark
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Transcriptomic plasticity of the hypothalamic osmoregulatory control centre of the Arabian dromedary camel. Commun Biol 2022; 5:1008. [PMID: 36151304 PMCID: PMC9508118 DOI: 10.1038/s42003-022-03857-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/17/2022] [Indexed: 11/08/2022] Open
Abstract
Water conservation is vital for life in the desert. The dromedary camel (Camelus dromedarius) produces low volumes of highly concentrated urine, more so when water is scarce, to conserve body water. Two hormones, arginine vasopressin and oxytocin, both produced in the supraoptic nucleus, the core hypothalamic osmoregulatory control centre, are vital for this adaptive process, but the mechanisms that enable the camel supraoptic nucleus to cope with osmotic stress are not known. To investigate the central control of water homeostasis in the camel, we first build three dimensional models of the camel supraoptic nucleus based on the expression of the vasopressin and oxytocin mRNAs in order to facilitate sampling. We then compare the transcriptomes of the supraoptic nucleus under control and water deprived conditions and identified genes that change in expression due to hyperosmotic stress. By comparing camel and rat datasets, we have identified common elements of the water deprivation transcriptomic response network, as well as elements, such as extracellular matrix remodelling and upregulation of angiotensinogen expression, that appear to be unique to the dromedary camel and that may be essential adaptations necessary for life in the desert. Comparative transcriptomic analyses between dromedary camels and rats provide insight into water homeostasis gene responses in animals under water stress conditions.
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N-Methyl-D-aspartate Glutamate Receptor Modulates Cardiovascular and Neuroendocrine Responses Evoked by Hemorrhagic Shock in Rats. BIOMED RESEARCH INTERNATIONAL 2021; 2021:1156031. [PMID: 34423030 PMCID: PMC8378978 DOI: 10.1155/2021/1156031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/12/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Here, we report the participation of N-methyl-D-aspartate (NMDA) glutamate receptor in the mediation of cardiovascular and circulating vasopressin responses evoked by a hemorrhagic stimulus. In addition, once NMDA receptor activation is a prominent mechanism involved in nitric oxide (NO) synthesis in the brain, we investigated whether control of hemorrhagic shock by NMDA glutamate receptor was followed by changes in NO synthesis in brain supramedullary structures involved in cardiovascular and neuroendocrine control. Thus, we observed that intraperitoneal administration of the selective NMDA glutamate receptor antagonist dizocilpine maleate (MK801, 0.3 mg/kg) delayed and reduced the magnitude of hemorrhage-induced hypotension. Besides, hemorrhage induced a tachycardia response in the posthemorrhage period (i.e., recovery period) in control animals, and systemic treatment with MK801 caused a bradycardia response during hemorrhagic shock. Hemorrhagic stimulus increased plasma vasopressin levels during the recovery period and NMDA receptor antagonism increased concentration of this hormone during both the hemorrhage and postbleeding periods in relation to control animals. Moreover, hemorrhagic shock caused a decrease in NOx levels in the paraventricular nucleus of the hypothalamus (PVN), amygdala, bed nucleus of the stria terminalis (BNST), and ventral periaqueductal gray matter (vPAG). Nevertheless, treatment with MK801 did not affect these effects. Taken together, these results indicate that the NMDA glutamate receptor is involved in the hemorrhagic shock by inhibiting circulating vasopressin release. Our data also suggest a role of the NMDA receptor in tachycardia, but not in the decreased NO synthesis in the brain evoked by hemorrhage.
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Brown CH, Ludwig M, Tasker JG, Stern JE. Somato-dendritic vasopressin and oxytocin secretion in endocrine and autonomic regulation. J Neuroendocrinol 2020; 32:e12856. [PMID: 32406599 PMCID: PMC9134751 DOI: 10.1111/jne.12856] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/29/2020] [Accepted: 04/11/2020] [Indexed: 12/29/2022]
Abstract
Somato-dendritic secretion was first demonstrated over 30 years ago. However, although its existence has become widely accepted, the function of somato-dendritic secretion is still not completely understood. Hypothalamic magnocellular neurosecretory cells were among the first neuronal phenotypes in which somato-dendritic secretion was demonstrated and are among the neurones for which the functions of somato-dendritic secretion are best characterised. These neurones secrete the neuropeptides, vasopressin and oxytocin, in an orthograde manner from their axons in the posterior pituitary gland into the blood circulation to regulate body fluid balance and reproductive physiology. Retrograde somato-dendritic secretion of vasopressin and oxytocin modulates the activity of the neurones from which they are secreted, as well as the activity of neighbouring populations of neurones, to provide intra- and inter-population signals that coordinate the endocrine and autonomic responses for the control of peripheral physiology. Somato-dendritic vasopressin and oxytocin have also been proposed to act as hormone-like signals in the brain. There is some evidence that somato-dendritic secretion from magnocellular neurosecretory cells modulates the activity of neurones beyond their local environment where there are no vasopressin- or oxytocin-containing axons but, to date, there is no conclusive evidence for, or against, hormone-like signalling throughout the brain, although it is difficult to imagine that the levels of vasopressin found throughout the brain could be underpinned by release from relatively sparse axon terminal fields. The generation of data to resolve this issue remains a priority for the field.
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Affiliation(s)
- Colin H. Brown
- Department of Physiology, Brain Health Research Centre, Centre for Neuroendocrinology, University of Otago, Dunedin, New Zealand
| | - Mike Ludwig
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
- Department of Immunology, Centre for Neuroendocrinology, University of Pretoria, Pretoria, South Africa
| | - Jeffrey G. Tasker
- Department of Cell and Molecular Biology, Brain Institute, Tulane University, New Orleans, LA, USA
| | - Javier E. Stern
- Neuroscience Institute, Georgia State University, Atlanta, GA, USA
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Abstract
The posterior pituitary gland secretes oxytocin and vasopressin (the antidiuretic hormone) into the blood system. Oxytocin is required for normal delivery of the young and for delivery of milk to the young during lactation. Vasopressin increases water reabsorption in the kidney to maintain body fluid balance and causes vasoconstriction to increase blood pressure. Oxytocin and vasopressin secretion occurs from the axon terminals of magnocellular neurons whose cell bodies are principally found in the hypothalamic supraoptic nucleus and paraventricular nucleus. The physiological functions of oxytocin and vasopressin depend on their secretion, which is principally determined by the pattern of action potentials initiated at the cell bodies. Appropriate secretion of oxytocin and vasopressin to meet the challenges of changing physiological conditions relies mainly on integration of afferent information on reproductive, osmotic, and cardiovascular status with local regulation of magnocellular neurons by glia as well as intrinsic regulation by the magnocellular neurons themselves. This review focuses on the control of magnocellular neuron activity with a particular emphasis on their regulation by reproductive function, body fluid balance, and cardiovascular status. © 2016 American Physiological Society. Compr Physiol 6:1701-1741, 2016.
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Affiliation(s)
- Colin H Brown
- Brain Health Research Centre, Centre for Neuroendocrinology and Department of Physiology, University of Otago, Dunedin, New Zealand
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Greenwood MP, Mecawi AS, Hoe SZ, Mustafa MR, Johnson KR, Al-Mahmoud GA, Elias LLK, Paton JFR, Antunes-Rodrigues J, Gainer H, Murphy D, Hindmarch CCT. A comparison of physiological and transcriptome responses to water deprivation and salt loading in the rat supraoptic nucleus. Am J Physiol Regul Integr Comp Physiol 2015; 308:R559-68. [PMID: 25632023 DOI: 10.1152/ajpregu.00444.2014] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/21/2015] [Indexed: 01/16/2023]
Abstract
Salt loading (SL) and water deprivation (WD) are experimental challenges that are often used to study the osmotic circuitry of the brain. Central to this circuit is the supraoptic nucleus (SON) of the hypothalamus, which is responsible for the biosynthesis of the hormones, arginine vasopressin (AVP) and oxytocin (OXT), and their transport to terminals that reside in the posterior lobe of the pituitary. On osmotic challenge evoked by a change in blood volume or osmolality, the SON undergoes a function-related plasticity that creates an environment that allows for an appropriate hormone response. Here, we have described the impact of SL and WD compared with euhydrated (EU) controls in terms of drinking and eating behavior, body weight, and recorded physiological data including circulating hormone data and plasma and urine osmolality. We have also used microarrays to profile the transcriptome of the SON following SL and remined data from the SON that describes the transcriptome response to WD. From a list of 2,783 commonly regulated transcripts, we selected 20 genes for validation by qPCR. All of the 9 genes that have already been described as expressed or regulated in the SON by osmotic stimuli were confirmed in our models. Of the 11 novel genes, 5 were successfully validated while 6 were false discoveries.
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Affiliation(s)
| | - Andre S Mecawi
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; Department of Physiological Sciences, Institute of Biology, Federal Rural University of Rio de Janeiro, Seropedica, Brazil
| | - See Ziau Hoe
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Rais Mustafa
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kory R Johnson
- Clinical Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Ghada A Al-Mahmoud
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Al Tarfa, Doha, Qatar
| | - Lucila L K Elias
- Department of Physiology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Julian F R Paton
- School of Physiology and Pharmacology, University Walk, Bristol, United Kingdom; and
| | - Jose Antunes-Rodrigues
- Department of Physiology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Harold Gainer
- Laboratory of Neurochemistry, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - David Murphy
- School of Clinical Sciences, University of Bristol, Bristol, United Kingdom; Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Charles C T Hindmarch
- School of Clinical Sciences, University of Bristol, Bristol, United Kingdom; Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia;
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