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Wen J, Ding Z, Wei Z, Xia H, Zhang Y, Zhu X. NeuroPpred-SHE: An interpretable neuropeptides prediction model based on selected features from hand-crafted features and embeddings of T5 model. Comput Biol Med 2024; 181:109048. [PMID: 39182368 DOI: 10.1016/j.compbiomed.2024.109048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 08/13/2024] [Accepted: 08/18/2024] [Indexed: 08/27/2024]
Abstract
Neuropeptides are the most ubiquitous neurotransmitters in the immune system, regulating various biological processes. Neuropeptides play a significant role for the discovery of new drugs and targets for nervous system disorders. Traditional experimental methods for identifying neuropeptides are time-consuming and costly. Although several computational methods have been developed to predict the neuropeptides, the accuracy is still not satisfactory due to the representability of the extracted features. In this work, we propose an efficient and interpretable model, NeuroPpred-SHE, for predicting neuropeptides by selecting the optimal feature subset from both hand-crafted features and embeddings of a protein language model. Specially, we first employed a pre-trained T5 protein language model to extract embedding features and twelve other encoding methods to extract hand-crafted features from peptide sequences, respectively. Secondly, we fused both embedding features and hand-crafted features to enhance the feature representability. Thirdly, we utilized random forest (RF), Max-Relevance and Min-Redundancy (mRMR) and eXtreme Gradient Boosting (XGBoost) methods to select the optimal feature subset from the fused features. Finally, we employed five machine learning methods (GBDT, XGBoost, SVM, MLP, and LightGBM) to build the models. Our results show that the model based on GBDT achieves the best performance. Furthermore, our final model was compared with other state-of-the-art methods on an independent test set, the results indicate that our model achieves an AUROC of 97.8 % which is higher than all the other state-of-the-art predictors. Our model is available at: https://github.com/wenjean/NeuroPpred-SHE.
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Affiliation(s)
- Jian Wen
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - Zhijie Ding
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - Zhuoyu Wei
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - Hongwei Xia
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - Yong Zhang
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China.
| | - Xiaolei Zhu
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China.
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Zhou B, Ran H, Zhang Q, Chen H, Han F, Xu C, Zhao Q. Unveiling the Impact of Rapeseed Meal on Feeding Behavior and Anorexigenic Endocrine in Litopenaeus vannamei. Animals (Basel) 2024; 14:540. [PMID: 38396508 PMCID: PMC10886117 DOI: 10.3390/ani14040540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Litopenaeus vannamei, with high plant protein acceptance and high global aquaculture production, is a potential species for rapeseed meal application. However, rapeseed meal has been associated with anorexia in fish, and whether the same occurs in L. vannamei remains unknown. This study demonstrated the effects of rapeseed meal on the feeding and anorexigenic endocrine of L. vannamei based on feeding behavior and transcriptomics. Soybean meal was replaced with fermented rapeseed meal (50%), and a significant increase in remaining diet and dietary discard was observed with a significant reduction in dietary visits. Transcriptome analysis revealed that the pathways involved in rapeseed meal-induced anorexia mainly included signal transduction, the digestive system, the sensory system, the endocrine system, phototransduction-fly, the thyroid hormone signaling pathway and pancreatic secretion. Moreover, this study further analyzed and identified seven neuropeptides involved in rapeseed meal-induced anorexia, and it explored the complex expression regulation strategies of these neuropeptides. In summary, this study confirmed through feeding behavior that rapeseed meal causes anorexia in L. vannamei, and it identified seven neuropeptides that were closely related to the anorexia process.
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Affiliation(s)
- Bo Zhou
- Fisheries Research Institute of Sichuan Academy of Agricultural Sciences, Yibin 644000, China;
| | - Hongmei Ran
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 570228, China (F.H.); (C.X.); (Q.Z.)
| | - Qijun Zhang
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 570228, China (F.H.); (C.X.); (Q.Z.)
| | - Hu Chen
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 570228, China (F.H.); (C.X.); (Q.Z.)
| | - Fenglu Han
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 570228, China (F.H.); (C.X.); (Q.Z.)
| | - Chang Xu
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 570228, China (F.H.); (C.X.); (Q.Z.)
| | - Qun Zhao
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 570228, China (F.H.); (C.X.); (Q.Z.)
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Phetsanthad A, Vu NQ, Yu Q, Buchberger AR, Chen Z, Keller C, Li L. Recent advances in mass spectrometry analysis of neuropeptides. MASS SPECTROMETRY REVIEWS 2023; 42:706-750. [PMID: 34558119 PMCID: PMC9067165 DOI: 10.1002/mas.21734] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 05/08/2023]
Abstract
Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.
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Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Amanda R. Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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Cook AP, Nusbaum MP. Feeding state-dependent modulation of feeding-related motor patterns. J Neurophysiol 2021; 126:1903-1924. [PMID: 34669505 PMCID: PMC8715047 DOI: 10.1152/jn.00387.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 11/22/2022] Open
Abstract
Studies elucidating modulation of microcircuit activity in isolated nervous systems have revealed numerous insights regarding neural circuit flexibility, but this approach limits the link between experimental results and behavioral context. To bridge this gap, we studied feeding behavior-linked modulation of microcircuit activity in the isolated stomatogastric nervous system (STNS) of male Cancer borealis crabs. Specifically, we removed hemolymph from a crab that was unfed for ≥24 h ("unfed" hemolymph) or fed 15 min to 2 h before hemolymph removal ("fed" hemolymph). After feeding, the first significant foregut emptying occurred >1 h later and complete emptying required ≥6 h. We applied the unfed or fed hemolymph to the stomatogastric ganglion (STG) in an isolated STNS preparation from a separate, unfed crab to determine its influence on the VCN (ventral cardiac neuron)-triggered gastric mill (chewing) and pyloric (filtering of chewed food) rhythms. Unfed hemolymph had little influence on these rhythms, but fed hemolymph from each examined time-point (15 min, 1 h, or 2 h after feeding) slowed one or both rhythms without weakening circuit neuron activity. There were also distinct parameter changes associated with each time-point. One change unique to the 1-h time-point (i.e., reduced activity of one circuit neuron during the transition from the gastric mill retraction to protraction phase) suggested that the fed hemolymph also enhanced the influence of a projection neuron that innervates the STG from a ganglion isolated from the applied hemolymph. Hemolymph thus provides a feeding state-dependent modulation of the two feeding-related motor patterns in the C. borealis STG.NEW & NOTEWORTHY Little is known about behavior-linked modulation of microcircuit activity. We show that the VCN-triggered gastric mill (chewing) and pyloric (food filtering) rhythms in the isolated crab Cancer borealis stomatogastric nervous system were changed by applying hemolymph from recently fed but not unfed crabs. This included some distinct parameter changes during each examined post-fed hemolymph time-point. These results suggest the presence of feeding-related changes in circulating hormones that regulate consummatory microcircuit activity.
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Affiliation(s)
- Aaron P Cook
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael P Nusbaum
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Mass spectrometry profiling and quantitation of changes in circulating hormones secreted over time in Cancer borealis hemolymph due to feeding behavior. Anal Bioanal Chem 2021; 414:533-543. [PMID: 34184104 DOI: 10.1007/s00216-021-03479-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
The crustacean stomatogastric ganglion (STG) is a valuable model for understanding circuit dynamics in neuroscience as it contains a small number of neurons, all easily distinguishable and most of which contribute to two complementary feeding-related neural circuits. These circuits are modulated by numerous neuropeptides, with many gaining access to the STG as hemolymph-transported hormones. Previous work characterized neuropeptides in the hemolymph of the crab Cancer borealis but was limited by low peptide abundance in the presence of a complex biological matrix and the propensity for rapid peptide degradation. To improve their detection, a data-independent acquisition (DIA) mass spectrometry (MS) method was implemented. This approach improved the number of neuropeptides detected by approximately twofold and showed greater reproducibility between experimental and biological replicates. This method was then used to profile neuropeptides at different stages of the feeding process, including hemolymph from crabs that were unfed, or 0 min, 15 min, 1 h, and 2 h post-feeding. The results show differences both in the presence and relative abundance of neuropeptides at the various time points. Additionally, 96 putative neuropeptide sequences were identified with de novo sequencing, indicating there may be more key modulators within this system than is currently known. These results suggest that a distinct cohort of neuropeptides provides modulation to the STG at different times in the feeding process, providing groundwork for targeted follow-up electrophysiological studies to better understand the functional role of circulating hormones in the neural basis of feeding behavior.
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Ben-Shushan S, Miller Y. Neuropeptides: Roles and Activities as Metal Chelators in Neurodegenerative Diseases. J Phys Chem B 2021; 125:2796-2811. [PMID: 33570949 PMCID: PMC8389909 DOI: 10.1021/acs.jpcb.0c11151] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Neurodegenerative diseases, such as Alzheimer's disease (AD) and Parkinson's disease (PD), are characterized by deposits of amyloid proteins. The homeostasis of metal ions is crucial for the normal biological functions in the brain. However, in AD and PD, the imbalance of metal ions leads to formation of amyloid deposits. In the past four decades, there has been extensive effort to design compound agents than can chelate metal ions with the aim of preventing the formation of the amyloid deposits. Unfortunately, the compounds to date that were designed were not successful candidates to be used in clinical trials. Neuropeptides are small molecules that are produced and released by neurons. It has been shown that neuropeptides have neuroprotective effects in the brain and reduce the formation of amyloid deposits. This Review Article is focused on the function of neuropeptides as metal chelators. Experimental and computational studies demonstrated that neuropeptides could bind metal ions, such as Cu2+ and Zn2+. This Review Article provides perspectives and initiates future studies to investigate the role of neuropeptides as metal chelators in neurodegenerative diseases.
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Affiliation(s)
- Shira Ben-Shushan
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
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7
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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: 4.8] [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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8
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Rainey AN, Fukui SM, Mark K, King HM, Blitz DM. Intrinsic sources of tachykinin-related peptide in the thoracic ganglion mass of the crab, Cancer borealis. Gen Comp Endocrinol 2021; 302:113688. [PMID: 33275935 DOI: 10.1016/j.ygcen.2020.113688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 11/30/2022]
Abstract
Neuropeptides comprise the largest class of neural and neuroendocrine signaling molecules. Vertebrate tachykinins (TKs) and the structurally-related invertebrate tachykinin-related peptides (TRPs) together form the largest neuropeptide superfamily, with a number of conserved neural and neuroendocrine functions across species. Arthropods, including crustaceans, have provided many insights into neuropeptide signaling and function. Crustacean tachykinin-related peptide occurs in endocrine organs and cells and in two of the major crustacean CNS components, the supraoesophageal ganglion ("brain") and the stomatogastric nervous system. However, little is known about TRP sources in the remaining major CNS component, the thoracic ganglion mass (TGM). To gain further insight into the function of this peptide, we aimed to identify intrinsic TRP sources in the TGM of the Jonah crab, Cancer borealis. We first adapted a clearing protocol to improve TRP immunoreactivity specifically in the TGM, which is a dense, fused mass of multiple ganglia in short-bodied crustaceans such as Cancer species of crabs. We verified that the clearing protocol avoided distortion of cell body morphology yet increased visibility of TRP immunoreactivity. Using confocal microscopy, we found TRP-immunoreactive (TRP-IR) axon tracts running the length of the TGM, TRP-IR neuropil in all ganglia, and approximately 110 TRP-IR somata distributed throughout the TGM, within and between ganglia. These somata likely represent both neural and neuroendocrine sources of TRP. Thus, there are many potential intrinsic sources of TRP in the TGM that are positioned to regulate behaviors such as food intake, locomotion, respiration, and reproduction.
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Affiliation(s)
- Amanda N Rainey
- Department of Biology and Center for Neuroscience, Miami University, Oxford, OH 45056, United States
| | - Stephanie M Fukui
- Department of Biology and Center for Neuroscience, Miami University, Oxford, OH 45056, United States
| | - Katie Mark
- Department of Biology and Center for Neuroscience, Miami University, Oxford, OH 45056, United States
| | - Hailey M King
- Department of Biology and Center for Neuroscience, Miami University, Oxford, OH 45056, United States
| | - Dawn M Blitz
- Department of Biology and Center for Neuroscience, Miami University, Oxford, OH 45056, United States.
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Vu NQ, DeLaney K, Li L. Neuropeptidomics: Improvements in Mass Spectrometry Imaging Analysis and Recent Advancements. Curr Protein Pept Sci 2021; 22:158-169. [PMID: 33200705 PMCID: PMC8330971 DOI: 10.2174/1389203721666201116115708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/29/2020] [Accepted: 07/23/2020] [Indexed: 12/13/2022]
Abstract
Neuropeptides are an important class of endogenous peptides in the nervous system that regulate physiological functions such as feeding, glucose homeostasis, pain, memory, reproduction, and many others. In order to understand the functional role of neuropeptides in diseases or disorders, studies investigating their dysregulation in terms of changes in abundance and localization must be carried out. As multiple neuropeptides are believed to play a functional role in each physiological process, techniques capable of global profiling multiple neuropeptides simultaneously are desired. Mass spectrometry is well-suited for this goal due to its ability to perform untargeted measurements without prior comprehensive knowledge of the analytes of interest. Mass spectrometry imaging (MSI) is particularly useful because it has the capability to image a large variety of peptides in a single experiment without labeling. Like all analytical techniques, careful sample preparation is critical to successful MSI analysis. The first half of this review focuses on recent developments in MSI sample preparation and instrumentation for analyzing neuropeptides and other biomolecules in which the sample preparation technique may be directly applicable for neuropeptide analysis. The benefit offered by incorporating these techniques is shown as improvement in a number of observable neuropeptides, enhanced signal to noise, increased spatial resolution, or a combination of these aspects. The second half of this review focuses on recent biological discoveries about neuropeptides resulting from these improvements in MSI analysis. The recent progress in neuropeptide detection and analysis methods, including the incorporation of various tissue washes, matrices, instruments, ionization sources, and computation approaches combined with the advancements in understanding neuropeptide function in a variety of model organisms, indicates the potential for the utilization of MSI analysis of neuropeptides in clinical settings.
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Affiliation(s)
- Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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Buchberger AR, DeLaney K, Liu Y, Vu NQ, Helfenbein K, Li L. Mass Spectrometric Profiling of Neuropeptides in Callinectes sapidus during Hypoxia Stress. ACS Chem Neurosci 2020; 11:3097-3106. [PMID: 32840999 DOI: 10.1021/acschemneuro.0c00439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Oxygen (O2) is a critical component of life; without proper O2 levels, cells are unable to respire, meaning glucose cannot be utilized. Thus, hypoxia (low O2 levels) is a well-documented stressor, especially in aquatic environments. Neuropeptides are a major class of regulators for stress-induced responses; however, their global expression changes during stress are not well characterized due to the natural complexity of the nervous system. Beyond being a neurological model organism, crustaceans are regularly exposed to hypoxia, making them a relevant system for this study. Several neuropeptide families, including orcokinins, RFamides, and allatostatin A-types, show dynamic dysregulation due to hypoxic stress. In particular, the brain showed the most dynamic changes with a survival mechanism "switching" (i.e., significant increase to decrease) of neuropeptide content between moderate and severe hypoxia (e.g., NFDEDRSGFA, FDAFTTGFGHS, NRNFLRFamide, and APSGFLGMRamide). Globally, neuropeptides in different tissues appeared to exhibit unique expression patterns at the various severities of hypoxia, including LSSSNSPSSTPL and NFDEIDRSSFGF. Overall, this study provides clear evidence for the benefits of globally analyzing biomolecules and that neuropeptides play a critical role in how crustaceans adapt due to hypoxic stress.
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Affiliation(s)
- Amanda R. Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53705, United States
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53705, United States
| | - Yang Liu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53705, United States
| | - Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53705, United States
| | - Kylie Helfenbein
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53705, United States
- School of Pharmacy, University of Wisconsin-Madison, 5125 Rennebohm Hall, 777 Highland Drive, Madison, Wisconsin 53706, United States
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Abou El Asrar R, Cools D, Vanden Broeck J. Role of peptide hormones in insect gut physiology. CURRENT OPINION IN INSECT SCIENCE 2020; 41:71-78. [PMID: 32814267 DOI: 10.1016/j.cois.2020.07.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/09/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
Nutrient uptake and digestion are essential for optimal growth and development. In insects, these processes are regulated by the gut-brain axis, which is a neurohumoral communication system for maintaining gut homeostasis. The insect gut is a complex organ consisting of three distinct structures, denominated foregut, midgut and hindgut, each with their specific specializations. These specializations are tightly regulated by the interplay of several neuropeptides: a versatile group of signalling molecules involved in a multitude of processes including gut physiology. Neuropeptides take part in the regulation of gut processes ranging from digestive enzyme release to muscle activity and satiety. Some neuropeptide mimetics are a promising strategy for ecological pest management. This review focuses on a selection of neuropeptides that are well-known for their role in gut physiology, and neuropeptides for which the mode of action is yet to be unravelled.
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Affiliation(s)
- Rania Abou El Asrar
- KU Leuven, Department of Biology, Research Group of Molecular Developmental Physiology and Signal Transduction, Naamsestraat 59 Box 2465, 3000 Leuven, Belgium
| | - Dorien Cools
- KU Leuven, Department of Biology, Research Group of Molecular Developmental Physiology and Signal Transduction, Naamsestraat 59 Box 2465, 3000 Leuven, Belgium
| | - Jozef Vanden Broeck
- KU Leuven, Department of Biology, Research Group of Molecular Developmental Physiology and Signal Transduction, Naamsestraat 59 Box 2465, 3000 Leuven, Belgium.
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Cao Q, Yu Q, Liu Y, Chen Z, Li L. Signature-Ion-Triggered Mass Spectrometry Approach Enabled Discovery of N- and O-Linked Glycosylated Neuropeptides in the Crustacean Nervous System. J Proteome Res 2020; 19:634-643. [PMID: 31875397 DOI: 10.1021/acs.jproteome.9b00525] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Crustaceans are commonly used model organisms to study neuromodulation. Despite numerous reported crustacean neuropeptide families and their functions, there has been no report on neuropeptide glycosylation. This is in part due to a lack of sensitive methods that enable deciphering this intricate low-abundance post-translational modification, even though glycosylation has been shown to play an important role in neuromodulation. Here, we describe the discovery of glycosylated neuropeptides with an enrichment-free approach, taking advantage of signature oxonium ions produced in higher-energy collision dissociation (HCD) MS/MS spectra. The detection of the oxonium ions in the HCD scans suggests glycan attachment to peptides, allowing electron-transfer/higher-energy collision dissociation (EThcD) to be performed to selectively elucidate structural information of glycosylated neuropeptides that are buried in nonglycosylated peptides. Overall, 4 N-linked and 14 O-linked glycosylated neuropeptides have been identified for the first time in the crustacean nervous system. In addition, 91 novel putative neuropeptides have been discovered based on the collected HCD scans. This hybrid approach, coupling a shotgun method for neuropeptide discovery and targeted strategy for glycosylation characterization, enables the first report on glycosylated neuropeptides in crustaceans and the discovery of additional neuropeptides simultaneously. The elucidation of novel glycosylated neuropeptides sheds light on the crustacean peptidome and offers novel insights into future neuropeptide functional studies.
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Affiliation(s)
- Qinjingwen Cao
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| | - Qing Yu
- School of Pharmacy , University of Wisconsin-Madison , 777 Highland Avenue , Madison , Wisconsin 53705 , United States
| | - Yang Liu
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| | - Zhengwei Chen
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| | - Lingjun Li
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States.,School of Pharmacy , University of Wisconsin-Madison , 777 Highland Avenue , Madison , Wisconsin 53705 , United States
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13
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Jiang X, Xiang F, Jia C, Buchberger AR, Li L. Relative Quantitation of Neuropeptides at Multiple Developmental Stages of the American Lobster Using N, N-Dimethyl Leucine Isobaric Tandem Mass Tags. ACS Chem Neurosci 2018; 9:2054-2063. [PMID: 29357224 DOI: 10.1021/acschemneuro.7b00521] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Neuromodulators and neurotransmitters play important roles in neural network development. The quantitative changes of these signaling molecules often reflect their regulatory roles in physiological processes. Currently, several commercial tags (e.g., iTRAQ and TMT) have been widely used in proteomics. With reduced cost and higher labeling efficiency, we employed a set of custom-developed N, N-dimethyl leucine (DiLeu) 4-plex isobaric tandem mass tags as an attractive alternative for the relative quantitation of neuropeptides in brain tissue of American lobster Homarus americanus at multiple developmental stages. A general workflow for isobaric labeling of neuropeptides followed by LC-MS/MS analysis has been developed, including optimized sample handling procedures. Overall, we were able to quantify 18 trace-amount neuropeptides from 6 different families using a single adult brain as a control. The quantitation results indicated that the expressions of different neuropeptide families had significant changes over distinct developmental stages. Additionally, our data revealed intriguing elevated expression of neuropeptides in the early juvenile development stage. The methodology presented here advanced the workflow of DiLeu as an alternative labeling approach and the application of DiLeu-based quantitative peptidomics, which can be extended to areas beyond neuroscience.
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Affiliation(s)
- Xiaoyue Jiang
- School of Pharmacy, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Feng Xiang
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Chenxi Jia
- School of Pharmacy, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Amanda Rae Buchberger
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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14
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Zhang Y, DeLaney K, Hui L, Wang J, Sturm RM, Li L. A Multifaceted Mass Spectrometric Method to Probe Feeding Related Neuropeptide Changes in Callinectes sapidus and Carcinus maenas. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:948-960. [PMID: 29435768 PMCID: PMC5959843 DOI: 10.1007/s13361-017-1888-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 05/07/2023]
Abstract
Food intake is regulated by various neuromodulators, including numerous neuropeptides. However, it remains elusive at the molecular and cellular level as to how these important chemicals regulate internal processes and which regions of the neuronal organs are responsible for regulating the behavior. Here we report a comparative neuropeptidomic analysis of the brain and pericardial organ (PO) in response to feeding in two well-studied crustacean physiology model organisms, Callinectes sapidus and Carcinus maenas, using mass spectrometry (MS) techniques. A multifaceted MS-based approach has been developed to obtain complementary information on the expression changes of a large array of neuropeptides in the brain and PO. The method employs stable isotope labeling of brain and PO extracts for relative MS quantitation, capillary electrophoresis (CE)-MS for fractionation and high-specificity analysis, and mass spectrometric imaging (MSI) for in-situ molecular mapping of peptides. A number of neuropeptides, including RFamides, B-type allatostatins (AST-B), RYamides, and orcokinins exhibit significant changes in abundance after feeding in this investigation. Peptides from the AST-B family found in PO tissue were shown to have both altered expression and localization changes after feeding, indicating that they may be a class of vital neuropeptide regulators involved in feeding behavior. Graphical Abstract ᅟ.
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Affiliation(s)
- Yuzhuo Zhang
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705-2222, USA
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI, 53706-1322, USA
| | - Limei Hui
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705-2222, USA
| | - Junhua Wang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI, 53706-1322, USA
| | - Robert M Sturm
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705-2222, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705-2222, USA.
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI, 53706-1322, USA.
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15
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Cao Q, Ouyang C, Zhong X, Li L. Profiling of small molecule metabolites and neurotransmitters in crustacean hemolymph and neuronal tissues using reversed-phase LC-MS/MS. Electrophoresis 2018; 39:1241-1248. [PMID: 29579349 PMCID: PMC7382969 DOI: 10.1002/elps.201800058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/04/2018] [Accepted: 03/07/2018] [Indexed: 12/14/2022]
Abstract
Crustaceans have been long used as model animals for neuromodulation studies because of their well-defined neural circuitry. The identification of small molecule metabolites and signaling molecules in circulating fluids and neuronal tissues presents unique challenges due to their diverse structures, biological functions, and wide range of concentrations. LC combined with high resolution MS/MS is one of the most powerful tools to uncover endogenous small molecules. Here we explored several sample preparation techniques (solid-phase extraction and denaturing) and MS data acquisition strategies (data-dependent acquisition and targeted MS2-based acquisition) that provided complementary coverage and improved overall identification rate in C18 LC-MS/MS experiment. By MS/MS spectral matching with mzCloud database and those generated from standard compounds, a total of 129 small molecule metabolites and neurotransmitters were identified from crustacean hemolymph and neuronal tissues. These confidently identified small molecules covered predominant biosynthetic pathways for major neurotransmitters, validating the effectiveness of the high-throughput RPLC-MS/MS approach in studying the metabolism of neurotransmitters.
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Affiliation(s)
- Qinjingwen Cao
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin, 53706, United States
| | - Chuanzi Ouyang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin, 53706, United States
| | - Xuefei Zhong
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin, 53705, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin, 53706, United States
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin, 53705, United States
- School of Life Sciences, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
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16
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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: 4.7] [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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17
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Boonen K, De Haes W, Van Houtven J, Verdonck R, Baggerman G, Valkenborg D, Schoofs L. Quantitative Peptidomics with Isotopic and Isobaric Tags. Methods Mol Biol 2018; 1719:141-159. [PMID: 29476509 DOI: 10.1007/978-1-4939-7537-2_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In differential peptidomics, peptide profiles are compared between biological samples and the resulting expression levels are correlated to a phenotype of interest. This, in turn, allows us insight into how peptides may affect the phenotype of interest. In quantitative differential peptidomics, both label-based and label-free techniques are often employed. Label-based techniques have several advantages over label-free methods, primarily that labels allow for various samples to be pooled prior to liquid chromatography-mass spectrometry (LC-MS) analysis, reducing between-run variation. Here, we detail a method for performing quantitative peptidomics using stable amine-binding isotopic and isobaric tags.
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Affiliation(s)
- Kurt Boonen
- Research Group of Functional Genomics and Proteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Wouter De Haes
- Research Group of Functional Genomics and Proteomics, Department of Biology, KU Leuven, Leuven, Belgium
- Research Group of Molecular and Functional Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Joris Van Houtven
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven, Belgium
| | - Rik Verdonck
- Research Group of Molecular Developmental Physiology and Signal Transduction, Department of Biology, KU Leuven, Leuven, Belgium
| | - Geert Baggerman
- Center for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Dirk Valkenborg
- Center for Proteomics, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Liliane Schoofs
- Research Group of Functional Genomics and Proteomics, Department of Biology, KU Leuven, Leuven, Belgium.
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18
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Ohno H, Yoshida M, Sato T, Kato J, Miyazato M, Kojima M, Ida T, Iino Y. Luqin-like RYamide peptides regulate food-evoked responses in C. elegans. eLife 2017; 6:e28877. [PMID: 28847365 PMCID: PMC5576490 DOI: 10.7554/elife.28877] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/08/2017] [Indexed: 12/25/2022] Open
Abstract
Peptide signaling controls many processes involving coordinated actions of multiple organs, such as hormone-mediated appetite regulation. However, the extent to which the mode of action of peptide signaling is conserved in different animals is largely unknown, because many peptides and receptors remain orphan and many undiscovered peptides still exist. Here, we identify two novel Caenorhabditis elegans neuropeptides, LURY-1-1 and LURY-1-2, as endogenous ligands for the neuropeptide receptor-22 (NPR-22). Both peptides derive from the same precursor that is orthologous to invertebrate luqin/arginine-tyrosine-NH2 (RYamide) proneuropeptides. LURY-1 peptides are secreted from two classes of pharyngeal neurons and control food-related processes: feeding, lifespan, egg-laying, and locomotory behavior. We propose that LURY-1 peptides transmit food signals to NPR-22 expressed in feeding pacemaker neurons and a serotonergic neuron. Our results identified a critical role for luqin-like RYamides in feeding-related processes and suggested that peptide-mediated negative feedback is important for satiety regulation in C. elegans.
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Affiliation(s)
- Hayao Ohno
- Department of Biological SciencesGraduate School of Science, The University of TokyoTokyoJapan
| | - Morikatsu Yoshida
- Department of BiochemistryNational Cerebral and Cardiovascular Center Research InstituteOsakaJapan
| | - Takahiro Sato
- Molecular GeneticsInstitute of Life Sciences, Kurume UniversityFukuokaJapan
| | - Johji Kato
- Department of Bioactive PeptidesFrontier Science Research Center, University of MiyazakiMiyazakiJapan
| | - Mikiya Miyazato
- Department of BiochemistryNational Cerebral and Cardiovascular Center Research InstituteOsakaJapan
| | - Masayasu Kojima
- Molecular GeneticsInstitute of Life Sciences, Kurume UniversityFukuokaJapan
| | - Takanori Ida
- Department of Bioactive PeptidesFrontier Science Research Center, University of MiyazakiMiyazakiJapan
- Center for Animal Disease ControlUniversity of MiyazakiMiyazakiJapan
| | - Yuichi Iino
- Department of Biological SciencesGraduate School of Science, The University of TokyoTokyoJapan
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19
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Verdonck R, De Haes W, Cardoen D, Menschaert G, Huhn T, Landuyt B, Baggerman G, Boonen K, Wenseleers T, Schoofs L. Fast and Reliable Quantitative Peptidomics with labelpepmatch. J Proteome Res 2016; 15:1080-9. [DOI: 10.1021/acs.jproteome.5b00845] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Gerben Menschaert
- Research
Group of Bio-informatics and Computational Genomics, Ghent University, Ghent, Belgium
| | - Thomas Huhn
- Chemistry
Department, University of Konstanz, Konstanz, Germany
| | | | - Geert Baggerman
- CFP/CeProMa, Antwerp University, Antwerp, Belgium
- Applied Bio & Molecular Systems, Vito, Mol, Belgium
| | - Kurt Boonen
- Biology
Department, KU Leuven, Leuven, Belgium
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20
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OuYang C, Chen B, Li L. High Throughput In Situ DDA Analysis of Neuropeptides by Coupling Novel Multiplex Mass Spectrometric Imaging (MSI) with Gas-Phase Fractionation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1992-2001. [PMID: 26438126 PMCID: PMC4837696 DOI: 10.1007/s13361-015-1265-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 08/22/2015] [Accepted: 08/24/2015] [Indexed: 05/05/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometric imaging (MSI) is a powerful tool to map the spatial distribution of biomolecules on tissue sections. Recent developments of hybrid MS instruments allow combination of different types of data acquisition by various mass analyzers into a single MSI analysis, which reduces experimental time and sample consumptions. Here, using the well-characterized crustacean nervous system as a test-bed, we explore the utility of high resolution and accurate mass (HRAM) MALDI Orbitrap platform for enhanced in situ characterization of the neuropeptidome with improved chemical information. Specifically, we report on a multiplex-MSI method, which combines HRAM MSI with data dependent acquisition (DDA) tandem MS analysis in a single experiment. This method enables simultaneous mapping of neuropeptide distribution, sequence validation, and novel neuropeptide discovery in crustacean neuronal tissues. To enhance the dynamic range and efficiency of in situ DDA, we introduced a novel approach of fractionating full m/z range into several sub-mass ranges and embedding the setup using the multiplex-DDA-MSI scan events to generate pseudo fractionation before MS/MS scans. The division of entire m/z into multiple segments of m/z sub-ranges for MS interrogation greatly decreased the complexity of molecular species from tissue samples and the heterogeneity of the distribution and variation of intensities of m/z peaks. By carefully optimizing the experimental conditions such as the dynamic exclusion, the multiplex-DDA-MSI approach demonstrates better performance with broader precursor coverage, less biased MS/MS scans towards high abundance molecules, and improved quality of tandem mass spectra for low intensity molecular species. Graphical Abstract ᅟ.
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Affiliation(s)
- Chuanzi OuYang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Bingming Chen
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA.
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53705, USA.
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21
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Zhang Y, Buchberger A, Muthuvel G, Li L. Expression and distribution of neuropeptides in the nervous system of the crab Carcinus maenas and their roles in environmental stress. Proteomics 2015; 15:3969-79. [PMID: 26475201 DOI: 10.1002/pmic.201500256] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 10/07/2015] [Accepted: 10/12/2015] [Indexed: 01/05/2023]
Abstract
Environmental fluctuations, such as salinity, impose serious challenges to marine animal survival. Neuropeptides, signaling molecules involved in the regulation process, and the dynamic changes of their full complement in the stress response have yet to be investigated. Here, a MALDI-MS-based stable isotope labeling quantitation strategy was used to investigate the relationship between neuropeptide expression and adaptability of Carcinus maenas to various salinity levels, including high (60 parts per thousand [p.p.t.]) and low (0 p.p.t.) salinity, in both the crustacean pericardial organ (PO) and brain. Moreover, a high salinity stress time course study was conducted. MS imaging (MSI) of neuropeptide localization in C. maenas PO was also performed. As a result of salinity stress, multiple neuropeptide families exhibited changes in their relative abundances, including RFamides (e.g. APQGNFLRFamide), RYamides (e.g. SSFRVGGSRYamide), B-type allatostatins (AST-B; e.g. VPNDWAHFRGSWamide), and orcokinins (e.g. NFDEIDRSSFGFV). The MSI data revealed distribution differences in several neuropeptides (e.g. SGFYANRYamide) between color morphs, but salinity stress appeared to not have a major effect on the localization of the neuropeptides.
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Affiliation(s)
- Yuzhuo Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Amanda Buchberger
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
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22
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De Haes W, Van Sinay E, Detienne G, Temmerman L, Schoofs L, Boonen K. Functional neuropeptidomics in invertebrates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:812-26. [PMID: 25528324 DOI: 10.1016/j.bbapap.2014.12.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/27/2014] [Accepted: 12/10/2014] [Indexed: 10/24/2022]
Abstract
Neuropeptides are key messengers in almost all physiological processes. They originate from larger precursors and are extensively processed to become bioactive. Neuropeptidomics aims to comprehensively identify the collection of neuropeptides in an organism, organ, tissue or cell. The neuropeptidome of several invertebrates is thoroughly explored since they are important model organisms (and models for human diseases), disease vectors and pest species. The charting of the neuropeptidome is the first step towards understanding peptidergic signaling. This review will first discuss the latest developments in exploring the neuropeptidome. The physiological roles and modes of action of neuropeptides can be explored in two ways, which are largely orthogonal and therefore complementary. The first way consists of inferring the functions of neuropeptides by a forward approach where neuropeptide profiles are compared under different physiological conditions. Second is the reverse approach were neuropeptide collections are used to screen for receptor-binding. This is followed by localization studies and functional tests. This review will focus on how these different functional screening methods contributed to the field of invertebrate neuropeptidomics and expanded our knowledge of peptidergic signaling. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Wouter De Haes
- Functional Genomics and Proteomics, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000 Leuven, Belgium
| | - Elien Van Sinay
- Functional Genomics and Proteomics, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000 Leuven, Belgium
| | - Giel Detienne
- Functional Genomics and Proteomics, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000 Leuven, Belgium
| | - Liesbet Temmerman
- Functional Genomics and Proteomics, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000 Leuven, Belgium
| | - Liliane Schoofs
- Functional Genomics and Proteomics, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000 Leuven, Belgium
| | - Kurt Boonen
- Functional Genomics and Proteomics, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000 Leuven, Belgium.
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23
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Frost DC, Greer T, Li L. High-resolution enabled 12-plex DiLeu isobaric tags for quantitative proteomics. Anal Chem 2014; 87:1646-54. [PMID: 25405479 PMCID: PMC4318621 DOI: 10.1021/ac503276z] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Multiplex
isobaric tags (e.g., tandem mass tags (TMT) and isobaric
tags for relative and absolute quantification (iTRAQ)) are a valuable
tool for high-throughput mass spectrometry based quantitative proteomics.
We have developed our own multiplex isobaric tags, DiLeu, that feature
quantitative performance on par with commercial offerings but can
be readily synthesized in-house as a cost-effective alternative. In
this work, we achieve a 3-fold increase in the multiplexing capacity
of the DiLeu reagent without increasing structural complexity by exploiting
mass defects that arise from selective incorporation of 13C, 15N, and 2H stable isotopes in the reporter
group. The inclusion of eight new reporter isotopologues that differ
in mass from the existing four reporters by intervals of 6 mDa yields
a 12-plex isobaric set that preserves the synthetic simplicity and
quantitative performance of the original implementation. We show that
the new reporter variants can be baseline-resolved in high-resolution
higher-energy C-trap dissociation (HCD) spectra, and we demonstrate
accurate 12-plex quantitation of a DiLeu-labeled Saccharomyces
cerevisiae lysate digest via high-resolution nano
liquid chromatography–tandem mass spectrometry (nanoLC–MS2) analysis on an Orbitrap Elite mass spectrometer.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin , 777 Highland Avenue, Madison, Wisconsin 53705, United States
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24
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Chen R, Ouyang C, Xiao M, Li L. In situ identification and mapping of neuropeptides from the stomatogastric nervous system of Cancer borealis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2437-2444. [PMID: 25303472 PMCID: PMC4216564 DOI: 10.1002/rcm.7037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 08/26/2014] [Accepted: 08/31/2014] [Indexed: 06/02/2023]
Abstract
RATIONALE The crustacean stomatogastric nervous system (STNS) is a classic experimental model to derive basic knowledge about neuronal functions and how they coordinate with each other to generate neural circuits. To investigate the components of the neuromodulators and how they are distributed in such a system is essential to understand the underlying mechanism. In this study, in situ mass spectrometry based techniques were employed to fulfill this goal. METHODS Offline high-performance liquid chromatography (HPLC) separation was coupled with matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) to analyze the neuropeptides in the stomatogastric ganglion (STG) tissue extract from the Jonah crab Cancer borealis. Direct tissue analysis was employed to investigate the neuropeptides present in the STNS. MALDI imaging was also applied to map the localization of multiple neuropeptide families in the STG and the upstream nerve fibers. RESULTS Fifty-seven neuropeptides were detected from a single desheathed STG using direct tissue analysis, and they were from eleven different neuropeptide families, including FaRP, AST-A, AST-B, etc. Differential neuropeptide profiles from three different types of ganglia and two types of nerve fiber tissues from the STNS were documented. The direct tissue analysis was shown better for studying neuropeptides from small neural organs like the STG as compared to the large-scale HPLC/MALDI analysis. MALDI images were also acquired to study the distribution of neuropeptides in the STG. CONCLUSIONS In this study, the components and distribution of neuropeptides have been analyzed in the STNS from C. borealis using direct tissue profiling and MALDI imaging. The results show that the direct tissue analysis of desheathed neural tissues can provide higher sensitivity for neuropeptide study compared to large-scale HPLC/MALDI analysis of pooled tissues. The results are valuable for understanding the functions of neuropeptides in neural network generation.
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Affiliation(s)
- Ruibing Chen
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Chuanzi Ouyang
- Department of Chemistry and Pharmacy School, University of Wisconsin at Madison, WI 53705, USA
| | - Mingming Xiao
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Lingjun Li
- Department of Chemistry and Pharmacy School, University of Wisconsin at Madison, WI 53705, USA
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Mass spectrometric analysis of spatio-temporal dynamics of crustacean neuropeptides. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:798-811. [PMID: 25448012 DOI: 10.1016/j.bbapap.2014.10.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/23/2014] [Accepted: 10/28/2014] [Indexed: 12/13/2022]
Abstract
Neuropeptides represent one of the largest classes of signaling molecules used by nervous systems to regulate a wide range of physiological processes. Over the past several years, mass spectrometry (MS)-based strategies have revolutionized the discovery of neuropeptides in numerous model organisms, especially in decapod crustaceans. Here, we focus our discussion on recent advances in the use of MS-based techniques to map neuropeptides in the spatial domain and monitoring their dynamic changes in the temporal domain. These MS-enabled investigations provide valuable information about the distribution, secretion and potential function of neuropeptides with high molecular specificity and sensitivity. In situ MS imaging and in vivo microdialysis are highlighted as key technologies for probing spatio-temporal dynamics of neuropeptides in the crustacean nervous system. This review summarizes the latest advancement in MS-based methodologies for neuropeptide analysis including typical workflow and sample preparation strategies as well as major neuropeptide families discovered in decapod crustaceans. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Challenges and recent advances in mass spectrometric imaging of neurotransmitters. Bioanalysis 2014; 6:525-40. [PMID: 24568355 DOI: 10.4155/bio.13.341] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mass spectrometric imaging (MSI) is a powerful tool that grants the ability to investigate a broad mass range of molecules, from small molecules to large proteins, by creating detailed distribution maps of selected compounds. To date, MSI has demonstrated its versatility in the study of neurotransmitters and neuropeptides of different classes toward investigation of neurobiological functions and diseases. These studies have provided significant insight in neurobiology over the years and current technical advances are facilitating further improvements in this field. Herein, we briefly review new MSI studies of neurotransmitters, focusing specifically on the challenges and recent advances of MSI of neurotransmitters.
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Chen R, Xiao M, Buchberger A, Li L. Quantitative neuropeptidomics study of the effects of temperature change in the crab Cancer borealis. J Proteome Res 2014; 13:5767-76. [PMID: 25214466 PMCID: PMC4261957 DOI: 10.1021/pr500742q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Temperature changes influence the
reaction rates of all biological
processes, which can pose dramatic challenges to cold-blooded organisms,
and the capability to adapt to temperature fluctuations is crucial
for the survival of these animals. In order to understand the roles
that neuropeptides play in the temperature stress response, we employed
a mass spectrometry-based approach to investigate the neuropeptide
changes associated with acute temperature elevation in three neural
tissues from the Jonah crab Cancer borealis. At high temperature, members from two neuropeptide families, including
RFamide and RYamide, were observed to be significantly reduced in
one of the neuroendocrine structures, the pericardial organ, while
several orcokinin peptides were detected to be decreased in another
major neuroendocrine organ, the sinus gland. These results implicate
that the observed neuropeptides may be involved with temperature perturbation
response via hormonal regulation. Furthermore, a temperature stress
marker peptide with the primary sequence of SFRRMGGKAQ (m/z 1137.7) was detected and de novo sequenced in
the circulating fluid (hemolymph) from animals under thermal perturbation.
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Affiliation(s)
- Ruibing Chen
- Research Center of Basic Medical Sciences, Tianjin Medical University , Tianjin 300070, China
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28
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Zhang Z, Kuang J, Li L. Liquid chromatography-matrix-assisted laser desorption/ionization mass spectrometric imaging with sprayed matrix for improved sensitivity, reproducibility and quantitation. Analyst 2014; 138:6600-6. [PMID: 24003441 DOI: 10.1039/c3an01225e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometric imaging (MSI) has been employed as a detection method for both capillary electrophoresis (CE)-MALDI and liquid chromatography (LC)-MALDI analyses. Based on our previous studies, here we report a new interface to couple LC with MSI by employing an automated matrix sprayer. The LC trace is directly collected on a ground stainless steel MALDI plate and dried. The matrix is sprayed on the MALDI plate using a programmable matrix sprayer. With the highly uniform matrix layers produced from the sprayer, the MS image signal quality is significantly improved with enhanced signal-to-noise ratios for analyte peaks. With the programmable matrix application and imaging MS data acquisition, the new LC-MSI platform exhibits highly stable and reproducible performance. A total of 87 bovine serum albumin (BSA) tryptic peptides and 295 putative neuropeptides from blue crab pericardial organs have been observed with LC-MSI analysis, exhibiting better performance in terms of peptide coverage than regular LC-MALDI with discrete spot collection and our previously reported LC-MSI interface with the matrix being delivered by a capillary. In addition to relative quantitation with isotopic labeling as we have previously demonstrated, we performed the first absolute quantitation using the new LC-MSI platform and obtained accurate quantitation results for neuropeptides, indicating great potential for quantitative analysis of complex samples.
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Affiliation(s)
- Zichuan Zhang
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705, USA.
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29
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30
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Jia C, Yu Q, Wang J, Li L. Qualitative and quantitative top-down mass spectral analysis of crustacean hyperglycemic hormones in response to feeding. Proteomics 2014; 14:1185-94. [PMID: 24532205 DOI: 10.1002/pmic.201300331] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 12/07/2013] [Accepted: 02/10/2014] [Indexed: 12/13/2022]
Abstract
An efficient pipeline for peptide discovery accelerates peptidomic analysis and facilitates a better understanding of the functional roles of neuropeptides. However, qualitative and quantitative analysis of large neuropeptides is challenging due to the bigger molecular sizes, multiple PTMs, and interference by homologous isoforms. Herein, we refined two methodologies in the pipeline for highly confident and efficient MS-based peptide discovery. For the qualitative analysis, the so-called "high resolution/accurate mass" measurement on Orbitrap mass spectrometers was integrated with computer-assisted homology search, which was successfully applied to decipher the substituted amino acid residues in large neuropeptides by referring to homologous sequences. For the quantitative analysis, a new isotopic labeling-assisted top-down MS strategy was developed, which enabled direct monitoring of the abundance changes of endogenous large neuropeptides. By using the refined peptide discovery pipeline, one novel crustacean hyperglycemic hormone (CHH) from the Dungeness crab sinus glands was confidently identified and de novo sequenced, and its relative abundance was quantified. Comparative analysis of CHHs in unfed and fed crabs revealed that the peptide abundance in the sinus glands was significantly increased after food intake, suggesting that the release of CHHs might be altered by feeding behavior.
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Affiliation(s)
- Chenxi Jia
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, WI, USA
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31
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Salisbury JP, Boggio KJ, Hsu YWA, Quijada J, Sivachenko A, Gloeckner G, Kowalski PJ, Easterling ML, Rosbash M, Agar JN. A rapid MALDI-TOF mass spectrometry workflow for Drosophila melanogaster differential neuropeptidomics. Mol Brain 2013; 6:60. [PMID: 24373546 PMCID: PMC4022047 DOI: 10.1186/1756-6606-6-60] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 12/20/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Neuropeptides are a diverse category of signaling molecules in the nervous system regulating a variety of processes including food intake, social behavior, circadian rhythms, learning, and memory. Both the identification and functional characterization of specific neuropeptides are ongoing fields of research. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis of nervous tissues from a variety of organisms allows direct detection and identification of neuropeptides. Here, we demonstrate an analysis workflow that allows for the detection of differences in specific neuropeptides amongst a variety of neuropeptides being simultaneously measured. For sample preparation, we describe a straight-forward and rapid (minutes) method where individual adult Drosophila melanogaster brains are analyzed. Using a MATLAB-based data analysis workflow, also compatible with MALDI-TOF mass spectra obtained from other sample preparations and instrumentation, we demonstrate how changes in neuropeptides levels can be detected with this method. RESULTS Over fifty isotopically resolved ion signals in the peptide mass range are reproducibly observed across experiments. MALDI-TOF MS profile spectra were used to statistically identify distinct relative differences in organ-wide endogenous levels of detected neuropeptides between biological conditions. In particular, three distinct levels of a particular neuropeptide, pigment dispersing factor, were detected by comparing groups of preprocessed spectra obtained from individual brains across three different D. melanogaster strains, each of which express different amounts of this neuropeptide. Using the same sample preparation, MALDI-TOF/TOF tandem mass spectrometry confirmed that at least 14 ion signals observed across experiments are indeed neuropeptides. Among the identified neuropeptides were three products of the neuropeptide-like precursor 1 gene previously not identified in the literature. CONCLUSIONS Using MALDI-TOF MS and preprocessing/statistical analysis, changes in relative levels of a particular neuropeptide in D. melanogaster tissue can be statistically detected amongst a variety of neuropeptides. While the data analysis methods should be compatible with other sample preparations, the presented sample preparation method was sufficient to identify previously unconfirmed D. melanogaster neuropeptides.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jeffrey N Agar
- Depts of Chemistry and Chemical Biology and Pharmaceutical Sciences and Barnett Institute of Chemical and Biological Analysis, Northeastern University, 140 The Fenway, Boston, MA 02115, USA.
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Zhang X, Zhang F, Guo L, Wang Y, Zhang P, Wang R, Zhang N, Chen R. Interactome analysis reveals that C1QBP (complement component 1, q subcomponent binding protein) is associated with cancer cell chemotaxis and metastasis. Mol Cell Proteomics 2013; 12:3199-209. [PMID: 23924515 DOI: 10.1074/mcp.m113.029413] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The complement component 1, q subcomponent binding protein (C1QBP/p32/HABP1) is a ubiquitously expressed and multicompartmental cellular protein involved in various biological processes. In order to further understand its biological functions, we conducted proteomics analysis of its interactome in this study. An improved sample preparation and mass spectrometric identification strategy was developed combining high-speed centrifugation, formaldehyde labeling, and two-dimensional reverse-phase liquid chromatography. Using this approach, we identified 187 interacting proteins and constructed a highly connected interacting network for C1QBP. Moreover, we explored the interaction between C1QBP and protein kinase C ζ, a key regulator of cell polarity and migration. The results indicated that C1QBP regulated the activity of protein kinase C ζ and modulated EGF-induced cancer cell chemotaxis. In addition, C1QBP was required for breast cancer metastasis in a severe combined immunodeficiency mouse model. Furthermore, C1QBP was observed to be overexpressed in breast cancer tissues, and its expression level was closely linked with distant metastasis and TNM stages. In summary, C1QBP was identified as a novel regulator of cancer metastasis that may serve as a therapeutic target for breast cancer treatment.
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Affiliation(s)
- Xiaofang Zhang
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
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Jia C, Lietz CB, Ye H, Hui L, Yu Q, Yoo S, Li L. A multi-scale strategy for discovery of novel endogenous neuropeptides in the crustacean nervous system. J Proteomics 2013; 91:1-12. [PMID: 23806756 DOI: 10.1016/j.jprot.2013.06.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/26/2013] [Accepted: 06/16/2013] [Indexed: 12/18/2022]
Abstract
UNLABELLED The conventional mass spectrometry (MS)-based strategy is often inadequate for the comprehensive characterization of various size neuropeptides without the assistance of genomic information. This study evaluated sequence coverage of different size neuropeptides in two crustacean species, blue crab Callinectes sapidus and Jonah crab Cancer borealis using conventional MS methodologies and revealed limitations to mid- and large-size peptide analysis. Herein we attempt to establish a multi-scale strategy for simultaneous and confident sequence elucidation of various sizes of peptides in the crustacean nervous system. Nine novel neuropeptides spanning a wide range of molecular weights (0.9-8.2kDa) were fully sequenced from a major neuroendocrine organ, the sinus gland of the spiny lobster Panulirus interruptus. These novel neuropeptides included seven allatostatin (A- and B-type) peptides, one crustacean hyperglycemic hormone precursor-related peptide, and one crustacean hyperglycemic hormone. Highly accurate multi-scale characterization of a collection of varied size neuropeptides was achieved by integrating traditional data-dependent tandem MS, improved bottom-up sequencing, multiple fragmentation technique-enabled top-down sequencing, chemical derivatization, and in silico homology search. Collectively, the ability to characterize a neuropeptidome with vastly differing molecule sizes from a neural tissue extract could find great utility in unraveling complex signaling peptide mixtures employed by other biological systems. BIOLOGICAL SIGNIFICANCE Mass spectrometry (MS)-based neuropeptidomics aims to completely characterize the neuropeptides in a target organism as an important first step toward a better understanding of the structure and function of these complex signaling molecules. Although liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) with data-dependent acquisition is a powerful tool in peptidomic research, it often lacks the capability for de novo sequencing of mid-size and large peptides due to inefficient fragmentation of peptides larger than 4kDa. This study describes a multi-scale strategy for complete and confident sequence elucidation of various sizes of neuropeptides in the crustacean nervous system. The aim is to fill a technical gap where the conventional strategy is inefficient for comprehensive characterization of a complex neuropeptidome without assistance of genomic information. Nine novel neuropeptides in a wide range of molecular weights (0.9-8.2kDa) were fully sequenced from a major neuroendocrine organ of the spiny lobster, P. interruptus. The resulting molecular information extracted from such multi-scale peptidomic analysis will greatly accelerate functional studies of these novel neuropeptides.
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Affiliation(s)
- Chenxi Jia
- School of Pharmacy, University of Wisconsin-Madison, WI, USA; Department of Chemistry, University of Wisconsin-Madison, WI, USA
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Sturm RM, Greer T, Woodards N, Gemperline E, Li L. Mass spectrometric evaluation of neuropeptidomic profiles upon heat stabilization treatment of neuroendocrine tissues in crustaceans. J Proteome Res 2013; 12:743-52. [PMID: 23227893 DOI: 10.1021/pr300805f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tissue heat stabilization is a vital component in successful mammalian neuropeptidomic studies. Heat stabilization using focused microwave irradiation, conventional microwave irradiation, boiling, and treatment with the Denator Stabilizor T1 have all proven effective in arresting post-mortem protein degradation. Although research has reported the presence of protein fragments in crustacean hemolymph when protease inhibitors were not added to the sample, the degree to which post-mortem protease activity affects neuropeptidomic tissue studies in crustacean species has not been investigated in depth. This work examines the need for Stabilizor T1 or boiling tissue stabilization methods for neuropeptide studies of Callinectes sapidus (blue crab) pericardial organ tissue. Neuropeptides in stabilized and nonstabilized tissue were extracted using acidified methanol or N,N-dimethylformamide (DMF) and analyzed by MALDI-TOF and nanoLC-ESI-MS/MS platforms. Post-mortem fragments did not dramatically affect MALDI analysis in the range m/z 650-1600, but observations in ESI MS/MS experiments suggest that putative post-mortem fragments can mask neuropeptide signal and add spectral complexity to crustacean neuropeptidomic studies. The impact of the added spectral complexity did not dramatically affect the number of detected neuropeptides between stabilized and nonstabilized tissues. However, it is prudent that neuropeptidomic studies of crustacean species include a preliminary experiment using the heat stabilization method to assess the extent of neuropeptide masking by larger, highly charged molecular species.
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Affiliation(s)
- Robert M Sturm
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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35
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Jia C, Hui L, Cao W, Lietz CB, Jiang X, Chen R, Catherman AD, Thomas PM, Ge Y, Kelleher NL, Li L. High-definition de novo sequencing of crustacean hyperglycemic hormone (CHH)-family neuropeptides. Mol Cell Proteomics 2012; 11:1951-64. [PMID: 23028060 DOI: 10.1074/mcp.m112.020537] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A complete understanding of the biological functions of large signaling peptides (>4 kDa) requires comprehensive characterization of their amino acid sequences and post-translational modifications, which presents significant analytical challenges. In the past decade, there has been great success with mass spectrometry-based de novo sequencing of small neuropeptides. However, these approaches are less applicable to larger neuropeptides because of the inefficient fragmentation of peptides larger than 4 kDa and their lower endogenous abundance. The conventional proteomics approach focuses on large-scale determination of protein identities via database searching, lacking the ability for in-depth elucidation of individual amino acid residues. Here, we present a multifaceted MS approach for identification and characterization of large crustacean hyperglycemic hormone (CHH)-family neuropeptides, a class of peptide hormones that play central roles in the regulation of many important physiological processes of crustaceans. Six crustacean CHH-family neuropeptides (8-9.5 kDa), including two novel peptides with extensive disulfide linkages and PTMs, were fully sequenced without reference to genomic databases. High-definition de novo sequencing was achieved by a combination of bottom-up, off-line top-down, and on-line top-down tandem MS methods. Statistical evaluation indicated that these methods provided complementary information for sequence interpretation and increased the local identification confidence of each amino acid. Further investigations by MALDI imaging MS mapped the spatial distribution and colocalization patterns of various CHH-family neuropeptides in the neuroendocrine organs, revealing that two CHH-subfamilies are involved in distinct signaling pathways.
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Affiliation(s)
- Chenxi Jia
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
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Hui L, Xiang F, Zhang Y, Li L. Mass spectrometric elucidation of the neuropeptidome of a crustacean neuroendocrine organ. Peptides 2012; 36:230-9. [PMID: 22627023 PMCID: PMC3402701 DOI: 10.1016/j.peptides.2012.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/14/2012] [Accepted: 05/14/2012] [Indexed: 01/23/2023]
Abstract
The blue crab Callinectes sapidus has been used as an experimental model organism for the study of regulation of cardiac activity and other physiological processes. Moreover, it is an economically and ecologically important crustacean species. However, there was no previous report on the characterization of its neuropeptidome. To fill in this gap, we employed multiple sample preparation methods including direct tissue profiling, crude tissue extraction and tissue extract fractionation by HPLC to obtain a complete description of the neuropeptidome of C. sapidus. Matrix-assisted laser desorption/ionization (MALDI)-Fourier transform mass spectrometry (FTMS) and MALDI-time-of-flight (TOF)/TOF were utilized initially to obtain a quick snapshot of the neuropeptide profile, and subsequently nanoflow liquid chromatography (nanoLC) coupled with electrospray ionization quadrupole time-of-flight (ESI-Q-TOF) tandem MS analysis of neuropeptide extracts was conducted for de novo sequencing. Simultaneously, the pericardial organ (PO) tissue extract was labeled by a novel N,N-dimethylated leucine (DiLeu) reagent, offering enhanced fragmentation efficiency of peptides. In total, 130 peptide sequences belonging to 11 known neuropeptide families including orcomyotropin, pyrokinin, allatostatin A (AST-A), allatostatin B (AST-B), FMRFamide-like peptides (FLPs), and orcokinin were identified. Among these 130 sequences, 44 are novel peptides and 86 are previously identified. Overall, our results lay the groundwork for future physiological studies of neuropeptides in C. sapidus and other crustaceans.
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Affiliation(s)
- Limei Hui
- Department of Chemistry, University of Wisconsin-Madison, WI, USA
| | - Feng Xiang
- School of Pharmacy, University of Wisconsin-Madison, WI, USA
| | - Yuzhuo Zhang
- Department of Chemistry, University of Wisconsin-Madison, WI, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, WI, USA
- School of Pharmacy, University of Wisconsin-Madison, WI, USA
- Address correspondence to: Dr. Lingjun Li, School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI 53705-2222. Phone: (608)265-8491; Fax: (608)262-5345;
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Hui L, Zhang Y, Wang J, Cook A, Ye H, Nusbaum MP, Li L. Discovery and functional study of a novel crustacean tachykinin neuropeptide. ACS Chem Neurosci 2011; 2:711-722. [PMID: 22247794 DOI: 10.1021/cn200042p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Tachykinin-related peptide (TRP) refers to a large and structurally diverse family of neuropeptides found in vertebrate and invertebrate nervous systems. These peptides have various important physiological functions, from regulating stress in mammals to exciting the pyloric (food filtering) rhythm in the stomatogastric nervous system (STNS) of decapod crustaceans. Here, a novel TRP, which we named CalsTRP (Callinectes sapidus TRP), YPSGFLGMRamide (m/z 1026.52), was identified and de novo sequenced using a multifaceted mass spectrometry-based platform in both the central nervous system (CNS) and STNS of C. sapidus. We also found, using isotopic formaldehyde labeling, that CalsTRP in the C. sapidus brain and commissural ganglion (CoG) was up-regulated after food-intake, suggesting that TRPs in the CNS and STNS are involved in regulating feeding in Callinectes. Using imaging mass spectrometry, we determined that the previously identified CabTRP Ia (APSGFLGMRamide) and CalsTRP were co-localized in the C. sapidus brain. Lastly, our electrophysiological studies show that bath-applied CalsTRP and CabTRP Ia each activates the pyloric and gastric mill rhythms in C. sapidus, as shown previously for pyloric rhythm activation by CabTRP Ia in the crab Cancer borealis. In summary, the newly identified CalsTRP joins CabTRP Ia as a TRP family member in the decapod crustacean nervous system, whose actions include regulating feeding behavior.
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Affiliation(s)
| | | | | | - Aaron Cook
- Department of Neuroscience, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Michael P. Nusbaum
- Department of Neuroscience, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Sterkel M, Urlaub H, Rivera-Pomar R, Ons S. Functional Proteomics of Neuropeptidome Dynamics during the Feeding Process of Rhodnius prolixus. J Proteome Res 2011; 10:3363-71. [DOI: 10.1021/pr2001012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcos Sterkel
- Laboratorio de Genética y Genómica Funcional, Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Laboratory, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Rolando Rivera-Pomar
- Laboratorio de Genética y Genómica Funcional, Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, Buenos Aires, Argentina
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Pergamino, Argentina
| | - Sheila Ons
- Laboratorio de Genética y Genómica Funcional, Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, Buenos Aires, Argentina
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Christie AE, Stemmler EA, Dickinson PS. Crustacean neuropeptides. Cell Mol Life Sci 2010; 67:4135-69. [PMID: 20725764 PMCID: PMC11115526 DOI: 10.1007/s00018-010-0482-8] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 07/09/2010] [Accepted: 07/28/2010] [Indexed: 10/19/2022]
Abstract
Crustaceans have long been used for peptide research. For example, the process of neurosecretion was first formally demonstrated in the crustacean X-organ-sinus gland system, and the first fully characterized invertebrate neuropeptide was from a shrimp. Moreover, the crustacean stomatogastric and cardiac nervous systems have long served as models for understanding the general principles governing neural circuit functioning, including modulation by peptides. Here, we review the basic biology of crustacean neuropeptides, discuss methodologies currently driving their discovery, provide an overview of the known families, and summarize recent data on their control of physiology and behavior.
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Affiliation(s)
- Andrew E Christie
- Program in Neuroscience, John W. and Jean C. Boylan Center for Cellular and Molecular Physiology, Mount Desert Island Biological Laboratory, Old Bar Harbor Road, P.O. Box 35, Salisbury Cove, ME 04672, USA.
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Wang J, Zhang Y, Xiang F, Zhang Z, Li L. Combining capillary electrophoresis matrix-assisted laser desorption/ionization mass spectrometry and stable isotopic labeling techniques for comparative crustacean peptidomics. J Chromatogr A 2010; 1217:4463-70. [PMID: 20334868 PMCID: PMC2882495 DOI: 10.1016/j.chroma.2010.02.084] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 02/23/2010] [Accepted: 02/26/2010] [Indexed: 11/27/2022]
Abstract
Herein we describe a sensitive and straightforward off-line capillary electrophoresis (CE) matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) interface in conjunction with stable isotopic labeling (SIL) technique for comparative neuropeptidomic analysis in crustacean model organisms. Two SIL schemes, including a binary H/D formaldehyde labeling technique and novel, laboratory-developed multiplexed dimethylated leucine-based isobaric tagging reagents, have been evaluated in these proof-of-concept experiments. We employ these isotopic labeling techniques in conjunction with CE-MALDI-MS for quantitative peptidomic analyses of the pericardial organs isolated from two crustacean species, the European green crab Carcinus maenas and the blue crab Callinectes sapidus. Isotopically labeled peptide pairs are found to co-migrate in CE fractions and quantitative changes in relative abundances of peptide pairs are obtained by comparing peak intensities of respective peptide pairs. Several neuropeptide families exhibit changes in response to salinity stress, suggesting potential physiological functions of these signaling peptides.
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Affiliation(s)
- Junhua Wang
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705-2222, USA.
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