Multifaceted Mass Spectrometric Investigation of Neuropeptide Changes in Atlantic Blue Crab, Callinectes sapidus, in Response to Low pH Stress

An Updated Guide to the Identification, Quantitation, and Imaging of the Crustacean Neuropeptidome

Crustaceans serve as a useful, simplified model for studying peptides and neuromodulation, as they contain numerous neuropeptide homologs to mammals and enable electrophysiological studies at the single-cell and neural circuit levels. Crustaceans contain well-defined neural networks, including the stomatogastric ganglion, oesophageal ganglion, commissural ganglia, and several neuropeptide-rich organs such as the brain, pericardial organs, and sinus glands. As existing mass spectrometry (MS) methods are not readily amenable to neuropeptide studies, there is a great need for optimized sample preparation, data acquisition, and data analysis methods. Herein, we present a general workflow and detailed methods for MS-based neuropeptidomic analysis of crustacean tissue samples and circulating fluids. In conjunction with profiling, quantitation can also be performed with isotopic or isobaric labeling. Information regarding the localization patterns and changes of peptides can be studied via mass spectrometry imaging. Combining these sample preparation strategies and MS analytical techniques allows for a multi-faceted approach to obtaining deep knowledge of crustacean peptidergic signaling pathways.

Recent advances in mass spectrometry analysis of neuropeptides

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.

ADVANCES IN HIGH-RESOLUTION MALDI MASS SPECTROMETRY FOR NEUROBIOLOGY

Research in the field of neurobiology and neurochemistry has seen a rapid expansion in the last several years due to advances in technologies and instrumentation, facilitating the detection of biomolecules critical to the complex signaling of neurons. Part of this growth has been due to the development and implementation of high-resolution Fourier transform (FT) mass spectrometry (MS), as is offered by FT ion cyclotron resonance (FTICR) and Orbitrap mass analyzers, which improves the accuracy of measurements and helps resolve the complex biological mixtures often analyzed in the nervous system. The coupling of matrix-assisted laser desorption/ionization (MALDI) with high-resolution MS has drastically expanded the information that can be obtained with these complex samples. This review discusses notable technical developments in MALDI-FTICR and MALDI-Orbitrap platforms and their applications toward molecules in the nervous system, including sequence elucidation and profiling with de novo sequencing, analysis of post-translational modifications, in situ analysis, key advances in sample preparation and handling, quantitation, and imaging. Notable novel applications are also discussed to highlight key developments critical to advancing our understanding of neurobiology and providing insight into the exciting future of this field. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Developing mass spectrometry for the quantitative analysis of neuropeptides

INTRODUCTION

Neuropeptides are signaling molecules originating in the neuroendocrine system that can act as neurotransmitters and hormones in many biochemical processes. Their exact function is difficult to characterize, however, due to dependence on concentration, post-translational modifications, and the presence of other comodulating neuropeptides. Mass spectrometry enables sensitive, accurate, and global peptidomic analyses that can profile neuropeptide expression changes to understand their roles in many biological problems, such as neurodegenerative disorders and metabolic function.

AREAS COVERED

We provide a brief overview of the fundamentals of neuropeptidomic research, limitations of existing methods, and recent progress in the field. This review is focused on developments in mass spectrometry and encompasses labeling strategies, post-translational modification analysis, mass spectrometry imaging, and integrated multi-omic workflows, with discussion emphasizing quantitative advancements.

EXPERT OPINION

Neuropeptidomics is critical for future clinical research with impacts in biomarker discovery, receptor identification, and drug design. While advancements are being made to improve sensitivity and accuracy, there is still room for improvement. Better quantitative strategies are required for clinical analyses, and these methods also need to be amenable to mass spectrometry imaging, post-translational modification analysis, and multi-omics to facilitate understanding and future treatment of many diseases.

Mass spectrometry profiling and quantitation of changes in circulating hormones secreted over time in Cancer borealis hemolymph due to feeding behavior

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.

Hemolymph proteins: An overview across marine arthropods and molluscs

In this compilation we collect information about the main protein components in hemolymph and stress the continued interest in their study. The reasons for such an attention span several areas of biological, veterinarian and medical applications: from the notions for better dealing with the species - belonging to phylum Arthropoda, subphylum Crustacea, and to phylum Mollusca - of economic interest, to the development of 'marine drugs' from the peptides that, in invertebrates, act as antimicrobial, antifungal, antiprotozoal, and/or antiviral agents. Overall, the topic most often on focus is that of innate immunity operated by classes of pattern-recognition proteins. SIGNIFICANCE: The immune response in invertebrates relies on innate rather than on adaptive/acquired effectors. At a difference from the soluble and membrane-bound immunoglobulins and receptors in vertebrates, the antimicrobial, antifungal, antiprotozoal and/or antiviral agents in invertebrates interact with non-self material by targeting some common (rather than some highly specific) structural motifs. Developing this paradigm into (semi) synthetic pharmaceuticals, possibly optimized through the modeling opportunities offered by computational biochemistry, is one of the lessons today's science may learn from the study of marine invertebrates, and specifically of the proteins and peptides in their hemolymph.

Targeted Top-Down Mass Spectrometry for the Characterization and Tissue-Specific Functional Discovery of Crustacean Hyperglycemic Hormones (CHH) and CHH Precursor-Related Peptides in Response to Low pH Stress

Crustacean hyperglycemic hormones (CHHs) are a family of neuropeptides that were discovered in multiple tissues in crustaceans, but the function of most isoforms remains unclear. Functional discovery often requires comprehensive qualitative profiling and quantitative analysis. The conventional enzymatic digestion method has several limitations, such as missing post-translational modification (PTM) information, homology interference, and incomplete sequence coverage. Herein, by using a targeted top-down method, facilitated by higher sensitivity instruments and hybrid fragmentation modes, we achieved the characterization of two CHH isoforms from the sinus glands (SG-CHH) and the pericardial organs (PO-CHH) from the Atlantic blue crab, Callinectes sapidus, with improved sequence coverage compared to earlier studies. In this study, both label-free and isotopic labeling approaches were adopted to monitor the response of CHHs and CHH precursor-related peptide (CPRP) under low pH stress. The identical trends of CPRP and CHH expression indicated that CPRP could serve as an ideal probe in tracking the CHH expression level changes, which would greatly simplify the quantitative analysis of large peptides. Furthermore, the distinct patterns of changes in the expression of CHHs in the SG and the PO suggested their tissue-specific functions in the regulation of low pH stress. Ion mobility-mass spectrometry (IM-MS) was also employed in this study to provide conformation analysis of both CHHs and CPRPs from different tissues.

Mass Spectrometric Profiling of Neuropeptides in Response to Copper Toxicity via Isobaric Tagging

Copper is a necessary nutrient but quickly becomes toxic at elevated levels. To properly handle environmental copper influxes and maintain metal homeostasis, organisms utilize various methods to chelate, excrete, and metabolize heavy metals. These mechanisms are believed to involve complex signaling pathways mediated by neuropeptides. This study incorporates custom N,N-dimethyl leucine isobaric tags to characterize the neuropeptidomic changes after different time points (1, 2, and 4 h) of copper exposure in a model organism, blue crab, Callinectes sapidus. Using a modified simplex optimization strategy, the number of identifiable and quantifiable neuropeptides was increased 3-fold to facilitate a deeper understanding of the signaling pathways involved in responding to heavy metal exposure. The time course exposure showed many interesting findings, including upregulation of inhibitory allatostatin peptides in the pericardial organs. Additionally, there was evidence of transport of a pigment dispersing hormone from the sinus glands to the brain. Overall, this study improves the multiplexing capabilities of neuropeptidomic studies to understand the temporal changes associated with copper toxicity.

Exploring the Sexual Dimorphism of Crustacean Neuropeptide Expression Using Callinectes sapidus as a Model Organism

The impact of numerous diseases has been linked to differences in sex between organisms, including various neurological diseases. As neuropeptides are known to be key players in the nervous system, studying the variation of neuropeptidomic profiles between males and females in a crustacean model organism is of interest. By using high-resolution mass spectrometry with two complementary ionization sources in conjunction with quantitative chemical labeling (isotopic reductive dimethylation), differences were observed in five key neural tissues and hemolymph. Interestingly, while males and females possess numerous neuropeptide isoforms that are unique to their sex, the represented families of each sex remain largely consistent. However, some differences in familial isoforms were also observed, such as the relative numbers of neuropeptides belonging to RFamide and allatostatin A-type families. Additionally, >100 neuropeptides detected across five neural tissues and hemolymph were found to have statistically significant differences in abundance between male and female blue crab samples. Also, hundreds of putative peptide sequences were identified by de novo sequencing that may be indicative of previously undiscovered neuropeptides, highlighting the power of using a multifaceted MS approach.

Mass Spectrometry Quantification, Localization, and Discovery of Feeding-Related Neuropeptides in Cancer borealis

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.

Neuropeptidomic Profiling and Localization in the Crustacean Cardiac Ganglion Using Mass Spectrometry Imaging with Multiple Platforms

The crustacean cardiac neuromuscular system is a useful model for studying how neural circuits generate behavior, as it is comprised of a simple ganglion containing nine neurons, yet acts as a robust central pattern generator. The crustacean heart is neurogenic, receiving input from neuropeptides. However, the specific effects of neuropeptides on cardiac output is not fully understood, and the large degree of comodulation between multiple neuropeptides makes studying these effects more challenging. To address this challenge, matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) imaging was used to localize neuropeptides within the cardiac ganglion (CG), providing information about the identity and localization of neuropeptides being present. CG extracts were also profiled using liquid chromatography coupled to tandem mass spectrometry (MS/MS) with a data independent acquisition method, resulting in the confirmation of 316 neuropeptides. Two MS imaging (MSI) platforms were compared to provide comprehensive results, including a MALDI-Orbitrap instrument for high mass spectral resolution for accurate identifications and a MALDI TOF/TOF instrument for improved spatial resolution and sensitivity, providing more descriptive MS images. MS images for 235 putative neuropeptides were obtained, with the identification of 145 of these being confirmed by either complementary MS/MS data or accurate mass matching. The MSI studies demonstrate the sensitivity and power of this MALDI-based in situ analytical strategy for unraveling the chemical complexity present in a small nine-cell neuronal system. The results of this study will enable more informative assays of the functions of neuropeptides within this important neural circuit.

Mass Spectrometric Profiling of Neuropeptides in Callinectes sapidus during Hypoxia Stress

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.

PRESnovo: Prescreening Prior to de novo Sequencing to Improve Accuracy and Sensitivity of Neuropeptide Identification

Identification of peptides in species lacking fully sequenced genomes is challenging due to the lack of prior knowledge. De novo sequencing is the method of choice, but its performance is less than satisfactory due to algorithmic bias and interference in complex MS/MS spectra. The task becomes even more challenging for endogenous peptides that do not involve an enzymatic digestion step, such as neuropeptides. However, many neuropeptides possess common sequence motifs that are conserved across members of the same family. Taking advantage of this feature to improve de novo sequencing of neuropeptides, we have developed a method named PRESnovo (prescreening precursors prior to de novo sequencing) to predict the motif from a MS/MS spectrum. A neuropeptide sequence is broken into a motif with conserved amino acid residues and the remaining partial sequence. By searching against a predefined motif database constructed from known homologous sequences, PRESnovo assigns the most probable motif to each precursor via a sophisticated scoring function. Performance analysis was conducted with 15 neuropeptide standards, and 11 neuropeptides were correctly identified with PRESnovo compared to 1 identification by PEAKS only. We applied PRESnovo to assign motifs to peptide sequences in conjunction with PEAKS for assigning the rest of the peptide sequence in order to discover neuropeptides in tissue samples of green crab, C. maenas, and Jonah crab, C. borealis. Collectively, a large number of neuropeptides were identified, including 13 putative neuropeptides identified in green crab brain, 77 in Jonah crab brain, and 47 in Jonah crab sinus glands for the first time. This PRESnovo strategy greatly simplifies de novo sequencing and enhances the accuracy and sensitivity of neuropeptide identification when common motifs are present.