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Dong T, Wang X, Jia Z, Yang J, Liu Y. Assessing the associations of 1,400 blood metabolites with major depressive disorder: a Mendelian randomization study. Front Psychiatry 2024; 15:1391535. [PMID: 38903637 PMCID: PMC11187323 DOI: 10.3389/fpsyt.2024.1391535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Background and objectives Major Depressive Disorder (MDD) is one of the most prevalent and debilitating health conditions worldwide. Previous studies have reported a link between metabolic dysregulation and MDD. However, evidence for a causal relationship between blood metabolites and MDD is lacking. Methods Using a two-sample bidirectional Mendelian randomization analysis (MR), we assessed the causal relationship between 1,400 serum metabolites and Major Depressive Disorder (MDD). The Inverse Variance Weighted method (IVW) was employed to estimate the causal association between exposures and outcomes. Additionally, MR-Egger regression, weighted median, simple mode, and weighted mode methods were used as supplementary approaches for a comprehensive appraisal of the causality between blood metabolites and MDD. Pleiotropy and heterogeneity tests were also conducted. Lastly, the relevant metabolites were subjected to metabolite function analysis, and a reverse MR was implemented to explore the potential influence of MDD on these metabolites. Results After rigorous screening, we identified 34 known metabolites, 13 unknown metabolites, and 18 metabolite ratios associated with Major Depressive Disorder (MDD). Among all metabolites, 33 were found to have positive associations, and 32 had negative associations. The top five metabolites that increased the risk of MDD were the Arachidonate (20:4n6) to linoleate (18:2n6) ratio, LysoPE(18:0/0:0), N-acetyl-beta-alanine levels, Arachidonate (20:4n6) to oleate to vaccenate (18:1) ratio, Glutaminylglutamine, and Threonine to pyruvate ratio. Conversely, the top five metabolites that decreased the risk of MDD were N6-Acetyl-L-lysine, Oleoyl-linoleoyl-glycerol (18:1 to 18:2) [2] to linoleoyl-arachidonoyl-glycerol (18:2 to 20:4) [2] ratio, Methionine to phosphate ratio, Pregnanediol 3-O-glucuronide, and 6-Oxopiperidine-2-carboxylic acid. Metabolite function enrichment was primarily concentrated in pathways such as Bile Acid Biosynthesis (FDR=0.177), Glutathione Metabolism (FDR=0.177), Threonine, and 2-Oxobutanoate Degradation (FDR=0.177). In addition, enrichment was noted in pathways like Valine, Leucine, and Isoleucine Biosynthesis (p=0.04), as well as Ascorbate and Aldarate Metabolism (p=0.04). Discussion Within a pool of 1,400 blood metabolites, we identified 34 known metabolites and 13 unknown metabolites, as well as 18 metabolite ratios associated with Major Depressive Disorder (MDD). Additionally, three functionally enriched groups and two metabolic pathways were selected. The integration of genomics and metabolomics has provided significant insights for the screening and prevention of MDD.
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Affiliation(s)
- Tiantian Dong
- Center for External Treatment of Traditional Chinese Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- College of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Xingxin Wang
- College of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Zhixia Jia
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jiguo Yang
- College of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yuanxiang Liu
- Department of Neurology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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Cheng X, Xie H, Xiong Y, Sun P, Xue Y, Li K. Lipidomics profiles of human spermatozoa: insights into capacitation and acrosome reaction using UPLC-MS-based approach. Front Endocrinol (Lausanne) 2023; 14:1273878. [PMID: 38027124 PMCID: PMC10660817 DOI: 10.3389/fendo.2023.1273878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Lipidomics elucidates the roles of lipids in both physiological and pathological processes, intersecting with many diseases and cellular functions. The maintenance of lipid homeostasis, essential for cell health, significantly influences the survival, maturation, and functionality of sperm during fertilization. While capacitation and the acrosome reaction, key processes before fertilization, involve substantial lipidomic alterations, a comprehensive understanding of the changes in human spermatozoa's lipidomic profiles during these processes remains unknown. This study aims to explicate global lipidomic changes during capacitation and the acrosome reaction in human sperm, employing an untargeted lipidomic strategy using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). Methods Twelve semen specimens, exceeding the WHO reference values for semen parameters, were collected. After discontinuous density gradient separation, sperm concentration was adjusted to 2 x 106 cells/ml and divided into three groups: uncapacitated, capacitated, and acrosome-reacted. UPLC-MS analysis was performed after lipid extraction from these groups. Spectral peak alignment and statistical analysis, using unsupervised principal component analysis (PCA), bidirectional orthogonal partial least squares discriminant analysis (O2PLS-DA) analysis, and supervised partial least-squares-latent structure discriminate analysis (PLS-DA), were employed to identify the most discriminative lipids. Results The 1176 lipid peaks overlapped across the twelve individuals in the uncapacitated, capacitated, and acrosome-reacted groups: 1180 peaks between the uncapacitated and capacitated groups, 1184 peaks between the uncapacitated and acrosome-reacted groups, and 1178 peaks between the capacitated and acrosome-reacted groups. The count of overlapping peaks varied among individuals, ranging from 739 to 963 across sperm samples. Moreover, 137 lipids had VIP values > 1.0 and twenty-two lipids had VIP > 1.5, based on the O2PLS-DA model. Furthermore, the identified twelve lipids encompassed increases in PI 44:10, LPS 20:4, LPA 20:5, and LPE 20:4, and decreases in 16-phenyl-tetranor-PGE2, PC 40:6, PS 35:4, PA 29:1, 20-carboxy-LTB4, and 2-oxo-4-methylthio-butanoic acid. Discussion This study has been the first time to investigate the lipidomics profiles associated with acrosome reaction and capacitation in human sperm, utilizing UPLC-MS in conjunction with multivariate data analysis. These findings corroborate earlier discoveries on lipids during the acrosome reaction and unveil new metabolites. Furthermore, this research highlights the effective utility of UPLC-MS-based lipidomics for exploring diverse physiological states in sperm. This study offers novel insights into lipidomic changes associated with capacitation and the acrosome reaction in human sperm, which are closely related to male reproduction.
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Affiliation(s)
- Xiaohong Cheng
- School of Pharmacy, Hangzhou Medical College, Hangzhou, China
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Haifeng Xie
- School of Pharmacy, Hangzhou Medical College, Hangzhou, China
| | - Yuping Xiong
- School of Pharmacy, Hangzhou Medical College, Hangzhou, China
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Peibei Sun
- School of Pharmacy, Hangzhou Medical College, Hangzhou, China
| | - Yamei Xue
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kun Li
- School of Pharmacy, Hangzhou Medical College, Hangzhou, China
- Zhejiang Provincial Laboratory of Experimental Animal’s & Nonclinical Laboratory Studies, Hangzhou Medical College, Hangzhou, Zhejiang, China
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The Role of Primary Cilia-Associated Phosphoinositide Signaling in Development. J Dev Biol 2022; 10:jdb10040051. [PMID: 36547473 PMCID: PMC9785882 DOI: 10.3390/jdb10040051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/07/2022] Open
Abstract
Primary cilia are microtube-based organelles that extend from the cell surface and function as biochemical and mechanical extracellular signal sensors. Primary cilia coordinate a series of signaling pathways during development. Cilia dysfunction leads to a pleiotropic group of developmental disorders, termed ciliopathy. Phosphoinositides (PIs), a group of signaling phospholipids, play a crucial role in development and tissue homeostasis by regulating membrane trafficking, cytoskeleton reorganization, and organelle identity. Accumulating evidence implicates the involvement of PI species in ciliary defects and ciliopathies. The abundance and localization of PIs in the cell are tightly regulated by the opposing actions of kinases and phosphatases, some of which are recently discovered in the context of primary cilia. Here, we review several cilium-associated PI kinases and phosphatases, including their localization along cilia, function in regulating the ciliary biology under normal conditions, as well as the connection of their disease-associated mutations with ciliopathies.
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Wang Z, Sun Y, Bian L, Zhang Y, Zhang Y, Wang C, Tian J, Lu T. The crosstalk signals of Sodium Tanshinone ⅡA Sulfonate in rats with cerebral ischemic stroke: Insights from proteomics. Biomed Pharmacother 2022; 151:113059. [PMID: 35561426 DOI: 10.1016/j.biopha.2022.113059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/06/2022] [Accepted: 04/26/2022] [Indexed: 11/02/2022] Open
Abstract
BACKGROUND Stroke could cause long-term disability, even mortality around the world. Recently, Sodium tanshinone IIA sulfonate (STS), identified from Salvia miltiorrhiza Bunge and was found to have unique efficiency in clinical practice as a potential therapeutic agent for ischemic cerebral infarction. However, systematic investigation about the biological mechanism is still lacking. Herein, we utilized high-throughput proteomics approach to identify the underlying targets for the treatment of STS in stroke. METHODS We investigated the effect of STS on stroke outcomes on rat model of the Middle Cerebral Artery Occlusion and Reperfusion (MCAO/R), assessing by Z-Longa score, infarct volume and HE staining. Pharmacoproteomic profiling of ischemic penumbra in cortical (IPC) was performed using DIA-based label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique. Bioinformatics analysis was processed for further investigation. The expression of core proteins was semi-quantified by DIA, and the major protein correlating with stroke was examined using parallel reaction monitoring (PRM). RESULTS Rats in the MCAO/R group showed neurological function deterioration, which was improved by STS. There were 423 differentially expressed proteins (DEPs) in IPC being detected and quantified in both the sham group and the MCAO/R group. Meanwhile, 285 proteins were significantly changed in the STS treated group, compared to the MCAO/R model. Protein-protein interaction (PPI) network, pathway and biological function enrichment were processed for the DEPs across each two groups, the results of which were integrated for analysis. Alb, mTOR, Dync1h1, Stxbp1, Cltc, and Sptan1 were contained as the core proteins. Altered molecules were discovered to be enriched in 18 signal pathways such as phosphatidylinositol signaling system, PI3K/AKT signal pathway and HIF-1 signal pathway. The results also showed the correlation with sleep disturbances and depression post-stroke. CONCLUSIONS We concluded that STS could prevent penumbra from progressively ongoing damage and improve neurological deficits in MCAO/R model rats. The intersected pathways and protein networks predicted by proteomics might provide much more detailed information for the therapeutic mechanisms of STS in the treatment of CIS.
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Affiliation(s)
- Zheyi Wang
- Qilu Hospital, Shandong University, Jinan, Shandong 250012, China; Beijing University of Chinese Medicine, Beijing 100029, China; School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100026, China; Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100010, China
| | - Yize Sun
- Beijing University of Chinese Medicine, Beijing 100029, China
| | - Lihua Bian
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejing 32500, China
| | - Yiling Zhang
- Xiamen Municipal Health Commission, Xiamen, Fujian 361000, China
| | - Yue Zhang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100026, China
| | - Chunguo Wang
- Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jinzhou Tian
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100010, China
| | - Tao Lu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100026, China.
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Dickson EJ. Phosphoinositide transport and metabolism at membrane contact sites. Biochim Biophys Acta Mol Cell Biol Lipids 2022; 1867:159107. [PMID: 34995791 DOI: 10.1016/j.bbalip.2021.159107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 11/18/2022]
Abstract
Phosphoinositides are a family of signaling lipids that play a profound role in regulating protein function at the membrane-cytosol interface of all cellular membranes. Underscoring their importance, mutations or alterations in phosphoinositide metabolizing enzymes lead to host of developmental, neurodegenerative, and metabolic disorders that are devastating for human health. In addition to lipid enzymes, phosphoinositide metabolism is regulated and controlled at membrane contact sites (MCS). Regions of close opposition typically between the ER and other cellular membranes, MCS are non-vesicular lipid transport portals that engage in extensive communication to influence organelle homeostasis. This review focuses on lipid transport, specifically phosphoinositide lipid transport and metabolism at MCS.
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Affiliation(s)
- Eamonn J Dickson
- Department of Physiology and Membrane Biology, University of California, Davis, CA 95616, United States of America.
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First insights into the honey bee (Apis mellifera) brain lipidome and its neonicotinoid-induced alterations associated with reduced self-grooming behavior. J Adv Res 2021; 37:75-89. [PMID: 35499051 PMCID: PMC9039751 DOI: 10.1016/j.jare.2021.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/21/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
First bee brain characterization shows distinctive low plasmalogens and high alkyl-ether levels. PC 20:3e/15:0, PC 16:0/18:3, PA 18:0/24:1 increased by the highest dose of clothianidin. Levels of CL 18:3/18:1/14:0/22:6, TG 6:0/11:2/18:1 and eLPE 18:0e were linked to intense grooming. Membrane lipids, like PC 18:1e/20:3, ePC 8:1e/20:3, and pPE 16:1p/24:1 were up-regulated by clothianidin. Clothianidin exposure up-regulated genes linked to GPI-anchor biosynthesis pathway. Lipids can be used as biomarkers to assess the effect of neurotoxins on behaviors.
Introduction Honey bees (Apis mellifera) play key roles in food production performing complex behaviors, like self-grooming to remove parasites. However, the lipids of their central nervous system have not been examined, even though they likely play a crucial role in the performance of cognitive process to perform intricate behaviors. Lipidomics has greatly advanced our understanding of neuropathologies in mammals and could provide the same for honey bees. Objectives The objectives of this study were to characterize the brain lipidome of adult honey bees and to assess the effect of clothianidin (a neurotoxic insecticide) on the brain lipid composition, gene expression, and performance of self-grooming behavior under controlled conditions (cage experiments). Methods After seven days of exposure to oral sublethal doses of clothianidin, the bees were assessed for self-grooming behavior; their brains were dissected to analyze the lipidome using an untargeted lipidomics approach and to perform a high throughput RNAseq analysis. Results Compared to all other organisms, healthy bee brain lipidomes contain unusually high levels of alkyl-ether linked (plasmanyl) phospholipids (51.42%) and low levels of plasmalogens (plasmenyl phospholipids; 3.46%). This could make it more susceptible to the effects of toxins in the environment. A positive correlation between CL 18:3/18:1/14:0/22:6, TG 6:0/11:2/18:1, LPE 18:0e and intense self-grooming was found. Sublethal doses of a neonicotinoid altered PC 20:3e/15:0, PC 16:0/18:3, PA 18:0/24:1, and TG 18:1/18:1/18/1 levels, and affected gene expression linked to GPI-anchor biosynthesis pathway and energy metabolism that may be partially responsible for the altered lipid composition. Conclusion This study showed that lipidomics can reveal honey bee neuropathologies associated with reduced grooming behavior due to sublethal neonicotinoid exposure. The ease of use, unusual brain lipidome as well as characterized behaviors that are affected by the environment make honey bees a promising model organism for studying the neurolipidome and associations with neurobehavioral disorders.
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Garcia Corrales AV, Haidar M, Bogie JFJ, Hendriks JJA. Fatty Acid Synthesis in Glial Cells of the CNS. Int J Mol Sci 2021; 22:ijms22158159. [PMID: 34360931 PMCID: PMC8348209 DOI: 10.3390/ijms22158159] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
Fatty acids (FAs) are of crucial importance for brain homeostasis and neural function. Glia cells support the high demand of FAs that the central nervous system (CNS) needs for its proper functioning. Additionally, FAs can modulate inflammation and direct CNS repair, thereby contributing to brain pathologies such Alzheimer’s disease or multiple sclerosis. Intervention strategies targeting FA synthesis in glia represents a potential therapeutic opportunity for several CNS diseases.
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Affiliation(s)
- Aida V Garcia Corrales
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium
| | - Mansour Haidar
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium
| | - Jeroen F J Bogie
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium
| | - Jerome J A Hendriks
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium
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Li P, Lämmerhofer M. Isomer Selective Comprehensive Lipidomics Analysis of Phosphoinositides in Biological Samples by Liquid Chromatography with Data Independent Acquisition Tandem Mass Spectrometry. Anal Chem 2021; 93:9583-9592. [PMID: 34191474 DOI: 10.1021/acs.analchem.1c01751] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Phosphoinositides (PIPx) play central roles in membrane dynamics and signal transduction of key functions like cellular growth, proliferation, differentiation, migration, and adhesion. They are highly regulated through a network of distinct phosphatidylinositol phosphates consisting of seven groups and three regioisomers in two groups (PIP and PIP2), which arise from phosphorylation at 3', 4', and 5' positions of the inositol ring. Numerous studies have revealed the importance of both fatty acyl chains, degree of phosphorylation, and phosphorylation positions under physiological and pathological states. However, a comprehensive analytical method that allows differentiation of all regioisomeric forms with different acyl side chains and degrees of phosphorylation is still lacking. Here, we present an integrated comprehensive workflow of PIPx analysis utilizing a chiral polysaccharide stationary phase coupled with electrospray ionization high-resolution mass spectrometry with a data independent acquisition technique using the SWATH technology. Correspondingly, a targeted data mining strategy in the untargeted comprehensively acquired MS and MS/MS data was developed. This powerful highly selective method gives a full picture of PIPx profiles in biological samples. Herein, we present for the first time the full PIPx profiles of NIST SRM1950 plasma, Pichia pastoris lipid extract, and HeLa cell extract, including profile changes upon treatment with potential PI3K inhibitor wortmannin. We also illustrate using this inhibitor that measurements of the PIPx profile averaged over the distinct regioisomers by analytical procedures, which cannot differentiate between the individual PIPx isomers, can easily lead to biased conclusions.
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Affiliation(s)
- Peng Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
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Kruse M, Whitten RJ. Control of Neuronal Excitability by Cell Surface Receptor Density and Phosphoinositide Metabolism. Front Pharmacol 2021; 12:663840. [PMID: 33967808 PMCID: PMC8097148 DOI: 10.3389/fphar.2021.663840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/29/2021] [Indexed: 12/27/2022] Open
Abstract
Phosphoinositides are members of a family of minor phospholipids that make up about 1% of all lipids in most cell types. Despite their low abundance they have been found to be essential regulators of neuronal activities such as action potential firing, release and re-uptake of neurotransmitters, and interaction of cytoskeletal proteins with the plasma membrane. Activation of several different neurotransmitter receptors can deplete phosphoinositide levels by more than 90% in seconds, thereby profoundly altering neuronal behavior; however, despite the physiological importance of this mechanism we still lack a profound quantitative understanding of the connection between phosphoinositide metabolism and neuronal activity. Here, we present a model that describes phosphoinositide metabolism and phosphoinositide-dependent action potential firing in sympathetic neurons. The model allows for a simulation of activation of muscarinic acetylcholine receptors and its effects on phosphoinositide levels and their regulation of action potential firing in these neurons. In this paper, we describe the characteristics of the model, its calibration to experimental data, and use the model to analyze how alterations of surface density of muscarinic acetylcholine receptors or altered activity levels of a key enzyme of phosphoinositide metabolism influence action potential firing of sympathetic neurons. In conclusion, the model provides a comprehensive framework describing the connection between muscarinic acetylcholine signaling, phosphoinositide metabolism, and action potential firing in sympathetic neurons which can be used to study the role of these signaling systems in health and disease.
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Affiliation(s)
- Martin Kruse
- Department of Biology, Bates College, Lewiston, ME, United States.,Program in Neuroscience, Bates College, Lewiston, ME, United States
| | - Rayne J Whitten
- Program in Neuroscience, Bates College, Lewiston, ME, United States
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Lopes I, Altab G, Raina P, de Magalhães JP. Gene Size Matters: An Analysis of Gene Length in the Human Genome. Front Genet 2021; 12:559998. [PMID: 33643374 PMCID: PMC7905317 DOI: 10.3389/fgene.2021.559998] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/06/2021] [Indexed: 12/23/2022] Open
Abstract
While it is expected for gene length to be associated with factors such as intron number and evolutionary conservation, we are yet to understand the connections between gene length and function in the human genome. In this study, we show that, as expected, there is a strong positive correlation between gene length, transcript length, and protein size as well as a correlation with the number of genetic variants and introns. Among tissue-specific genes, we find that the longest transcripts tend to be expressed in the blood vessels, nerves, thyroid, cervix uteri, and the brain, while the smallest transcripts tend to be expressed in the pancreas, skin, stomach, vagina, and testis. We report, as shown previously, that natural selection suppresses changes for genes with longer transcripts and promotes changes for genes with smaller transcripts. We also observe that genes with longer transcripts tend to have a higher number of co-expressed genes and protein-protein interactions, as well as more associated publications. In the functional analysis, we show that bigger transcripts are often associated with neuronal development, while smaller transcripts tend to play roles in skin development and in the immune system. Furthermore, pathways related to cancer, neurons, and heart diseases tend to have genes with longer transcripts, with smaller transcripts being present in pathways related to immune responses and neurodegenerative diseases. Based on our results, we hypothesize that longer genes tend to be associated with functions that are important in the early development stages, while smaller genes tend to play a role in functions that are important throughout the whole life, like the immune system, which requires fast responses.
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Affiliation(s)
| | | | | | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
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Schäfer J, Förster L, Mey I, Papadopoulos T, Brose N, Steinem C. Neuroligin-2 dependent conformational activation of collybistin reconstituted in supported hybrid membranes. J Biol Chem 2020; 295:18604-18613. [PMID: 33127642 PMCID: PMC7939476 DOI: 10.1074/jbc.ra120.015347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/27/2020] [Indexed: 12/23/2022] Open
Abstract
The assembly of the postsynaptic transmitter sensing machinery at inhibitory nerve cell synapses requires the intimate interplay between cell adhesion proteins, scaffold and adaptor proteins, and γ-aminobutyric acid (GABA) or glycine receptors. We developed an in vitro membrane system to reconstitute this process, to identify the essential protein components, and to define their mechanism of action, with a specific focus on the mechanism by which the cytosolic C terminus of the synaptic cell adhesion protein Neuroligin-2 alters the conformation of the adaptor protein Collybistin-2 and thereby controls Collybistin-2-interactions with phosphoinositides (PtdInsPs) in the plasma membrane. Supported hybrid membranes doped with different PtdInsPs and 1,2-dioleoyl-sn-glycero-3-{[N-(5-amino-1-carboxypentyl)iminodiacetic acid]succinyl} nickel salt (DGS-NTA(Ni)) to allow for the specific adsorption of the His6-tagged intracellular domain of Neuroligin-2 (His-cytNL2) were prepared on hydrophobically functionalized silicon dioxide substrates via vesicle spreading. Two different collybistin variants, the WT protein (CB2SH3) and a mutant that adopts an intrinsically 'open' and activated conformation (CB2SH3/W24A-E262A), were bound to supported membranes in the absence or presence of His-cytNL2. The corresponding binding data, obtained by reflectometric interference spectroscopy, show that the interaction of the C terminus of Neuroligin-2 with Collybistin-2 induces a conformational change in Collybistin-2 that promotes its interaction with distinct membrane PtdInsPs.
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Affiliation(s)
- Jonas Schäfer
- Institute for Organic and Biomolecular Chemistry, Georg August University, Göttingen, Germany
| | - Lucas Förster
- Institute for Organic and Biomolecular Chemistry, Georg August University, Göttingen, Germany
| | - Ingo Mey
- Institute for Organic and Biomolecular Chemistry, Georg August University, Göttingen, Germany
| | | | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany.
| | - Claudia Steinem
- Institute for Organic and Biomolecular Chemistry, Georg August University, Göttingen, Germany; Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany.
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Tracey TJ, Kirk SE, Steyn FJ, Ngo ST. The role of lipids in the central nervous system and their pathological implications in amyotrophic lateral sclerosis. Semin Cell Dev Biol 2020; 112:69-81. [PMID: 32962914 DOI: 10.1016/j.semcdb.2020.08.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/11/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022]
Abstract
Lipids play an important role in the central nervous system (CNS). They contribute to the structural integrity and physical characteristics of cell and organelle membranes, act as bioactive signalling molecules, and are utilised as fuel sources for mitochondrial metabolism. The intricate homeostatic mechanisms underpinning lipid handling and metabolism across two major CNS cell types; neurons and astrocytes, are integral for cellular health and maintenance. Here, we explore the various roles of lipids in these two cell types. Given that changes in lipid metabolism have been identified in a number of neurodegenerative diseases, we also discuss changes in lipid handling and utilisation in the context of amyotrophic lateral sclerosis (ALS), in order to identify key cellular processes affected by the disease, and inform future areas of research.
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Affiliation(s)
- T J Tracey
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.
| | - S E Kirk
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - F J Steyn
- Centre for Clinical Research, The University of Queensland, Brisbane, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
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- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia; Centre for Clinical Research, The University of Queensland, Brisbane, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
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