1
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Zhai B, Ran W, Sun Y, Alcos A, Liu M, Chen J, Richardson CD, Sun D, Zhao J. Human SLAM-adapted canine distemper virus can enter human peripheral blood mononuclear cells and replicate in mice expressing human SLAM and defective for STAT1 expression. Virulence 2025; 16:2457967. [PMID: 39981650 PMCID: PMC11849921 DOI: 10.1080/21505594.2025.2457967] [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: 09/18/2024] [Revised: 12/24/2024] [Accepted: 01/20/2025] [Indexed: 02/22/2025] Open
Abstract
Canine distemper virus (CDV) is a member of the genus Morbillivirus with a worldwide distribution that causes fatal diseases in canids and marine mammals. In recent years, CDV has demonstrated the remarkable ability of pathogens to cross species barriers. The natural host range of CDV has expanded from Canidae to Primates, presumably attributed to ecological shifts and the emergence of viral variants. Therefore, it is important to investigate whether CDV can infect humans by adapting to the human signalling lymphocyte activation molecule (hSLAM) receptor to cross the species barrier. Through successive passaging and plaque cloning of a CDV wild-type strain (5804PeH) in Vero cells expressing hSLAM (Vero-hSLAM), we obtained an hSLAM adaptive strain, 5804PeH-VhS. The adapted CDV strain exhibited a D540G mutation within the receptor-binding domain (RBD) of the haemagglutinin (H) protein. The HD540G mutation has enhanced cell-cell fusion activity in Vero-hSLAM cells. This adaptation allowed the CDV strain to infect human peripheral blood mononuclear cells (PBMCs), particularly T lymphocytes and inhibited lymphocyte proliferation. Additionally, this strain could replicate in the lymphoid tissues of transgenic mice that express the hSLAM receptor, causing viraemia. However, the adapted strain did not spread to the epithelial cells or the central nervous system of the mice. While this adaptation indicates a potential risk, there is no definitive evidence that the virus can spread among humans.
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Affiliation(s)
- Boyu Zhai
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wei Ran
- Animal Husbandry and Fisheries, Guizhou Vocational College of Agriculture, Guiyang, China
| | - Yiyang Sun
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Angelita Alcos
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Mengjia Liu
- Institute of Special Animal and Plant Sciences, The Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jie Chen
- Institute of Special Animal and Plant Sciences, The Chinese Academy of Agricultural Sciences, Changchun, China
| | | | - Dongbo Sun
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jianjun Zhao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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2
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Simonian TL, Meyer AS, Guo J, Sha J, Wohlschlegel JA, Droujinine IA, Perrimon N, McMahon AP. Sex and Depot Specific Adipocyte Proteome Profiling In Vivo via Intracellular Proximity Labeling. Compr Physiol 2025; 15:e70007. [PMID: 40181252 PMCID: PMC11969033 DOI: 10.1002/cph4.70007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 02/22/2025] [Accepted: 02/27/2025] [Indexed: 04/05/2025]
Abstract
Adipose tissue has varying distributions and metabolic properties between the sexes. Inherent sex-specific differences in adipocytes may heighten the risk of metabolic disease in males. Analysis of the adipocyte proteome can potentially provide important insight. To enable cell-type specific proteomic profiling in vivo, we genetically engineered a mouse line for cell-type specific production of a promiscuous biotin ligase (BirA*G3) facilitating the rapid isolation of biotinylated cell-type specific proteomes. Adipocyte-specific activation of cytoplasmic BirA*G3 led to robust biotinylation of adipocyte proteins across all major fat depots. Comparison of brown adipose tissue (BAT) and subcutaneous white adipose tissue (SAT) proteomes identified 229 brown adipose-enriched and 35 white adipose-enriched proteins. Regional comparison of white fat depots revealed additional differences across depots. Comparison of male and female depots identified sexually dimorphic adipose proteins: AHNAK predominating in the male and ACOT2 in the female. These findings validate the genetic model and highlight insights to be gained through targeted profiling of adipocytes. The genetic tool adds to existing approaches for in vivo proximity profiling of cell-type specific proteome programs.
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Affiliation(s)
- Taylor L. Simonian
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Amanda S. Meyer
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Jihui Sha
- Department of Biological Chemistry, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Ilia A. Droujinine
- Department of Molecular MedicineScripps Research InstituteLa JollaCaliforniaUSA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik InstituteHarvard Medical SchoolCambridgeMassachusettsUSA
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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3
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van Oostrum M, Schuman EM. Understanding the molecular diversity of synapses. Nat Rev Neurosci 2025; 26:65-81. [PMID: 39638892 DOI: 10.1038/s41583-024-00888-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2024] [Indexed: 12/07/2024]
Abstract
Synapses are composed of thousands of proteins, providing the potential for extensive molecular diversity to shape synapse type-specific functional specializations. In this Review, we explore the landscape of synaptic diversity and describe the mechanisms that expand the molecular complexity of synapses, from the genotype to the regulation of gene expression to the production of specific proteoforms and the formation of localized protein complexes. We emphasize the importance of examining every molecular layer and adopting a systems perspective to understand how these interconnected mechanisms shape the diverse functional and structural properties of synapses. We explore current frameworks for classifying synapses and methodologies for investigating different synapse types at varying scales, from synapse-type-specific proteomics to advanced imaging techniques with single-synapse resolution. We highlight the potential of synapse-type-specific approaches for integrating molecular data with cellular functions, circuit organization and organismal phenotypes to enable a more holistic exploration of neuronal phenomena across different scales.
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Affiliation(s)
- Marc van Oostrum
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
- Biozentrum, University of Basel, Basel, Switzerland
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
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4
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Uchigashima M, Mikuni T. Single-cell synaptome mapping: its technical basis and applications in critical period plasticity research. Front Neural Circuits 2024; 18:1523614. [PMID: 39726910 PMCID: PMC11670323 DOI: 10.3389/fncir.2024.1523614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Accepted: 11/28/2024] [Indexed: 12/28/2024] Open
Abstract
Our brain adapts to the environment by optimizing its function through experience-dependent cortical plasticity. This plasticity is transiently enhanced during a developmental stage, known as the "critical period," and subsequently maintained at lower levels throughout adulthood. Thus, understanding the mechanism underlying critical period plasticity is crucial for improving brain adaptability across the lifespan. Critical period plasticity relies on activity-dependent circuit remodeling through anatomical and functional changes at individual synapses. However, it remains challenging to identify the molecular signatures of synapses responsible for critical period plasticity and to understand how these plasticity-related synapses are spatiotemporally organized within a neuron. Recent advances in genetic tools and genome editing methodologies have enabled single-cell endogenous protein labeling in the brain, allowing for comprehensive molecular profiling of individual synapses within a neuron, namely "single-cell synaptome mapping." This promising approach can facilitate insights into the spatiotemporal organization of synapses that are sparse yet functionally important within single neurons. In this review, we introduce the basics of single-cell synaptome mapping and discuss its methodologies and applications to investigate the synaptic and cellular mechanisms underlying circuit remodeling during the critical period.
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Affiliation(s)
- Motokazu Uchigashima
- Department of Cellular Neuropathology, Brain Research Institute, Niigata University, Niigata, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
| | - Takayasu Mikuni
- Department of Cellular Neuropathology, Brain Research Institute, Niigata University, Niigata, Japan
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5
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Fan N, Yang K, Bian X, Chen Y, Zhang L, Ai Z, Li X, Ding S, Li S, Cheng W. GlycoSS: A DNA Glycosignal Sieve for Deciphering Spatially Resolved EpCAM-Specific Glycoforms. ACS NANO 2024; 18:29106-29120. [PMID: 39374425 DOI: 10.1021/acsnano.4c10565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]
Abstract
Malignant transformation of cancer is often accompanied by aberrant glycopatterns. Epithelial-mesenchymal transition (EMT) is a crucial biological process in cancer migration and invasion, accelerating cancer deterioration. High-precision analysis of protein-glycan spatial profiling in the EMT process is essential for elucidating glycosylation functions and cancer progression. However, the diversity of glycans in composition and conformation complicates their spatial analysis. Here, we develop a DNA glycosignal sieve (GlycoSS) visualization platform for screening glycoform expression with a protein spatial dimension. GlycoSS utilizes protein-anchored DNA nanoscanners of distinct lengths to control glycosignal readout, enabling protein-glycan distance modulations, and simultaneously orthogonally amplify glycoform output through signal amplification by an exchange reaction. Using GlycoSS, we screened EpCAM-specific hypoglycosylated glycoform signals in different breast cancer cell subtypes, especially characterizing the spatial distribution of glycans on the MCF-7 cell surface. Considering that the EpCAM-specific N-glycan dysregulation in EMT is pivotal, GlycoSS revealed dynamic glycan fluctuations during IGF-1-induced EMT, revealing that the N-glycans were positively associated with tumor malignancy and metastasis. GlycoSS is anticipated to accelerate the identification of aberrant N-glycosylation in tumor progression, advancing systemic glycobiology insights. Notably, GlycoSS is capable of analyzing diverse glycoprotein profiles, offering additional dimensions into the role of glycoprotein nanoenvironments in regulating membrane protein function.
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Affiliation(s)
- Ningke Fan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Ketong Yang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xintong Bian
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yirong Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Lu Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Zhujun Ai
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xinyu Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Siqiao Li
- School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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6
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Bartolome A, Heiby JC, Di Fraia D, Heinze I, Knaudt H, Spaeth E, Omrani O, Minetti A, Hofmann M, Kirkpatrick JM, Dau T, Ori A. Quantitative mapping of proteasome interactomes and substrates using ProteasomeID. eLife 2024; 13:RP93256. [PMID: 39230574 PMCID: PMC11374303 DOI: 10.7554/elife.93256] [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] [Indexed: 09/05/2024] Open
Abstract
Proteasomes are essential molecular machines responsible for the degradation of proteins in eukaryotic cells. Altered proteasome activity has been linked to neurodegeneration, auto-immune disorders and cancer. Despite the relevance for human disease and drug development, no method currently exists to monitor proteasome composition and interactions in vivo in animal models. To fill this gap, we developed a strategy based on tagging of proteasomes with promiscuous biotin ligases and generated a new mouse model enabling the quantification of proteasome interactions by mass spectrometry. We show that biotin ligases can be incorporated in fully assembled proteasomes without negative impact on their activity. We demonstrate the utility of our method by identifying novel proteasome-interacting proteins, charting interactomes across mouse organs, and showing that proximity-labeling enables the identification of both endogenous and small-molecule-induced proteasome substrates.
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Affiliation(s)
| | - Julia C Heiby
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | | | - Ivonne Heinze
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Hannah Knaudt
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Ellen Spaeth
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Omid Omrani
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Alberto Minetti
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Maleen Hofmann
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | | | - Therese Dau
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
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7
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Wang YZ, Perez-Rosello T, Smukowski SN, Surmeier DJ, Savas JN. Neuron type-specific proteomics reveals distinct Shank3 proteoforms in iSPNs and dSPNs lead to striatal synaptopathy in Shank3B -/- mice. Mol Psychiatry 2024; 29:2372-2388. [PMID: 38486049 PMCID: PMC11412912 DOI: 10.1038/s41380-024-02493-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 09/21/2024]
Abstract
Combinatorial expression of postsynaptic proteins underlies synapse diversity within and between neuron types. Thus, characterization of neuron-type-specific postsynaptic proteomes is key to obtaining a deeper understanding of discrete synaptic properties and how selective dysfunction manifests in synaptopathies. To overcome the limitations associated with bulk measures of synaptic protein abundance, we developed a biotin proximity protein tagging probe to characterize neuron-type-specific postsynaptic proteomes in vivo. We found Shank3 protein isoforms are differentially expressed by direct and indirect pathway spiny projection neurons (dSPNs and iSPNs). Investigation of Shank3B-/- mice lacking exons 13-16 within the Shank3 gene, reveal distinct Shank3 protein isoform expression in iSPNs and dSPNs. In Shank3B-/- striatum, Shank3E and Shank3NT are expressed by dSPNs but are undetectable in iSPNs. Proteomic analysis indicates significant and selective alterations in the postsynaptic proteome of Shank3B-/- iSPNs. Correspondingly, the deletion of exons 13-16 diminishes dendritic spine density, reduces spine head diameter, and hampers corticostriatal synaptic transmission in iSPNs. Remarkably, reintroducing Shank3E in adult Shank3B-/- iSPNs significantly rectifies the observed dendritic spine morphological and corticostriatal synaptic transmission deficits. We report unexpected cell-type specific synaptic protein isoform expression which could play a key causal role in specifying synapse diversity and selective synapse dysfunction in synaptopathies.
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Affiliation(s)
- Yi-Zhi Wang
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Tamara Perez-Rosello
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Samuel N Smukowski
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - D James Surmeier
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Jeffrey N Savas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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8
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Kim JW, Yong AJH, Aisenberg EE, Lobel JH, Wang W, Dawson TM, Dawson VL, Gao R, Jan YN, Bateup HS, Ingolia NT. Molecular recording of calcium signals via calcium-dependent proximity labeling. Nat Chem Biol 2024; 20:894-905. [PMID: 38658655 DOI: 10.1038/s41589-024-01603-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024]
Abstract
Calcium ions serve as key intracellular signals. Local, transient increases in calcium concentrations can activate calcium sensor proteins that in turn trigger downstream effectors. In neurons, calcium transients play a central role in regulating neurotransmitter release and synaptic plasticity. However, it is challenging to capture the molecular events associated with these localized and ephemeral calcium signals. Here we present an engineered biotin ligase that generates permanent molecular traces in a calcium-dependent manner. The enzyme, calcium-dependent BioID (Cal-ID), biotinylates nearby proteins within minutes in response to elevated local calcium levels. The biotinylated proteins can be identified via mass spectrometry and visualized using microscopy. In neurons, Cal-ID labeling is triggered by neuronal activity, leading to prominent protein biotinylation that enables transcription-independent activity labeling in the brain. In summary, Cal-ID produces a biochemical record of calcium signals and neuronal activity with high spatial resolution and molecular specificity.
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Affiliation(s)
- J Wren Kim
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
| | - Adeline J H Yong
- Department of Physiology at the University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute at the University of California, San Francisco, San Francisco, CA, USA
| | - Erin E Aisenberg
- Helen Wills Neuroscience Institute at the University of California, Berkeley, Berkeley, CA, USA
| | - Joseph H Lobel
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
| | - Wei Wang
- Department of Chemistry at the University of Illinois, Chicago, Chicago, IL, USA
| | - Ted M Dawson
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruixuan Gao
- Department of Chemistry at the University of Illinois, Chicago, Chicago, IL, USA
| | - Yuh Nung Jan
- Department of Physiology at the University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute at the University of California, San Francisco, San Francisco, CA, USA
| | - Helen S Bateup
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute at the University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA.
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9
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Ge Y, Xiao B, Zhao R, Li B, Yang S, He KF, Gu HJ, Zuo S. CARMIL1 regulates liver cancer cell proliferation by activating the ERK/mTOR pathway through the TRIM27/p53 axis. Int Immunopharmacol 2024; 134:112139. [PMID: 38739978 DOI: 10.1016/j.intimp.2024.112139] [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: 02/05/2024] [Revised: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 05/16/2024]
Abstract
Capping protein regulatory factor and myosin 1 linker 1 is termed CARMIL1. CARMIL1 is involved in several physiological processes; it forms an actin filament network and plasma membrane-bound cellular projection tissues and positively regulates the cellular components and tissues. CARMIL1 exhibits important biological functions in cancer; nonetheless, these functions have not been completely explored. We aimed to investigate the novel functions of CARMIL1 in liver cancer, particularly in cell proliferation. The cell counting kit-8, 5-ethynyl-2'-deoxyuridine, Component A experiments, and subcutaneous tumor formation model suggest that CARMIL1 is central to the proliferation of liver cancer cells both in vivo and in vitro. We extracted CARMIL1 samples from The Cancer Genome Atlas Program and analyzed its enrichment. CARMIL1 regulated the pathway activity by affecting the expression of star molecular proteins of the extracellular signal-regulated kinase (ERK) and mammalian target of rapamycin (mTOR). Moreover, it influenced the proliferation ability of liver cancer cells. Western blotting suggested that CARMIL1 downregulation could affect ERK and mTOR phosphorylation. Results of the co-immunoprecipitation demonstrated that CARMIL1 binds to tripartite motif (TRIM)27, which in turn binds to p53. Subsequently, CARMIL1 can regulate p53 stability and promote its degradation through TRIM27. Additionally, CARMIL1 inhibition enhanced the sensitivity of liver cancer cells to sorafenib. Tumor growth was significantly inhibited in the group treated with sorafenib and CARMIL1, compared with the group treated with CARMIL1 alone. Sorafenib is a first-line targeted chemotherapeutic drug for hepatocellular carcinoma treatment. It increases the long-term survival of hepatocellular carcinoma by 44%. In this study, downregulated CARMIL1 combined with sorafenib significantly reduced the tumor volume and weight of the mouse subcutaneous tumor model, indicating the potential possibility of combining CARMIL1 with sorafenib in hepatocellular carcinoma treatment. In summary, CARMIL1 promotes liver cancer cell proliferation by regulating the TRIM27/p53 axis and activating the ERK/mTOR pathway.
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Affiliation(s)
- Yuzhen Ge
- Department of Prdiatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, PR China
| | - Benli Xiao
- Department of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, PR China
| | - Rui Zhao
- Department of Liver Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, PR China
| | - Bo Li
- Department of Liver Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, PR China
| | - Sibo Yang
- Department of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, PR China
| | - Kun Feng He
- Department of Prdiatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, PR China
| | - Hua Jian Gu
- Department of Prdiatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, PR China.
| | - Shi Zuo
- Department of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, PR China; Department of Liver Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, PR China; Precision Medicine Research Institute of Guizhou, The Affiliated Hospital of Guizhou Medical University, Guiyang, PR China.
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10
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Irala D, Wang S, Sakers K, Nagendren L, Ulloa Severino FP, Bindu DS, Savage JT, Eroglu C. Astrocyte-secreted neurocan controls inhibitory synapse formation and function. Neuron 2024; 112:1657-1675.e10. [PMID: 38574730 PMCID: PMC11098688 DOI: 10.1016/j.neuron.2024.03.007] [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: 04/18/2023] [Revised: 01/22/2024] [Accepted: 03/07/2024] [Indexed: 04/06/2024]
Abstract
Astrocytes strongly promote the formation and maturation of synapses by secreted proteins. Several astrocyte-secreted synaptogenic proteins controlling excitatory synapse development were identified; however, those that induce inhibitory synaptogenesis remain elusive. Here, we identify neurocan as an astrocyte-secreted inhibitory synaptogenic protein. After secretion from astrocytes, neurocan is cleaved into N- and C-terminal fragments. We found that these fragments have distinct localizations in the extracellular matrix. The neurocan C-terminal fragment localizes to synapses and controls cortical inhibitory synapse formation and function. Neurocan knockout mice lacking the whole protein or only its C-terminal synaptogenic domain have reduced inhibitory synapse numbers and function. Through super-resolution microscopy, in vivo proximity labeling by secreted TurboID, and astrocyte-specific rescue approaches, we discovered that the synaptogenic domain of neurocan localizes to somatostatin-positive inhibitory synapses and strongly regulates their formation. Together, our results unveil a mechanism through which astrocytes control circuit-specific inhibitory synapse development in the mammalian brain.
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Affiliation(s)
- Dolores Irala
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Shiyi Wang
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kristina Sakers
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Leykashree Nagendren
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Francesco Paolo Ulloa Severino
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Psychology and Neuroscience, Duke University, Durham, NC 27710, USA; Instituto Cajal, CSIC 28002 Madrid, Spain
| | | | - Justin T Savage
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cagla Eroglu
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Psychology and Neuroscience, Duke University, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Duke Institute for Brain Sciences (DIBS), Durham, NC 27710, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27710, USA.
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11
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Ito Y, Nagamoto S, Takano T. Synaptic proteomics decode novel molecular landscape in the brain. Front Mol Neurosci 2024; 17:1361956. [PMID: 38726307 PMCID: PMC11079194 DOI: 10.3389/fnmol.2024.1361956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
Synapses play a pivotal role in forming neural circuits, with critical implications for brain functions such as learning, memory, and emotions. Several advances in synaptic research have demonstrated the diversity of synaptic structure and function, which can form thousands of connections depending on the neuronal cell types. Moreover, synapses not only interconnect neurons but also establish connections with glial cells such as astrocytes, which play a key role in the architecture and function of neuronal circuits in the brain. Emerging evidence suggests that dysfunction of synaptic proteins contributes to a variety of neurological and psychiatric disorders. Therefore, it is crucial to determine the molecular networks within synapses in various neuronal cell types to gain a deeper understanding of how the nervous system regulates brain function. Recent advances in synaptic proteome approaches, such as fluorescence-activated synaptosome sorting (FASS) and proximity labeling, have allowed for a detailed and spatial analysis of many cell-type-specific synaptic molecules in vivo. In this brief review, we highlight these novel spatial proteomic approaches and discuss the regulation of synaptic formation and function in the brain. This knowledge of molecular networks provides new insight into the understanding of many neurological and psychiatric disorders.
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Affiliation(s)
- Yuki Ito
- Division of Molecular Systems for Brain Function, Institute for Advanced Study, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Division of Integrated Omics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Sayaka Nagamoto
- Division of Molecular Systems for Brain Function, Institute for Advanced Study, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Tetsuya Takano
- Division of Molecular Systems for Brain Function, Institute for Advanced Study, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Neurophysiology, Keio University School of Medicine, Tokyo, Japan
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
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12
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Shrestha HK, Sun H, Wang J, Peng J. Profiling Mouse Brain Single-Cell-Type Proteomes Via Adeno-Associated Virus-Mediated Proximity Labeling and Mass Spectrometry. Methods Mol Biol 2024; 2817:115-132. [PMID: 38907151 DOI: 10.1007/978-1-0716-3934-4_10] [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] [Indexed: 06/23/2024]
Abstract
Single-cell-type proteomics is an emerging field of research that combines cell-type specificity with the comprehensive proteome coverage offered by bulk proteomics. However, the extraction of single-cell-type proteomes remains a challenge, particularly for hard-to-isolate cells like neurons. In this chapter, we present an innovative technique for profiling single-cell-type proteomes using adeno-associated virus (AAV)-mediated proximity labeling (PL) and tandem-mass-tag (TMT) mass spectrometry. This technique eliminates the need for cell isolation and offers a streamlined workflow, including AAV delivery to express TurboID (an engineered biotin ligase) controlled by cell-type-specific promoters, biotinylated protein purification, on-bead digestion, TMT labeling, and liquid chromatography-mass spectrometry (LC-MS). We examined this method by analyzing distinct brain cell types in mice. Initially, recombinant AAVs were used to concurrently express TurboID and mCherry proteins driven by neuron- or astrocyte-specific promoters, which was validated through co-immunostaining with cellular markers. With biotin purification and TMT analysis, we successfully identified around 10,000 unique proteins from a few micrograms of protein samples with high reproducibility. Our statistical analyses revealed that these proteomes encompass cell-type-specific cellular pathways. By utilizing this technique, researchers can explore the proteomic landscape of specific cell types, paving the way for new insights into cellular processes, deciphering disease mechanisms, and identifying therapeutic targets in neuroscience and beyond.
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Affiliation(s)
- Him K Shrestha
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Huan Sun
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ju Wang
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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13
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van Oostrum M, Blok TM, Giandomenico SL, Tom Dieck S, Tushev G, Fürst N, Langer JD, Schuman EM. The proteomic landscape of synaptic diversity across brain regions and cell types. Cell 2023; 186:5411-5427.e23. [PMID: 37918396 PMCID: PMC10686415 DOI: 10.1016/j.cell.2023.09.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/18/2023] [Accepted: 09/28/2023] [Indexed: 11/04/2023]
Abstract
Neurons build synaptic contacts using different protein combinations that define the specificity, function, and plasticity potential of synapses; however, the diversity of synaptic proteomes remains largely unexplored. We prepared synaptosomes from 7 different transgenic mouse lines with fluorescently labeled presynaptic terminals. Combining microdissection of 5 different brain regions with fluorescent-activated synaptosome sorting (FASS), we isolated and analyzed the proteomes of 18 different synapse types. We discovered ∼1,800 unique synapse-type-enriched proteins and allocated thousands of proteins to different types of synapses (https://syndive.org/). We identify shared synaptic protein modules and highlight the proteomic hotspots for synapse specialization. We reveal unique and common features of the striatal dopaminergic proteome and discover the proteome signatures that relate to the functional properties of different interneuron classes. This study provides a molecular systems-biology analysis of synapses and a framework to integrate proteomic information for synapse subtypes of interest with cellular or circuit-level experiments.
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Affiliation(s)
- Marc van Oostrum
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Thomas M Blok
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | | | | | - Georgi Tushev
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Nicole Fürst
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
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14
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Chevet E, De Matteis MA, Eskelinen EL, Farhan H. Dynamic tandem proximity-based proteomics-Protein trafficking at the proteome-scale. Traffic 2023; 24:546-548. [PMID: 37581229 DOI: 10.1111/tra.12914] [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: 07/12/2023] [Accepted: 07/25/2023] [Indexed: 08/16/2023]
Abstract
TransitID is a new methodology based on proximity labeling allowing for the study of protein trafficking a the proteome scale.
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Affiliation(s)
- Eric Chevet
- INSERM U1242, University of Rennes, Rennes, France
- Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II-Medical School, Naples, Italy
| | | | - Hesso Farhan
- Institute of Pathophysiology, Medical University of Innsbruck, Innsbruck, Austria
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15
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Hromadkova L, Kim C, Haldiman T, Peng L, Zhu X, Cohen M, de Silva R, Safar JG. Evolving prion-like tau conformers differentially alter postsynaptic proteins in neurons inoculated with distinct isolates of Alzheimer's disease tau. Cell Biosci 2023; 13:174. [PMID: 37723591 PMCID: PMC10507869 DOI: 10.1186/s13578-023-01133-0] [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: 05/03/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023] Open
Abstract
OBJECTIVES Although accumulation of misfolded tau species has been shown to predict cognitive decline in patients with Alzheimer's disease (AD) and other tauopathies but with the remarkable diversity of clinical manifestations, neuropathology profiles, and time courses of disease progression remaining unexplained by current genetic data. We considered the diversity of misfolded tau conformers present in individual AD cases as an underlying driver of the phenotypic variations of AD and progressive loss of synapses. METHODS To model the mechanism of tau propagation and synaptic toxicity of distinct tau conformers, we inoculated wild-type primary mouse neurons with structurally characterized Sarkosyl-insoluble tau isolates from the frontal cortex of six AD cases and monitored the impact for fourteen days. We analyzed the accumulation rate, tau isoform ratio, and conformational characteristics of de novo-induced tau aggregates with conformationally sensitive immunoassays, and the dynamics of synapse formation, maintenance, and their loss using a panel of pre-and post-synaptic markers. RESULTS At the same concentrations of tau, the different AD tau isolates induced accumulation of misfolded predominantly 4-repeat tau aggregates at different rates in mature neurons, and demonstrated distinct conformational characteristics corresponding to the original AD brain tau. The time-course of the formation of misfolded tau aggregates and colocalization correlated with significant loss of synapses in tau-inoculated cell cultures and the reduction of synaptic connections implicated the disruption of postsynaptic compartment as an early event. CONCLUSIONS The data obtained with mature neurons expressing physiological levels and adult isoforms of tau protein demonstrate markedly different time courses of endogenous tau misfolding and differential patterns of post-synaptic alterations. These and previous biophysical data argue for an ensemble of various misfolded tau aggregates in individual AD brains and template propagation of their homologous conformations in neurons with different rates and primarily postsynaptic interactors. Modeling tau aggregation in mature differentiated neurons provides a platform for investigating divergent molecular mechanisms of tau strain propagation and for identifying common structural features of misfolded tau and critical interactors for new therapeutic targets and approaches in AD.
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Affiliation(s)
- Lenka Hromadkova
- Departments of Pathology, Case Western Reserve University School of Medicine, 2085 Adelbert Rd, Cleveland, OH, 44106, USA
| | - Chae Kim
- Departments of Pathology, Case Western Reserve University School of Medicine, 2085 Adelbert Rd, Cleveland, OH, 44106, USA
| | - Tracy Haldiman
- Departments of Pathology, Case Western Reserve University School of Medicine, 2085 Adelbert Rd, Cleveland, OH, 44106, USA
| | - Lihua Peng
- Departments of Pathology, Case Western Reserve University School of Medicine, 2085 Adelbert Rd, Cleveland, OH, 44106, USA
| | - Xiongwei Zhu
- Departments of Pathology, Case Western Reserve University School of Medicine, 2085 Adelbert Rd, Cleveland, OH, 44106, USA
- Departments of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Mark Cohen
- Departments of Pathology, Case Western Reserve University School of Medicine, 2085 Adelbert Rd, Cleveland, OH, 44106, USA
- National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Rohan de Silva
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, WC1N 1PJ, UK
| | - Jiri G Safar
- Departments of Pathology, Case Western Reserve University School of Medicine, 2085 Adelbert Rd, Cleveland, OH, 44106, USA.
- Departments of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Departments of Neuroscience, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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16
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Yim YY, Nestler EJ. Cell-Type-Specific Neuroproteomics of Synapses. Biomolecules 2023; 13:998. [PMID: 37371578 PMCID: PMC10296650 DOI: 10.3390/biom13060998] [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: 05/11/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
In the last two decades, our knowledge of synaptic proteomes and their relationship to normal brain function and neuropsychiatric disorders has been expanding rapidly through the use of more powerful neuroproteomic approaches. However, mass spectrometry (MS)-based neuroproteomic studies of synapses still require cell-type, spatial, and temporal proteome information. With the advancement of sample preparation and MS techniques, we have just begun to identify and understand proteomes within a given cell type, subcellular compartment, and cell-type-specific synapse. Here, we review the progress and limitations of MS-based neuroproteomics of synapses in the mammalian CNS and highlight the recent applications of these approaches in studying neuropsychiatric disorders such as major depressive disorder and substance use disorders. Combining neuroproteomic findings with other omics studies can generate an in-depth, comprehensive map of synaptic proteomes and possibly identify new therapeutic targets and biomarkers for several central nervous system disorders.
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Affiliation(s)
- Yun Young Yim
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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17
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Irala D, Wang S, Sakers K, Nagendren L, Ulloa-Severino FP, Bindu DS, Eroglu C. Astrocyte-Secreted Neurocan Controls Inhibitory Synapse Formation and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535448. [PMID: 37066164 PMCID: PMC10104008 DOI: 10.1101/2023.04.03.535448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Astrocytes strongly promote the formation and maturation of synapses by secreted proteins. To date, several astrocyte-secreted synaptogenic proteins controlling different stages of excitatory synapse development have been identified. However, the identities of astrocytic signals that induce inhibitory synapse formation remain elusive. Here, through a combination of in vitro and in vivo experiments, we identified Neurocan as an astrocyte-secreted inhibitory synaptogenic protein. Neurocan is a chondroitin sulfate proteoglycan that is best known as a protein localized to the perineuronal nets. However, Neurocan is cleaved into two after secretion from astrocytes. We found that the resulting N- and C-terminal fragments have distinct localizations in the extracellular matrix. While the N-terminal fragment remains associated with perineuronal nets, the Neurocan C-terminal fragment localizes to synapses and specifically controls cortical inhibitory synapse formation and function. Neurocan knockout mice lacking the whole protein or only its C-terminal synaptogenic region have reduced inhibitory synapse numbers and function. Through super-resolution microscopy and in vivo proximity labeling by secreted TurboID, we discovered that the synaptogenic domain of Neurocan localizes to somatostatin-positive inhibitory synapses and strongly regulates their formation. Together, our results unveil a mechanism through which astrocytes control circuit-specific inhibitory synapse development in the mammalian brain.
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18
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Kehrloesser S, Cast O, Elliott TS, Ernst RJ, Machel AC, Chen JX, Chin JW, Miller ML. Cell-of-origin-specific proteomics of extracellular vesicles. PNAS NEXUS 2023; 2:pgad107. [PMID: 37091541 PMCID: PMC10119638 DOI: 10.1093/pnasnexus/pgad107] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/21/2023] [Indexed: 04/25/2023]
Abstract
The ability to assign cellular origin to low-abundance secreted factors in extracellular vesicles (EVs) would greatly facilitate the analysis of paracrine-mediated signaling. Here, we report a method, named selective isolation of extracellular vesicles (SIEVE), which uses cell type-specific proteome labeling via stochastic orthogonal recoding of translation (SORT) to install bioorthogonal reactive groups into the proteins derived from the cells targeted for labeling. We establish the native purification of intact EVs from a target cell, via a bioorthogonal tetrazine ligation, leading to copurification of the largely unlabeled EV proteome from the same cell. SIEVE enables capture of EV proteins at levels comparable with those obtained by antibody-based methods, which capture all EVs regardless of cellular origin, and at levels 20× higher than direct capture of SORT-labeled proteins. Using proteomic analysis, we analyze nonlabeled cargo proteins of EVs and show that the enhanced sensitivity of SIEVE allows for unbiased and comprehensive analysis of EV proteins from subpopulations of cells as well as for cell-specific EV proteomics in complex coculture systems. SIEVE can be applied with high efficiency in a diverse range of existing model systems for cell-cell communication and has direct applications for cell-of-origin EV analysis and for protein biomarker discovery.
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Affiliation(s)
- Sebastian Kehrloesser
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Oliver Cast
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Thomas S Elliott
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Russell J Ernst
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Anne C Machel
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Jia-Xuan Chen
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Martin L Miller
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Oncology Data Science, Oncology R&D, AstraZeneca, 1 Francis Crick Ave, Cambridge CB2 0AA, UK
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19
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Kreissl FK, Banki MA, Droujinine IA. Molecular methods to study protein trafficking between organs. Proteomics 2023; 23:e2100331. [PMID: 36478633 DOI: 10.1002/pmic.202100331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
Interorgan communication networks are key regulators of organismal homeostasis, and their dysregulation is associated with a variety of pathologies. While mass spectrometry proteomics identifies circulating proteins and can correlate their abundance with disease phenotypes, the tissues of origin and destinations of these secreted proteins remain largely unknown. In vitro approaches to study protein secretion are valuable, however, they may not mimic the complexity of in vivo environments. More recently, the development of engineered promiscuous BirA* biotin ligase derivatives has enabled tissue-specific tagging of cellular secreted proteomes in vivo. The use of biotin as a molecular tag provides information on the tissue of origin and destination, and enables the enrichment of low-abundance hormone proteins. Therefore, promiscuous protein biotinylation is a valuable tool to study protein secretion in vivo.
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Affiliation(s)
- Felix K Kreissl
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
| | - Michael A Banki
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Ilia A Droujinine
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
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20
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Impaired OTUD7A-dependent Ankyrin regulation mediates neuronal dysfunction in mouse and human models of the 15q13.3 microdeletion syndrome. Mol Psychiatry 2023; 28:1747-1769. [PMID: 36604605 DOI: 10.1038/s41380-022-01937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023]
Abstract
Copy number variations (CNVs) are associated with psychiatric and neurodevelopmental disorders (NDDs), and most, including the recurrent 15q13.3 microdeletion disorder, have unknown disease mechanisms. We used a heterozygous 15q13.3 microdeletion mouse model and patient iPSC-derived neurons to reveal developmental defects in neuronal maturation and network activity. To identify the underlying molecular dysfunction, we developed a neuron-specific proximity-labeling proteomics (BioID2) pipeline, combined with patient mutations, to target the 15q13.3 CNV genetic driver OTUD7A. OTUD7A is an emerging independent NDD risk gene with no known function in the brain, but has putative deubiquitinase function. The OTUD7A protein-protein interaction network included synaptic, axonal, and cytoskeletal proteins and was enriched for ASD and epilepsy risk genes (Ank3, Ank2, SPTAN1, SPTBN1). The interactions between OTUD7A and Ankyrin-G (Ank3) and Ankyrin-B (Ank2) were disrupted by an epilepsy-associated OTUD7A L233F variant. Further investigation of Ankyrin-G in mouse and human 15q13.3 microdeletion and OTUD7AL233F/L233F models revealed protein instability, increased polyubiquitination, and decreased levels in the axon initial segment, while structured illumination microscopy identified reduced Ankyrin-G nanodomains in dendritic spines. Functional analysis of human 15q13.3 microdeletion and OTUD7AL233F/L233F models revealed shared and distinct impairments to axonal growth and intrinsic excitability. Importantly, restoring OTUD7A or Ankyrin-G expression in 15q13.3 microdeletion neurons led to a reversal of abnormalities. These data reveal a critical OTUD7A-Ankyrin pathway in neuronal development, which is impaired in the 15q13.3 microdeletion syndrome, leading to neuronal dysfunction. Furthermore, our study highlights the utility of targeting CNV genes using cell type-specific proteomics to identify shared and unexplored disease mechanisms across NDDs.
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21
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Oura S, Ninomiya A, Sugihara F, Matzuk MM, Ikawa M. Proximity-dependent biotin labeling in testicular germ cells identified TESMIN-associated proteins. Sci Rep 2022; 12:22198. [PMID: 36564444 PMCID: PMC9789103 DOI: 10.1038/s41598-022-26501-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Characterization of protein-protein interactions (PPI) is a key to understanding the functions of proteins of interest. Recently developed proximity-dependent biotin identification (BioID) has been actively investigated as an alternative PPI mapping method because of its usefulness in uncovering transient PPI. Here, as an example of proximity labeling proteomics application in the testis, we generated two transgenic mouse lines expressing two biotin ligases (BioID2 or TurboID) fused with TESMIN, which translocates from the cytosol to the nucleus during meiotic progression and is required for reproduction. The BioID2 transgene, albeit not the TurboID transgene, rescued fertility defects of the Tesmin KO male mice, indicating that the TESMIN-BioID2 fusion can physiologically replace TESMIN. Furthermore, biotinylated protein pull-down and affinity-purification followed by mass spectrometry using the TESMIN-BioID2 transgenic mice captured components of the MYBL1-MuvB complex that regulate cell-cycle gene expression. Thus, our study shows that proximity labeling proteomics can be applied in male germ cells, although the choice of biotin ligase needs to be carefully tested.
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Affiliation(s)
- Seiya Oura
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 565-0871, Japan
| | - Akinori Ninomiya
- Core Instrumentation Facility, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Martin M Matzuk
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan.
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 565-0871, Japan.
- The Institute of Medical Science, The University of Tokyo, Minato-Ku, Tokyo, 108-8639, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka, 565-0871, Japan.
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22
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Mathew B, Bathla S, Williams KR, Nairn AC. Deciphering Spatial Protein-Protein Interactions in Brain Using Proximity Labeling. Mol Cell Proteomics 2022; 21:100422. [PMID: 36198386 PMCID: PMC9650050 DOI: 10.1016/j.mcpro.2022.100422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 01/18/2023] Open
Abstract
Cellular biomolecular complexes including protein-protein, protein-RNA, and protein-DNA interactions regulate and execute most biological functions. In particular in brain, protein-protein interactions (PPIs) mediate or regulate virtually all nerve cell functions, such as neurotransmission, cell-cell communication, neurogenesis, synaptogenesis, and synaptic plasticity. Perturbations of PPIs in specific subsets of neurons and glia are thought to underly a majority of neurobiological disorders. Therefore, understanding biological functions at a cellular level requires a reasonably complete catalog of all physical interactions between proteins. An enzyme-catalyzed method to biotinylate proximal interacting proteins within 10 to 300 nm of each other is being increasingly used to characterize the spatiotemporal features of complex PPIs in brain. Thus, proximity labeling has emerged recently as a powerful tool to identify proteomes in distinct cell types in brain as well as proteomes and PPIs in structures difficult to isolate, such as the synaptic cleft, axonal projections, or astrocyte-neuron junctions. In this review, we summarize recent advances in proximity labeling methods and their application to neurobiology.
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Affiliation(s)
- Boby Mathew
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Shveta Bathla
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Department of Psychiatry, Yale University, New Haven, Connecticut, USA
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Department of Psychiatry, Yale University, New Haven, Connecticut, USA.
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23
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Murtaza N, Cheng AA, Brown CO, Meka DP, Hong S, Uy JA, El-Hajjar J, Pipko N, Unda BK, Schwanke B, Xing S, Thiruvahindrapuram B, Engchuan W, Trost B, Deneault E, Calderon de Anda F, Doble BW, Ellis J, Anagnostou E, Bader GD, Scherer SW, Lu Y, Singh KK. Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies. Cell Rep 2022; 41:111678. [DOI: 10.1016/j.celrep.2022.111678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/16/2022] [Accepted: 10/25/2022] [Indexed: 11/23/2022] Open
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24
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Dumrongprechachan V, Salisbury RB, Butler L, MacDonald ML, Kozorovitskiy Y. Dynamic proteomic and phosphoproteomic atlas of corticostriatal axons in neurodevelopment. eLife 2022; 11:e78847. [PMID: 36239373 PMCID: PMC9629834 DOI: 10.7554/elife.78847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022] Open
Abstract
Mammalian axonal development begins in embryonic stages and continues postnatally. After birth, axonal proteomic landscape changes rapidly, coordinated by transcription, protein turnover, and post-translational modifications. Comprehensive profiling of axonal proteomes across neurodevelopment is limited, with most studies lacking cell-type and neural circuit specificity, resulting in substantial information loss. We create a Cre-dependent APEX2 reporter mouse line and map cell-type-specific proteome of corticostriatal projections across postnatal development. We synthesize analysis frameworks to define temporal patterns of axonal proteome and phosphoproteome, identifying co-regulated proteins and phosphorylations associated with genetic risk for human brain disorders. We discover proline-directed kinases as major developmental regulators. APEX2 transgenic reporter proximity labeling offers flexible strategies for subcellular proteomics with cell type specificity in early neurodevelopment, a critical period for neuropsychiatric disease.
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Affiliation(s)
- Vasin Dumrongprechachan
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
- The Chemistry of Life Processes Institute, Northwestern UniversityEvanstonUnited States
| | - Ryan B Salisbury
- Department of Psychiatry, University of PittsburghPittsburghUnited States
| | - Lindsey Butler
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
| | | | - Yevgenia Kozorovitskiy
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
- The Chemistry of Life Processes Institute, Northwestern UniversityEvanstonUnited States
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25
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Myers KR, Fan Y, McConnell P, Cooper JA, Zheng JQ. Actin capping protein regulates postsynaptic spine development through CPI-motif interactions. Front Mol Neurosci 2022; 15:1020949. [PMID: 36245917 PMCID: PMC9557104 DOI: 10.3389/fnmol.2022.1020949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/12/2022] [Indexed: 12/02/2022] Open
Abstract
Dendritic spines are small actin-rich protrusions essential for the formation of functional circuits in the mammalian brain. During development, spines begin as dynamic filopodia-like protrusions that are then replaced by relatively stable spines containing an expanded head. Remodeling of the actin cytoskeleton plays a key role in the formation and modification of spine morphology, however many of the underlying regulatory mechanisms remain unclear. Capping protein (CP) is a major actin regulating protein that caps the barbed ends of actin filaments, and promotes the formation of dense branched actin networks. Knockdown of CP impairs the formation of mature spines, leading to an increase in the number of filopodia-like protrusions and defects in synaptic transmission. Here, we show that CP promotes the stabilization of dendritic protrusions, leading to the formation of stable mature spines. However, the localization and function of CP in dendritic spines requires interactions with proteins containing a capping protein interaction (CPI) motif. We found that the CPI motif-containing protein Twinfilin-1 (Twf1) also localizes to spines where it plays a role in CP spine enrichment. The knockdown of Twf1 leads to an increase in the density of filopodia-like protrusions and a decrease in the stability of dendritic protrusions, similar to CP knockdown. Finally, we show that CP directly interacts with Shank and regulates its spine accumulation. These results suggest that spatiotemporal regulation of CP in spines not only controls the actin dynamics underlying the formation of stable postsynaptic spine structures, but also plays an important role in the assembly of the postsynaptic apparatus underlying synaptic function.
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Affiliation(s)
- Kenneth R. Myers
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
| | - Yanjie Fan
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
| | - Patrick McConnell
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, United States
| | - John A. Cooper
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, United States
| | - James Q. Zheng
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
- Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
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26
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Yang R, Meyer AS, Droujinine IA, Udeshi ND, Hu Y, Guo J, McMahon JA, Carey DK, Xu C, Fang Q, Sha J, Qin S, Rocco D, Wohlschlegel J, Ting AY, Carr SA, Perrimon N, McMahon AP. A genetic model for in vivo proximity labelling of the mammalian secretome. Open Biol 2022; 12:220149. [PMID: 35946312 PMCID: PMC9364151 DOI: 10.1098/rsob.220149] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Organ functions are highly specialized and interdependent. Secreted factors regulate organ development and mediate homeostasis through serum trafficking and inter-organ communication. Enzyme-catalysed proximity labelling enables the identification of proteins within a specific cellular compartment. Here, we report a BirA*G3 mouse strain that enables CRE-dependent promiscuous biotinylation of proteins trafficking through the endoplasmic reticulum. When broadly activated throughout the mouse, widespread labelling of proteins was observed within the secretory pathway. Streptavidin affinity purification and peptide mapping by quantitative mass spectrometry (MS) proteomics revealed organ-specific secretory profiles and serum trafficking. As expected, secretory proteomes were highly enriched for signal peptide-containing proteins, highlighting both conventional and non-conventional secretory processes, and ectodomain shedding. Lower-abundance proteins with hormone-like properties were recovered and validated using orthogonal approaches. Hepatocyte-specific activation of BirA*G3 highlighted liver-specific biotinylated secretome profiles. The BirA*G3 mouse model demonstrates enhanced labelling efficiency and tissue specificity over viral transduction approaches and will facilitate a deeper understanding of secretory protein interplay in development, and in healthy and diseased adult states.
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Affiliation(s)
- Rui Yang
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Amanda S. Meyer
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | | | | | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Jill A. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | | | - Charles Xu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Qiao Fang
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada, M5S 3E1
| | - Jihui Sha
- Department of Biological Chemistry, Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shishang Qin
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, People's Republic of China
| | - David Rocco
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alice Y. Ting
- Chan Zuckerberg Biohub, San Francisco, CA, USA,Departments of Genetics, Biology, and Chemistry, Stanford University, Stanford, CA, USA
| | | | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA,Howard Hughes Medical Institute, Boston, MA, USA
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
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27
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Abstract
![]()
Proximity
labeling can be defined as an enzymatic “in-cell”
chemical reaction that catalyzes the proximity-dependent modification
of biomolecules in live cells. Since the modified proteins can be
isolated and identified via mass spectrometry, this method has been
successfully utilized for the characterization of local proteomes
such as the sub-mitochondrial proteome and the proteome at membrane
contact sites, or spatiotemporal interactome information in live cells,
which are not “accessible” via conventional methods.
Currently, proximity labeling techniques can be applied not only for
local proteome mapping but also for profiling local RNA and DNA, in
addition to showing great potential for elucidating spatial cell–cell
interaction networks in live animal models. We believe that proximity
labeling has emerged as an essential tool in “spatiomics,”
that is, for the extraction of spatially distributed biological information
in a cell or organism. Proximity labeling is a multidisciplinary
chemical technique. For
a decade, we and other groups have engineered it for multiple applications
based on the modulation of enzyme chemistry, chemical probe design,
and mass analysis techniques that enable superior mapping results.
The technique has been adopted in biology and chemistry. This “in-cell”
reaction has been widely adopted by biologists who modified it into
an in vivo reaction in animal models. In our laboratory, we conducted
in vivo proximity labeling reactions in mouse models and could successfully
obtain the liver-specific secretome and muscle-specific mitochondrial
matrix proteome. We expect that proximity reaction can further contribute
to revealing tissue-specific localized molecular information in live
animal models. Simultaneously, chemists have also adopted the
concept and employed
chemical “photocatalysts” as artificial enzymes to develop
new proximity labeling reactions. Under light activation, photocatalysts
can convert the precursor molecules to the reactive species via electron
transfer or energy transfer and the reactive molecules can react with
proximal biomolecules within a definite lifetime in an aqueous solution.
To identify the modified biomolecules by proximity labeling, the modified
biomolecules should be enriched after lysis and sequenced using sequencing
tools. In this analysis step, the direct detection of modified residue(s)
on the modified proteins or nucleic acids can be the proof of their
labeling event by proximal enzymes or catalysts in the cell. In this
Account, we introduce the basic concept of proximity labeling and
the multidirectional advances in the development of this method. We
believe that this Account may facilitate further utilization and modification
of the method in both biological and chemical research communities,
thereby revealing unknown spatially distributed molecular or cellular
information or spatiome.
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Affiliation(s)
- Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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28
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Lim D, Kim D, Um JW, Ko J. Reassessing synaptic adhesion pathways. Trends Neurosci 2022; 45:517-528. [DOI: 10.1016/j.tins.2022.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 01/19/2023]
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29
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Raeisossadati R, Ferrari MFR. Mitochondria-ER Tethering in Neurodegenerative Diseases. Cell Mol Neurobiol 2022; 42:917-930. [PMID: 33196974 PMCID: PMC11441217 DOI: 10.1007/s10571-020-01008-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022]
Abstract
Organelles juxtaposition has been detected for decades, although only recently gained importance due to a pivotal role in the regulation of cellular processes dependent on membrane contact sites. Endoplasmic reticulum (ER) and mitochondria interaction is a prime example of organelles contact sites. Mitochondria-associated membranes (MAM) are proposed to harbor ER-mitochondria tether complexes, mainly when these organelles are less than 30 nm apart. Dysfunctions of proteins located at the MAM are associated with neurodegenerative diseases such as Parkinson's, Alzheimer's and amyotrophic lateral sclerosis, as well as neurodevelopmental disorders; hence any malfunction in MAM can potentially trigger cell death. This review will focus on the role of ER-mitochondria contact sites, regarding calcium homeostasis, lipid metabolism, autophagy, morphology and dynamics of mitochondria, mainly in the context of neurodegenerative diseases. Approaches that have been employed so far to study organelles contact sites, as well as methods that were not used in neurosciences yet, but are promising and accurate ways to unveil the functions of MAM during neurodegeneration, is also discussed in the present review.
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Affiliation(s)
- Reza Raeisossadati
- Departamento de Genetica e Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
| | - Merari F R Ferrari
- Departamento de Genetica e Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
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30
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Proximity labeling methods for proteomic analysis of membrane proteins. J Proteomics 2022; 264:104620. [DOI: 10.1016/j.jprot.2022.104620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022]
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31
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Sun X, Sun H, Han X, Chen PC, Jiao Y, Wu Z, Zhang X, Wang Z, Niu M, Yu K, Liu D, Dey KK, Mancieri A, Fu Y, Cho JH, Li Y, Poudel S, Branon TC, Ting AY, Peng J. Deep Single-Cell-Type Proteome Profiling of Mouse Brain by Nonsurgical AAV-Mediated Proximity Labeling. Anal Chem 2022; 94:5325-5334. [PMID: 35315655 DOI: 10.1021/acs.analchem.1c05212] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Proteome profiling is a powerful tool in biological and biomedical studies, starting with samples at bulk, single-cell, or single-cell-type levels. Reliable methods for extracting specific cell-type proteomes are in need, especially for the cells (e.g., neurons) that cannot be readily isolated. Here, we present an innovative proximity labeling (PL) strategy for single-cell-type proteomics of mouse brain, in which TurboID (an engineered biotin ligase) is used to label almost all proteins in a specific cell type. This strategy bypasses the requirement of cell isolation and includes five major steps: (i) constructing recombinant adeno-associated viruses (AAVs) to express TurboID driven by cell-type-specific promoters, (ii) delivering the AAV to mouse brains by direct intravenous injection, (iii) enhancing PL labeling by biotin administration, (iv) purifying biotinylated proteins, followed by on-bead protein digestion, and (v) quantitative tandem-mass-tag (TMT) labeling. We first confirmed that TurboID can label a wide range of cellular proteins in human HEK293 cells and optimized the single-cell-type proteomic pipeline. To analyze specific brain cell types, we generated recombinant AAVs to coexpress TurboID and mCherry proteins, driven by neuron- or astrocyte-specific promoters and validated the expected cell expression by coimmunostaining of mCherry and cellular markers. Subsequent biotin purification and TMT analysis identified ∼10,000 unique proteins from a few micrograms of protein samples with excellent reproducibility. Comparative and statistical analyses indicated that these PL proteomes contain cell-type-specific cellular pathways. Although PL was originally developed for studying protein-protein interactions and subcellular proteomes, we extended it to efficiently tag the entire proteomes of specific cell types in the mouse brain using TurboID biotin ligase. This simple, effective in vivo approach should be broadly applicable to single-cell-type proteomics.
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Affiliation(s)
- Xiaojun Sun
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Huan Sun
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Xian Han
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Ping-Chung Chen
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Yun Jiao
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhiping Wu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Xue Zhang
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhen Wang
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Mingming Niu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kaiwen Yu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Danting Liu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kaushik Kumar Dey
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Ariana Mancieri
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Yingxue Fu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Tess C Branon
- Department of Genetics, Department of Chemistry, Department of Biology, Stanford University, Stanford, California 94305, United States
| | - Alice Y Ting
- Department of Genetics, Department of Chemistry, Department of Biology, Stanford University, Stanford, California 94305, United States
| | - Junmin Peng
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
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32
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Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. Subcellular Transcriptomics and Proteomics: A Comparative Methods Review. Mol Cell Proteomics 2022; 21:100186. [PMID: 34922010 PMCID: PMC8864473 DOI: 10.1016/j.mcpro.2021.100186] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
The internal environment of cells is molecularly crowded, which requires spatial organization via subcellular compartmentalization. These compartments harbor specific conditions for molecules to perform their biological functions, such as coordination of the cell cycle, cell survival, and growth. This compartmentalization is also not static, with molecules trafficking between these subcellular neighborhoods to carry out their functions. For example, some biomolecules are multifunctional, requiring an environment with differing conditions or interacting partners, and others traffic to export such molecules. Aberrant localization of proteins or RNA species has been linked to many pathological conditions, such as neurological, cancer, and pulmonary diseases. Differential expression studies in transcriptomics and proteomics are relatively common, but the majority have overlooked the importance of subcellular information. In addition, subcellular transcriptomics and proteomics data do not always colocate because of the biochemical processes that occur during and after translation, highlighting the complementary nature of these fields. In this review, we discuss and directly compare the current methods in spatial proteomics and transcriptomics, which include sequencing- and imaging-based strategies, to give the reader an overview of the current tools available. We also discuss current limitations of these strategies as well as future developments in the field of spatial -omics.
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Affiliation(s)
- Josie A Christopher
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Aikaterini Geladaki
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Department of Genetics, University of Cambridge, Cambridge, UK
| | - Charlotte S Dawson
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Owen L Vennard
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
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33
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Hong SA, Seo JH, Wi S, Jung ES, Yu J, Hwang GH, Yu JH, Baek A, Park S, Bae S, Cho SR. In vivo gene editing via homology-independent targeted integration for adrenoleukodystrophy treatment. Mol Ther 2022; 30:119-129. [PMID: 34058389 PMCID: PMC8753287 DOI: 10.1016/j.ymthe.2021.05.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 04/26/2021] [Accepted: 05/20/2021] [Indexed: 01/07/2023] Open
Abstract
Adrenoleukodystrophy (ALD) is caused by various pathogenic mutations in the X-linked ABCD1 gene, which lead to metabolically abnormal accumulations of very long-chain fatty acids in many organs. However, curative treatment of ALD has not yet been achieved. To treat ALD, we applied two different gene-editing strategies, base editing and homology-independent targeted integration (HITI), in ALD patient-derived fibroblasts. Next, we performed in vivo HITI-mediated gene editing using AAV9 vectors delivered via intravenous administration in the ALD model mice. We found that the ABCD1 mRNA level was significantly increased in HITI-treated mice, and the plasma levels of C24:0-LysoPC (lysophosphatidylcholine) and C26:0-LysoPC, sensitive diagnostic markers for ALD, were significantly reduced. These results suggest that HITI-mediated mutant gene rescue could be a promising therapeutic strategy for human ALD treatment.
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Affiliation(s)
- Sung-Ah Hong
- Department of Chemistry and Research Institute for Natural Sciences, Hanyang University, Seoul 04673, South Korea
| | - Jung Hwa Seo
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul 03722, South Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Soohyun Wi
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul 03722, South Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea; Department of Rehabilitation Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Eul Sik Jung
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, South Korea; JES Clinic, Incheon 21550, South Korea
| | - Jihyeon Yu
- Division of Life Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Gue-Ho Hwang
- Department of Chemistry and Research Institute for Natural Sciences, Hanyang University, Seoul 04673, South Korea
| | - Ji Hea Yu
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul 03722, South Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Ahreum Baek
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul 03722, South Korea; Department of Rehabilitation Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, South Korea
| | - Soeon Park
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea; Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Sangsu Bae
- Department of Chemistry and Research Institute for Natural Sciences, Hanyang University, Seoul 04673, South Korea.
| | - Sung-Rae Cho
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul 03722, South Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea; Graduate Program of Nano Science and Technology, Yonsei University, Seoul 03722, South Korea; Rehabilitation Institute of Neuromuscular Disease, Yonsei University College of Medicine, Seoul 03722, Korea.
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34
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Yeh SJ, Hsu PH, Yeh TY, Yang WK, Chang KP, Chiang CS, Tang SC, Tsai LK, Jeng JS, Hsieh ST. Capping Protein Regulator and Myosin 1 Linker 3 (CARMIL3) as a Molecular Signature of Ischemic Neurons in the DWI-T2 Mismatch Areas After Stroke. Front Mol Neurosci 2022; 14:754762. [PMID: 34975397 PMCID: PMC8716926 DOI: 10.3389/fnmol.2021.754762] [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: 08/07/2021] [Accepted: 11/29/2021] [Indexed: 11/15/2022] Open
Abstract
Ischemic stroke with a mismatch between diffusion-weighted imaging (DWI) and fluid-attenuated inversion recovery (FLAIR) or T2-weighted images indicates onset within 4.5 h, but the pathological substrates in the DWI-T2 mismatch and T2(+) areas remain elusive. In this study, proteomics was used to explore (1) the protein expression profiles in the T2(+), mismatch, and contralateral areas, and (2) the protein with the highest expression in the T2(+) area in the brains of male Sprague-Dawley rats within 4.5 h after middle cerebral artery occlusion (MCAO). The expression of the candidate protein was further validated in (1) rat brain subjected to MCAO, (2) rat primary cortical neuronal culture with oxygen-glucose deprivation (OGD), and (3) infarcted human brain tissues. This study showed that apoptosis was observed in the T2(+) and mismatch regions and necroptosis in the T2(+) region of rat brains after MCAO. We identified capping protein regulator and myosin 1 linker 3 (CARMIL3) as the candidate molecule in the T2(+) and mismatch areas, exclusively in neurons, predominantly in the cytoplasm, and most abundant in the mismatch area. The CARMIL3(+) neurons and neurites in the mismatch and T2(+) areas were larger than those in the control area, and associated with (1) increased expression of sulfonylurea receptor 1 (SUR1), indicating edema, (2) accumulation of p62, indicating impaired autophagy, and (3) increase in 8-hydroxy-2′-deoxyguanosine (8-OHdG), indicating oxidative stress. The increased expression of CARMIL3 was validated in a cell model of cortical neurons after OGD and in infarcted human brain tissues. In conclusion, this study shows that the mismatch and T2(+) areas within 4.5 h after ischemia are characterized by upregulated expression of CARMIL3 in neurons, particularly the mismatch area, which is associated with neuronal edema, impaired autophagy, and oxidative stress, indicating that CARMIL3 serves as a molecular signature of brain ischemia.
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Affiliation(s)
- Shin-Joe Yeh
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Pang-Hung Hsu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Ti-Yen Yeh
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wei-Kang Yang
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ko-Ping Chang
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Sung Chiang
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Sung-Chun Tang
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Kai Tsai
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan.,Department of Neurology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | - Jiann-Shing Jeng
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Sung-Tsang Hsieh
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.,Graduate Institute of Brain and Mind Sciences, National Taiwan University College of Medicine, Taipei, Taiwan
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35
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Stark BC, Gao Y, Sepich DS, Belk L, Culver MA, Hu B, Mekel M, Ferris W, Shin J, Solnica-Krezel L, Lin F, Cooper JA. CARMIL3 is important for cell migration and morphogenesis during early development in zebrafish. Dev Biol 2022; 481:148-159. [PMID: 34599906 PMCID: PMC8781030 DOI: 10.1016/j.ydbio.2021.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 01/03/2023]
Abstract
Cell migration is important during early animal embryogenesis. Cell migration and cell shape are controlled by actin assembly and dynamics, which depend on capping proteins, including the barbed-end heterodimeric actin capping protein (CP). CP activity can be regulated by capping-protein-interacting (CPI) motif proteins, including CARMIL (capping protein Arp2/3 myosin-I linker) family proteins. Previous studies of CARMIL3, one of the three highly conserved CARMIL genes in vertebrates, have largely been limited to cells in culture. Towards understanding CARMIL function during embryogenesis in vivo, we analyzed zebrafish lines carrying mutations of carmil3. Maternal-zygotic mutants showed impaired endodermal migration during gastrulation, along with defects in dorsal forerunner cell (DFC) cluster formation, which affected the morphogenesis of Kupffer's vesicle (KV). Mutant KVs were smaller, contained fewer cells and displayed decreased numbers of cilia, leading to defects in left/right (L/R) patterning with variable penetrance and expressivity. The penetrance and expressivity of the KV phenotype in carmil3 mutants correlated well with the L/R heart positioning defect at the end of embryogenesis. This in vivo animal study of CARMIL3 reveals its new role during morphogenesis of the vertebrate embryo. This role involves migration of endodermal cells and DFCs, along with subsequent morphogenesis of the KV and L/R asymmetry.
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Affiliation(s)
- Benjamin C. Stark
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO
| | - Yuanyuan Gao
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Diane S. Sepich
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO
| | - Lakyn Belk
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Matthew A. Culver
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Bo Hu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Marlene Mekel
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO
| | - Wyndham Ferris
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO
| | - Jimann Shin
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO,Corresponding authors. Email addresses for correspondence after publication: Fang Lin, ; Lilianna Solnica-Krezel, ; John Cooper,
| | - Fang Lin
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA.,Corresponding authors. Email addresses for correspondence after publication: Fang Lin, ; Lilianna Solnica-Krezel, ; John Cooper,
| | - John A. Cooper
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO,Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO,Corresponding authors. Email addresses for correspondence after publication: Fang Lin, ; Lilianna Solnica-Krezel, ; John Cooper,
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Abstract
INTRODUCTION The matrisome and adhesome comprise proteins that are found within or are associated with the extracellular matrix (ECM) and adhesion complexes, respectively. Interactions between cells and their microenvironment are mediated by key matrisome and adhesome proteins, which direct fundamental processes, including growth and development. Due to their underlying complexity, it has historically been challenging to undertake mass spectrometry (MS)-based profiling of these proteins. New developments in sample preparative workflows, informatics databases, and MS techniques have enabled in-depth proteomic characterization of the matrisome and adhesome, resulting in a comprehensive understanding of the interactomes, and cellular signaling that occur at the cell-ECM interface. AREA COVERED This review summarizes recent advances in proteomic characterization of the matrisome and adhesome. It focuses on the importance of curated databases and discusses key strengths and limitations of different workflows. EXPERT OPINION MS-based proteomics has shown promise in characterizing the matrisome and topology of adhesome networks in health and disease. Moving forward, it will be important to incorporate integrative analysis to define the bidirectional signaling between the matrisome and adhesome, and adopt new methods for post-translational modification and in vivo analyses to better dissect the critical roles that these proteins play in human pathophysiology.
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Affiliation(s)
- Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
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Gutman-Wei AY, Brown SP. Mechanisms Underlying Target Selectivity for Cell Types and Subcellular Domains in Developing Neocortical Circuits. Front Neural Circuits 2021; 15:728832. [PMID: 34630048 PMCID: PMC8497978 DOI: 10.3389/fncir.2021.728832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/25/2021] [Indexed: 11/25/2022] Open
Abstract
The cerebral cortex contains numerous neuronal cell types, distinguished by their molecular identity as well as their electrophysiological and morphological properties. Cortical function is reliant on stereotyped patterns of synaptic connectivity and synaptic function among these neuron types, but how these patterns are established during development remains poorly understood. Selective targeting not only of different cell types but also of distinct postsynaptic neuronal domains occurs in many brain circuits and is directed by multiple mechanisms. These mechanisms include the regulation of axonal and dendritic guidance and fine-scale morphogenesis of pre- and postsynaptic processes, lineage relationships, activity dependent mechanisms and intercellular molecular determinants such as transmembrane and secreted molecules, many of which have also been implicated in neurodevelopmental disorders. However, many studies of synaptic targeting have focused on circuits in which neuronal processes target different lamina, such that cell-type-biased connectivity may be confounded with mechanisms of laminar specificity. In the cerebral cortex, each cortical layer contains cell bodies and processes from intermingled neuronal cell types, an arrangement that presents a challenge for the development of target-selective synapse formation. Here, we address progress and future directions in the study of cell-type-biased synaptic targeting in the cerebral cortex. We highlight challenges to identifying developmental mechanisms generating stereotyped patterns of intracortical connectivity, recent developments in uncovering the determinants of synaptic target selection during cortical synapse formation, and current gaps in the understanding of cortical synapse specificity.
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Affiliation(s)
- Alan Y. Gutman-Wei
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Solange P. Brown
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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38
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Dynamic tracking and identification of tissue-specific secretory proteins in the circulation of live mice. Nat Commun 2021; 12:5204. [PMID: 34471136 PMCID: PMC8410947 DOI: 10.1038/s41467-021-25546-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 08/12/2021] [Indexed: 12/16/2022] Open
Abstract
Secretory proteins are an essential component of interorgan communication networks that regulate animal physiology. Current approaches for identifying secretory proteins from specific cell and tissue types are largely limited to in vitro or ex vivo models which often fail to recapitulate in vivo biology. As such, there is mounting interest in developing in vivo analytical tools that can provide accurate information on the origin, identity, and spatiotemporal dynamics of secretory proteins. Here, we describe iSLET (in situ Secretory protein Labeling via ER-anchored TurboID) which selectively labels proteins that transit through the classical secretory pathway via catalytic actions of Sec61b-TurboID, a proximity labeling enzyme anchored in the ER lumen. To validate iSLET in a whole-body system, we express iSLET in the mouse liver and demonstrate efficient labeling of liver secretory proteins which could be tracked and identified within circulating blood plasma. Furthermore, proteomic analysis of the labeled liver secretome enriched from liver iSLET mouse plasma is highly consistent with previous reports of liver secretory protein profiles. Taken together, iSLET is a versatile and powerful tool for studying spatiotemporal dynamics of secretory proteins, a valuable class of biomarkers and therapeutic targets. The in vivo identification of proteins secreted from a specific cell type or tissue remains challenging. Here, the authors develop a proximity labeling-based method to selectively label secreted proteins and combine it with proteomics to identify liver secretory proteins in mouse plasma.
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Pino L, Schilling B. Proximity labeling and other novel mass spectrometric approaches for spatiotemporal protein dynamics. Expert Rev Proteomics 2021; 18:757-765. [PMID: 34496693 PMCID: PMC8650568 DOI: 10.1080/14789450.2021.1976149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Proteins are highly dynamic and their biological function is controlled by not only temporal abundance changes but also via regulated protein-protein interaction networks, which respond to internal and external perturbations. A wealth of novel analytical reagents and workflows allow studying spatiotemporal protein environments with great granularity while maintaining high throughput and ease of analysis. AREAS COVERED We review technology advances for measuring protein-protein proximity interactions with an emphasis on proximity labeling, and briefly summarize other spatiotemporal approaches including protein localization, and their dynamic changes over time, specifically in human cells and mammalian tissues. We focus especially on novel technologies and workflows emerging within the past 5 years. This includes enrichment-based techniques (proximity labeling and crosslinking), separation-based techniques (organelle fractionation and size exclusion chromatography), and finally sorting-based techniques (laser capture microdissection and mass spectrometry imaging). EXPERT OPINION Spatiotemporal proteomics is a key step in assessing biological complexity, understanding refined regulatory mechanisms, and forming protein complexes and networks. Studying protein dynamics across space and time holds promise for gaining deep insights into how protein networks may be perturbed during disease and aging processes, and offer potential avenues for therapeutic interventions, drug discovery, and biomarker development.
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Affiliation(s)
- Lindsay Pino
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, CA 94945, USA
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40
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Dumrongprechachan V, Salisbury RB, Soto G, Kumar M, MacDonald ML, Kozorovitskiy Y. Cell-type and subcellular compartment-specific APEX2 proximity labeling reveals activity-dependent nuclear proteome dynamics in the striatum. Nat Commun 2021; 12:4855. [PMID: 34381044 PMCID: PMC8357913 DOI: 10.1038/s41467-021-25144-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
The vertebrate brain consists of diverse neuronal types, classified by distinct anatomy and function, along with divergent transcriptomes and proteomes. Defining the cell-type specific neuroproteomes is important for understanding the development and functional organization of neural circuits. This task remains challenging in complex tissue, due to suboptimal protein isolation techniques that often result in loss of cell-type specific information and incomplete capture of subcellular compartments. Here, we develop a genetically targeted proximity labeling approach to identify cell-type specific subcellular proteomes in the mouse brain, confirmed by imaging, electron microscopy, and mass spectrometry. We virally express subcellular-localized APEX2 to map the proteome of direct and indirect pathway spiny projection neurons in the striatum. The workflow provides sufficient depth to uncover changes in the proteome of striatal neurons following chemogenetic activation of Gαq-coupled signaling cascades. This method enables flexible, cell-type specific quantitative profiling of subcellular proteome snapshots in the mouse brain. Mapping neuronal proteomes with genetic, subcellular, and temporal specificity is a challenging task. This study uncovers proteome dynamics in two classes of striatal spiny projection neurons in the mouse brain using a genetically targeted APEX2-based proximity labeling approach.
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Affiliation(s)
- V Dumrongprechachan
- Department of Neurobiology, Northwestern University, Evanston, IL, USA.,The Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - R B Salisbury
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.,Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - G Soto
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - M Kumar
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - M L MacDonald
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA. .,Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Y Kozorovitskiy
- Department of Neurobiology, Northwestern University, Evanston, IL, USA. .,The Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
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41
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Rosenthal SM, Misra T, Abdouni H, Branon TC, Ting AY, Scott IC, Gingras AC. A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos. Mol Cell Proteomics 2021; 20:100128. [PMID: 34332124 PMCID: PMC8383115 DOI: 10.1016/j.mcpro.2021.100128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/07/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding how proteins are organized in compartments is essential to elucidating their function. While proximity-dependent approaches such as BioID have enabled a massive increase in information about organelles, protein complexes, and other structures in cell culture, to date there have been only a few studies on living vertebrates. Here, we adapted proximity labeling for protein discovery in vivo in the vertebrate model organism, zebrafish. Using lamin A (LMNA) as bait and green fluorescent protein (GFP) as a negative control, we developed, optimized, and benchmarked in vivo TurboID and miniTurbo labeling in early zebrafish embryos. We developed both an mRNA injection protocol and a transgenic system in which transgene expression is controlled by a heat shock promoter. In both cases, biotin is provided directly in the egg water, and we demonstrate that 12 h of labeling are sufficient for biotinylation of prey proteins, which should permit time-resolved analysis of development. After statistical scoring, we found that the proximal partners of LMNA detected in each system were enriched for nuclear envelope and nuclear membrane proteins and included many orthologs of human proteins identified as proximity partners of lamin A in mammalian cell culture. The tools and protocols developed here will allow zebrafish researchers to complement genetic tools with powerful proteomics approaches.
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Affiliation(s)
- Shimon M Rosenthal
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Tvisha Misra
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hala Abdouni
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Tess C Branon
- Department of Genetics, Stanford University, Stanford, California, USA; Department of Biology, Stanford University, Stanford, California, USA; Department of Chemistry, Stanford University, Stanford, California, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, California, USA; Department of Biology, Stanford University, Stanford, California, USA; Department of Chemistry, Stanford University, Stanford, California, USA; Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Ian C Scott
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada.
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42
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O'Neil SD, Rácz B, Brown WE, Gao Y, Soderblom EJ, Yasuda R, Soderling SH. Action potential-coupled Rho GTPase signaling drives presynaptic plasticity. eLife 2021; 10:63756. [PMID: 34269176 PMCID: PMC8285108 DOI: 10.7554/elife.63756] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 07/06/2021] [Indexed: 12/30/2022] Open
Abstract
In contrast to their postsynaptic counterparts, the contributions of activity-dependent cytoskeletal signaling to presynaptic plasticity remain controversial and poorly understood. To identify and evaluate these signaling pathways, we conducted a proteomic analysis of the presynaptic cytomatrix using in vivo biotin identification (iBioID). The resultant proteome was heavily enriched for actin cytoskeleton regulators, including Rac1, a Rho GTPase that activates the Arp2/3 complex to nucleate branched actin filaments. Strikingly, we find Rac1 and Arp2/3 are closely associated with synaptic vesicle membranes in adult mice. Using three independent approaches to alter presynaptic Rac1 activity (genetic knockout, spatially restricted inhibition, and temporal optogenetic manipulation), we discover that this pathway negatively regulates synaptic vesicle replenishment at both excitatory and inhibitory synapses, bidirectionally sculpting short-term synaptic depression. Finally, we use two-photon fluorescence lifetime imaging to show that presynaptic Rac1 activation is coupled to action potentials by voltage-gated calcium influx. Thus, this study uncovers a previously unrecognized mechanism of actin-regulated short-term presynaptic plasticity that is conserved across excitatory and inhibitory terminals. It also provides a new proteomic framework for better understanding presynaptic physiology, along with a blueprint of experimental strategies to isolate the presynaptic effects of ubiquitously expressed proteins.
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Affiliation(s)
| | - Bence Rácz
- Department of Anatomy and Histology, University of Veterinary Medicine, Budapest, Hungary
| | - Walter Evan Brown
- Department of Cell Biology, Duke University Medical Center, Durham, United States
| | - Yudong Gao
- Department of Cell Biology, Duke University Medical Center, Durham, United States
| | - Erik J Soderblom
- Department of Cell Biology, Duke University Medical Center, Durham, United States.,Proteomics and Metabolomics Shared Resource and Center for Genomic and Computational Biology, Duke University Medical Center, Durham, United States
| | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, United States
| | - Scott H Soderling
- Department of Neurobiology, Duke University Medical Center, Durham, United States.,Department of Cell Biology, Duke University Medical Center, Durham, United States
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43
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Tripartite synaptomics: Cell-surface proximity labeling in vivo. Neurosci Res 2021; 173:14-21. [PMID: 34019951 DOI: 10.1016/j.neures.2021.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/04/2021] [Accepted: 05/09/2021] [Indexed: 11/23/2022]
Abstract
The astrocyte is a central glial cell and plays a critical role in the architecture and activity of neuronal circuits and brain functions through forming a tripartite synapse with neurons. Emerging evidence suggests that dysfunction of tripartite synaptic connections contributes to a variety of psychiatric and neurodevelopmental disorders. Furthermore, recent advancements with transcriptome profiling, cell biological and physiological approaches have provided new insights into the molecular mechanisms into how astrocytes control synaptogenesis in the brain. In addition to these findings, we have recently developed in vivo cell-surface proximity-dependent biotinylation (BioID) approaches, TurboID-surface and Split-TurboID, to comprehensively understand the molecular composition between astrocytes and neuronal synapses. These proteomic approaches have discovered a novel molecular framework for understanding the tripartite synaptic cleft that arbitrates neuronal circuit formation and function. Here, this short review highlights novel in vivo cell-surface BioID approaches and recent advances in this rapidly evolving field, emphasizing how astrocytes regulate excitatory and inhibitory synapse formation in vitro and in vivo.
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44
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Aiken J, Holzbaur ELF. Cytoskeletal regulation guides neuronal trafficking to effectively supply the synapse. Curr Biol 2021; 31:R633-R650. [PMID: 34033795 DOI: 10.1016/j.cub.2021.02.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The development and proper function of the brain requires the formation of highly complex neuronal circuitry. These circuits are shaped from synaptic connections between neurons and must be maintained over a lifetime. The formation and continued maintenance of synapses requires accurate trafficking of presynaptic and postsynaptic components along the axon and dendrite, respectively, necessitating deliberate and specialized delivery strategies to replenish essential synaptic components. Maintenance of synaptic transmission also requires readily accessible energy stores, produced in part by localized mitochondria, that are tightly regulated with activity level. In this review, we focus on recent developments in our understanding of the cytoskeletal environment of axons and dendrites, examining how local regulation of cytoskeletal dynamics and organelle trafficking promotes synapse-specific delivery and plasticity. These new insights shed light on the complex and coordinated role that cytoskeletal elements play in establishing and maintaining neuronal circuitry.
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Affiliation(s)
- Jayne Aiken
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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45
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Pronobis MI, Zheng S, Singh SP, Goldman JA, Poss KD. In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration. eLife 2021; 10:e66079. [PMID: 33764296 PMCID: PMC8034980 DOI: 10.7554/elife.66079] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/25/2021] [Indexed: 01/04/2023] Open
Abstract
Strategies have not been available until recently to uncover interacting protein networks specific to key cell types, their subcellular compartments, and their major regulators during complex in vivo events. Here, we apply BioID2 proximity labeling to capture protein networks acting within cardiomyocytes during a key model of innate heart regeneration in zebrafish. Transgenic zebrafish expressing a promiscuous BirA2 localized to the entire myocardial cell or membrane compartment were generated, each identifying distinct proteomes in adult cardiomyocytes that became altered during regeneration. BioID2 profiling for interactors with ErbB2, a co-receptor for the cardiomyocyte mitogen Nrg1, implicated Rho A as a target of ErbB2 signaling in cardiomyocytes. Blockade of Rho A during heart regeneration, or during cardiogenic stimulation by the mitogenic influences Nrg1, Vegfaa, or vitamin D, disrupted muscle creation. Our findings reveal proximity labeling as a useful resource to interrogate cell proteomes and signaling networks during tissue regeneration in zebrafish.
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Affiliation(s)
- Mira I Pronobis
- Department of Cell Biology, Duke University Medical CenterDurhamUnited States
- Regeneration Next, Duke UniversityDurhamUnited States
| | - Susan Zheng
- Department of Cell Biology, Duke University Medical CenterDurhamUnited States
| | | | - Joseph A Goldman
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical CenterColumbusUnited States
| | - Kenneth D Poss
- Department of Cell Biology, Duke University Medical CenterDurhamUnited States
- Regeneration Next, Duke UniversityDurhamUnited States
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46
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Xu Y, Song X, Wang D, Wang Y, Li P, Li J. Proteomic insights into synaptic signaling in the brain: the past, present and future. Mol Brain 2021; 14:37. [PMID: 33596935 PMCID: PMC7888154 DOI: 10.1186/s13041-021-00750-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/09/2021] [Indexed: 12/29/2022] Open
Abstract
Chemical synapses in the brain connect neurons to form neural circuits, providing the structural and functional bases for neural communication. Disrupted synaptic signaling is closely related to a variety of neurological and psychiatric disorders. In the past two decades, proteomics has blossomed as a versatile tool in biological and biomedical research, rendering a wealth of information toward decoding the molecular machinery of life. There is enormous interest in employing proteomic approaches for the study of synapses, and substantial progress has been made. Here, we review the findings of proteomic studies of chemical synapses in the brain, with special attention paid to the key players in synaptic signaling, i.e., the synaptic protein complexes and their post-translational modifications. Looking toward the future, we discuss the technological advances in proteomics such as data-independent acquisition mass spectrometry (DIA-MS), cross-linking in combination with mass spectrometry (CXMS), and proximity proteomics, along with their potential to untangle the mystery of how the brain functions at the molecular level. Last but not least, we introduce the newly developed synaptomic methods. These methods and their successful applications marked the beginnings of the synaptomics era.
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Affiliation(s)
- Yalan Xu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Xiuyue Song
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Dong Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Jing Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China.
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47
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Basu A, Ash PEA, Wolozin B, Emili A. Protein Interaction Network Biology in Neuroscience. Proteomics 2021; 21:e1900311. [PMID: 33314619 PMCID: PMC7900949 DOI: 10.1002/pmic.201900311] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/27/2020] [Indexed: 01/04/2023]
Abstract
Mapping the intricate networks of cellular proteins in the human brain has the potential to address unsolved questions in molecular neuroscience, including the molecular basis of cognition, synaptic plasticity, long-term potentiation, learning, and memory. Perturbations to the protein-protein interaction networks (PPIN) present in neurons, glia, and other cell-types have been linked to multifactorial neurological disorders. Yet while knowledge of brain PPINs is steadily improving, the complexity and dynamic nature of the heterogeneous central nervous system in normal and disease contexts poses a formidable experimental challenge. In this review, the recent applications of functional proteomics and systems biology approaches to study PPINs central to normal neuronal function, during neurodevelopment, and in neurodegenerative disorders are summarized. How systematic PPIN analysis offers a unique mechanistic framework to explore intra- and inter-cellular functional modules governing neuronal activity and brain function is also discussed. Finally, future technological advancements needed to address outstanding questions facing neuroscience are outlined.
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Affiliation(s)
- Avik Basu
- Center for Network Systems BiologyBoston UniversityBostonMA02118USA
- Department of BiochemistryBoston University School of MedicineBostonMA02118USA
| | - Peter EA Ash
- Department of Pharmacology and Experimental TherapeuticsBoston University School of MedicineBostonMA02118USA
| | - Benjamin Wolozin
- Department of Pharmacology and Experimental TherapeuticsBoston University School of MedicineBostonMA02118USA
| | - Andrew Emili
- Center for Network Systems BiologyBoston UniversityBostonMA02118USA
- Department of BiochemistryBoston University School of MedicineBostonMA02118USA
- Department of BiologyBoston UniversityBostonMA02215USA
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48
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Xu Y, Fan X, Hu Y. In vivo interactome profiling by enzyme-catalyzed proximity labeling. Cell Biosci 2021; 11:27. [PMID: 33514425 PMCID: PMC7847152 DOI: 10.1186/s13578-021-00542-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/15/2021] [Indexed: 12/03/2022] Open
Abstract
Enzyme-catalyzed proximity labeling (PL) combined with mass spectrometry (MS) has emerged as a revolutionary approach to reveal the protein-protein interaction networks, dissect complex biological processes, and characterize the subcellular proteome in a more physiological setting than before. The enzymatic tags are being upgraded to improve temporal and spatial resolution and obtain faster catalytic dynamics and higher catalytic efficiency. In vivo application of PL integrated with other state of the art techniques has recently been adapted in live animals and plants, allowing questions to be addressed that were previously inaccessible. It is timely to summarize the current state of PL-dependent interactome studies and their potential applications. We will focus on in vivo uses of newer versions of PL and highlight critical considerations for successful in vivo PL experiments that will provide novel insights into the protein interactome in the context of human diseases.
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Affiliation(s)
- Yangfan Xu
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA.,Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, People's Republic of China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China.
| | - Yang Hu
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA.
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Sculpting Dendritic Spines during Initiation and Maintenance of Neuropathic Pain. J Neurosci 2021; 40:7578-7589. [PMID: 32998955 DOI: 10.1523/jneurosci.1664-20.2020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 08/21/2020] [Indexed: 12/21/2022] Open
Abstract
Accumulating evidence has established a firm role for synaptic plasticity in the pathogenesis of neuropathic pain. Recent advances have highlighted the importance of dendritic spine remodeling in driving synaptic plasticity within the CNS. Identifying the molecular players underlying neuropathic pain induced structural and functional maladaptation is therefore critical to understanding its pathophysiology. This process of dynamic reorganization happens in unique phases that have diverse pathologic underpinnings in the initiation and maintenance of neuropathic pain. Recent evidence suggests that pharmacological targeting of specific proteins during distinct phases of neuropathic pain development produces enhanced antinociception. These findings outline a potential new paradigm for targeted treatment and the development of novel therapies for neuropathic pain. We present a concise review of the role of dendritic spines in neuropathic pain and outline the potential for modulation of spine dynamics by targeting two proteins, srGAP3 and Rac1, critically involved in the regulation of the actin cytoskeleton.
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50
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Minehart JA, Speer CM. A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. Front Synaptic Neurosci 2021; 12:615059. [PMID: 33469427 PMCID: PMC7813761 DOI: 10.3389/fnsyn.2020.615059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
A key challenge in developmental neuroscience is identifying the local regulatory mechanisms that control neurite and synaptic refinement over large brain volumes. Innovative molecular techniques and high-resolution imaging tools are beginning to reshape our view of how local protein translation in subcellular compartments drives axonal, dendritic, and synaptic development and plasticity. Here we review recent progress in three areas of neurite and synaptic study in situ-compartment-specific transcriptomics/translatomics, targeted proteomics, and super-resolution imaging analysis of synaptic organization and development. We discuss synergies between sequencing and imaging techniques for the discovery and validation of local molecular signaling mechanisms regulating synaptic development, plasticity, and maintenance in circuits.
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Affiliation(s)
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, United States
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