1
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Evans HT, Ko T, Oliveira MM, Yu A, Kalavai SV, Golhan EN, Polavarapu A, Balamoti E, Wu V, Klann E, Trauner D. Light-Activatable, Cell-Type Specific Labeling of the Nascent Proteome. ACS Chem Neurosci 2024; 15:3473-3481. [PMID: 39307974 PMCID: PMC11450754 DOI: 10.1021/acschemneuro.4c00274] [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: 05/02/2024] [Revised: 08/27/2024] [Accepted: 09/06/2024] [Indexed: 10/03/2024] Open
Abstract
Elucidating the mechanisms by which protein synthesis contributes to complex biological processes has remained a challenging endeavor. This is particularly true in the field of neuroscience, where multiple, tightly regulated periods of new protein synthesis in different cell-types are thought to facilitate intricate neurological functions, such as memory formation. Current methods for labeling the de novo proteome have lacked the spatial and temporal resolution to accurately discriminate these overlapping and often competing windows of mRNA translation. To address this technological limitation, here we describe a novel, light-inducible specific method for labeling newly synthesized proteins within a targeted cell-type.By developing Opto-ANL, a photocaged version of the nonendogenous amino acid azidonorleucine (ANL), we can selectively label newly synthesized proteins in specific cell-types through the targeted expression of a mutant methionyl-tRNA synthetase (L274G-MetRS). We demonstrate that Opto-ANL can be rapidly uncaged by UV light treatment in both cell culture and mouse brain slices, with Opto-ANL labeled proteins being able to be visualized via fluorescent noncanonical amino acid tagging. We also reveal that pretreatment with Opto-ANL not only allows for the period of de novo proteomic labeling to be tightly controlled, but also improves labeling efficiency compared to regular ANL. To demonstrate the potential applications of this novel technique, we use Opto-ANL to detect insulin-induced increases in protein synthesis and to label the excitatory neuronal de novo proteome in mouse brain slices. We believe that this application of photopharmacology will allow researchers to generate novel insights into how the translational landscape is altered across cell-types during complex neurological phenomena such as memory formation.
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Affiliation(s)
- H. T. Evans
- Center
for Neural Science, New York University, New York, New York 10003, United States
| | - T. Ko
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - M. M. Oliveira
- Center
for Neural Science, New York University, New York, New York 10003, United States
| | - A. Yu
- Center
for Neural Science, New York University, New York, New York 10003, United States
| | - S. V. Kalavai
- Center
for Neural Science, New York University, New York, New York 10003, United States
| | - E. N. Golhan
- Center
for Neural Science, New York University, New York, New York 10003, United States
| | - A. Polavarapu
- Center
for Neural Science, New York University, New York, New York 10003, United States
| | - E. Balamoti
- Center
for Neural Science, New York University, New York, New York 10003, United States
| | - V. Wu
- Center
for Neural Science, New York University, New York, New York 10003, United States
| | - E. Klann
- Center
for Neural Science, New York University, New York, New York 10003, United States
| | - D. Trauner
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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2
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Scott-Hewitt N, Mahoney M, Huang Y, Korte N, Yvanka de Soysa T, Wilton DK, Knorr E, Mastro K, Chang A, Zhang A, Melville D, Schenone M, Hartigan C, Stevens B. Microglial-derived C1q integrates into neuronal ribonucleoprotein complexes and impacts protein homeostasis in the aging brain. Cell 2024; 187:4193-4212.e24. [PMID: 38942014 DOI: 10.1016/j.cell.2024.05.058] [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: 05/31/2023] [Revised: 01/08/2024] [Accepted: 05/31/2024] [Indexed: 06/30/2024]
Abstract
Neuroimmune interactions mediate intercellular communication and underlie critical brain functions. Microglia, CNS-resident macrophages, modulate the brain through direct physical interactions and the secretion of molecules. One such secreted factor, the complement protein C1q, contributes to complement-mediated synapse elimination in both developmental and disease models, yet brain C1q protein levels increase significantly throughout aging. Here, we report that C1q interacts with neuronal ribonucleoprotein (RNP) complexes in an age-dependent manner. Purified C1q protein undergoes RNA-dependent liquid-liquid phase separation (LLPS) in vitro, and the interaction of C1q with neuronal RNP complexes in vivo is dependent on RNA and endocytosis. Mice lacking C1q have age-specific alterations in neuronal protein synthesis in vivo and impaired fear memory extinction. Together, our findings reveal a biophysical property of C1q that underlies RNA- and age-dependent neuronal interactions and demonstrate a role of C1q in critical intracellular neuronal processes.
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Affiliation(s)
- Nicole Scott-Hewitt
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Matthew Mahoney
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Youtong Huang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nils Korte
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - T Yvanka de Soysa
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel K Wilton
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Emily Knorr
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kevin Mastro
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Allison Chang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Allison Zhang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - David Melville
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Monica Schenone
- The Broad Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christina Hartigan
- The Broad Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Beth Stevens
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Investigator, Boston Children's Hospital, Boston, MA 02115, USA.
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3
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McAndrews KM, Mahadevan KK, Kalluri R. Mouse Models to Evaluate the Functional Role of the Tumor Microenvironment in Cancer Progression and Therapy Responses. Cold Spring Harb Perspect Med 2024; 14:a041411. [PMID: 38191175 PMCID: PMC11216184 DOI: 10.1101/cshperspect.a041411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The tumor microenvironment (TME) is a complex ecosystem of both cellular and noncellular components that functions to impact the evolution of cancer. Various aspects of the TME have been targeted for the control of cancer; however, TME composition is dynamic, with the overall abundance of immune cells, endothelial cells (ECs), fibroblasts, and extracellular matrix (ECM) as well as subsets of TME components changing at different stages of progression and in response to therapy. To effectively treat cancer, an understanding of the functional role of the TME is needed. Genetically engineered mouse models have enabled comprehensive insight into the complex interactions within the TME ecosystem that regulate disease progression. Here, we review recent advances in mouse models that have been employed to understand how the TME regulates cancer initiation, progression, metastasis, and response to therapy.
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Affiliation(s)
- Kathleen M McAndrews
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Krishnan K Mahadevan
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Raghu Kalluri
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
- Department of Bioengineering, Rice University, Houston, Texas 77251, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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4
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Sridharan D, Dougherty JA, Ahmed U, Sanghvi SK, Alvi SB, Park KH, Islam H, Knoblaugh SE, Singh H, Kirby ED, Khan M. Bioorthogonal non-canonical amino acid tagging to track transplanted human induced pluripotent stem cell-specific proteome. Stem Cell Res Ther 2024; 15:186. [PMID: 38926849 PMCID: PMC11210150 DOI: 10.1186/s13287-024-03792-3] [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: 01/19/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Human induced pluripotent stem cells (hiPSCs) and their differentiated cell types have a great potential for tissue repair and regeneration. While the primary focus of using hiPSCs has historically been to regenerate damaged tissue, emerging studies have shown a more potent effect of hiPSC-derived paracrine factors on tissue regeneration. However, the precise contents of the transplanted hiPSC-derived cell secretome are ambiguous. This is mainly due to the lack of tools to distinguish cell-specific secretome from host-derived proteins in a complex tissue microenvironment in vivo. METHODS In this study, we present the generation and characterization of a novel hiPSC line, L274G-hiPSC, expressing the murine mutant methionyl-tRNA synthetase, L274GMmMetRS, which can be used for tracking the cell specific proteome via biorthogonal non-canonical amino acid tagging (BONCAT). We assessed the trilineage differentiation potential of the L274G-hiPSCs in vitro and in vivo. Furthermore, we assessed the cell-specific proteome labelling in the L274G-hiPSC derived cardiomyocytes (L274G-hiPSC-CMs) in vitro following co-culture with wild type human umbilical vein derived endothelial cells and in vivo post transplantation in murine hearts. RESULTS We demonstrated that the L274G-hiPSCs exhibit typical hiPSC characteristics and that we can efficiently track the cell-specific proteome in their differentiated progenies belonging to the three germ lineages, including L274G-hiPSC-CMs. Finally, we demonstrated cell-specific BONCAT in transplanted L274G-hiPSC-CMs. CONCLUSION The novel L274G-hiPSC line can be used to study the cell-specific proteome of hiPSCs in vitro and in vivo, to delineate mechanisms underlying hiPSC-based cell therapies for a variety of regenerative medicine applications.
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Affiliation(s)
- Divya Sridharan
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Julie A Dougherty
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Uzair Ahmed
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Shridhar K Sanghvi
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA
- Department of Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, USA
| | - Syed Baseeruddin Alvi
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Ki Ho Park
- Department of Surgery, University of Virginia, Charlottesville, VA, USA
| | - Helena Islam
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Sue E Knoblaugh
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Harpreet Singh
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA
| | - Elizabeth D Kirby
- Department of Psychology, The Ohio State University, Columbus, OH, USA
- Chronic Brain Injury Program, The Ohio State University, Columbus, OH, USA
| | - Mahmood Khan
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
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5
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Liu S, Deshmukh V, Wang F, Liang J, Cusick J, Li X, Martin JF. Myocardial Infarction Suppresses Protein Synthesis and Causes Decoupling of Transcription and Translation. JACC Basic Transl Sci 2024; 9:792-807. [PMID: 39070274 PMCID: PMC11282883 DOI: 10.1016/j.jacbts.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 07/30/2024]
Abstract
Gene expression involves transcription, translation, and mRNA and protein degradation. Advanced RNA sequencing measures mRNA levels for cell state assessment, but mRNA level does not fully reflect protein level. Identifying heart cell proteomes and their stress response is crucial. Using a cardiomyocyte-specific mouse model, we tracked protein synthesis after myocardial infarction. Our results showed that myocardial infarction suppresses protein synthesis and unveils a decoupling of translation and transcription regulation in cardiomyocytes.
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Affiliation(s)
- Shijie Liu
- Cardiomyocyte Renewal Laboratory, Texas Heart Institute, Houston, Texas, USA
- (currently) Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Vaibhav Deshmukh
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
| | - Fangfei Wang
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jie Liang
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jenna Cusick
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Xiao Li
- Gene Editing Laboratory, Texas Heart Institute, Houston, Texas, USA
| | - James F. Martin
- Cardiomyocyte Renewal Laboratory, Texas Heart Institute, Houston, Texas, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
- Gene Editing Laboratory, Texas Heart Institute, Houston, Texas, USA
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas, USA
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6
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Kumar P, Goettemoeller AM, Espinosa-Garcia C, Tobin BR, Tfaily A, Nelson RS, Natu A, Dammer EB, Santiago JV, Malepati S, Cheng L, Xiao H, Duong DD, Seyfried NT, Wood LB, Rowan MJM, Rangaraju S. Native-state proteomics of Parvalbumin interneurons identifies unique molecular signatures and vulnerabilities to early Alzheimer's pathology. Nat Commun 2024; 15:2823. [PMID: 38561349 PMCID: PMC10985119 DOI: 10.1038/s41467-024-47028-7] [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: 08/09/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Dysfunction in fast-spiking parvalbumin interneurons (PV-INs) may represent an early pathophysiological perturbation in Alzheimer's Disease (AD). Defining early proteomic alterations in PV-INs can provide key biological and translationally-relevant insights. We used cell-type-specific in-vivo biotinylation of proteins (CIBOP) coupled with mass spectrometry to obtain native-state PV-IN proteomes. PV-IN proteomic signatures include high metabolic and translational activity, with over-representation of AD-risk and cognitive resilience-related proteins. In bulk proteomes, PV-IN proteins were associated with cognitive decline in humans, and with progressive neuropathology in humans and the 5xFAD mouse model of Aβ pathology. PV-IN CIBOP in early stages of Aβ pathology revealed signatures of increased mitochondria and metabolism, synaptic and cytoskeletal disruption and decreased mTOR signaling, not apparent in whole-brain proteomes. Furthermore, we demonstrated pre-synaptic defects in PV-to-excitatory neurotransmission, validating our proteomic findings. Overall, in this study we present native-state proteomes of PV-INs, revealing molecular insights into their unique roles in cognitive resiliency and AD pathogenesis.
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Affiliation(s)
- Prateek Kumar
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Annie M Goettemoeller
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Neuroscience Graduate Program, Laney Graduate School, Emory University, Atlanta, USA
| | - Claudia Espinosa-Garcia
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Brendan R Tobin
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Ali Tfaily
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Ruth S Nelson
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Aditya Natu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric B Dammer
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Juliet V Santiago
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Neuroscience Graduate Program, Laney Graduate School, Emory University, Atlanta, USA
| | - Sneha Malepati
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lihong Cheng
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
| | - Hailian Xiao
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
| | - Duc D Duong
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Levi B Wood
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
- School of Chemical and Biological Engineering, GeoInsrgia titute of Technology, Atlanta, GA, 30322, USA
| | - Matthew J M Rowan
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA.
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA.
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA.
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7
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Bareja A, Lee DE, Ho T, Waitt G, McKay LH, Hannou SA, Orenduff MC, McGreevy KM, Binder A, Ryan CP, Soderblom EJ, Belsky DW, Ferrucci L, Das JK, Banskota N, Kraus VB, Huebner JL, Kraus WE, Huffman KM, Baht GS, Horvath S, Parmer RJ, Miles LA, White JP. Liver-derived plasminogen mediates muscle stem cell expansion during caloric restriction through the plasminogen receptor Plg-R KT. Cell Rep 2024; 43:113881. [PMID: 38442019 PMCID: PMC11075744 DOI: 10.1016/j.celrep.2024.113881] [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: 10/04/2022] [Revised: 08/08/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
An intriguing effect of short-term caloric restriction (CR) is the expansion of certain stem cell populations, including muscle stem cells (satellite cells), which facilitate an accelerated regenerative program after injury. Here, we utilized the MetRSL274G (MetRS) transgenic mouse to identify liver-secreted plasminogen as a candidate for regulating satellite cell expansion during short-term CR. Knockdown of circulating plasminogen prevents satellite cell expansion during short-term CR. Furthermore, loss of the plasminogen receptor KT (Plg-RKT) is also sufficient to prevent CR-related satellite cell expansion, consistent with direct signaling of plasminogen through the plasminogen receptor Plg-RKT/ERK kinase to promote proliferation of satellite cells. Importantly, we are able to replicate many of these findings in human participants from the CALERIE trial. Our results demonstrate that CR enhances liver protein secretion of plasminogen, which signals directly to the muscle satellite cell through Plg-RKT to promote proliferation and subsequent muscle resilience during CR.
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Affiliation(s)
- Akshay Bareja
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - David E Lee
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - Tricia Ho
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC, USA
| | - Greg Waitt
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC, USA
| | - Lauren H McKay
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of Chapel Hill, Chapel Hill, NC, USA
| | - Sarah A Hannou
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - Melissa C Orenduff
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - Kristen M McGreevy
- Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Alexandra Binder
- Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA; Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Calen P Ryan
- Columbia University Mailman School of Public Health, New York, NY, USA
| | - Erik J Soderblom
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC, USA
| | - Daniel W Belsky
- Columbia University Mailman School of Public Health, New York, NY, USA
| | - Luigi Ferrucci
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jayanta Kumar Das
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nirad Banskota
- Longitudinal Studies Section, Translation Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Virginia B Kraus
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA
| | - Janet L Huebner
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - William E Kraus
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA
| | - Kim M Huffman
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA
| | - Gurpreet S Baht
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA; Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC 27701, USA
| | - Steve Horvath
- Computational Biology and Genomics Core, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA; Altos Labs, San Diego, CA, USA
| | - Robert J Parmer
- Department of Medicine, Veterans Administration San Diego Healthcare System, San Diego, CA, USA; Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lindsey A Miles
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - James P White
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA.
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8
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Jacobson KR, Saleh AM, Lipp SN, Tian C, Watson AR, Luetkemeyer CM, Ocken AR, Spencer SL, Kinzer-Ursem TL, Calve S. Extracellular matrix protein composition dynamically changes during murine forelimb development. iScience 2024; 27:108838. [PMID: 38303699 PMCID: PMC10831947 DOI: 10.1016/j.isci.2024.108838] [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: 06/28/2023] [Revised: 10/02/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024] Open
Abstract
The extracellular matrix (ECM) is an integral part of multicellular organisms, connecting different cell layers and tissue types. During morphogenesis and growth, tissues undergo substantial reorganization. While it is intuitive that the ECM remodels in concert, little is known regarding how matrix composition and organization change during development. Here, we quantified ECM protein dynamics in the murine forelimb during appendicular musculoskeletal morphogenesis (embryonic days 11.5-14.5) using tissue fractionation, bioorthogonal non-canonical amino acid tagging, and mass spectrometry. Our analyses indicated that ECM protein (matrisome) composition in the embryonic forelimb changed as a function of development and growth, was distinct from other developing organs (brain), and was altered in a model of disease (osteogenesis imperfecta murine). Additionally, the tissue distribution for select matrisome was assessed via immunohistochemistry in the wild-type embryonic and postnatal musculoskeletal system. This resource will guide future research investigating the role of the matrisome during complex tissue development.
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Affiliation(s)
- Kathryn R. Jacobson
- Purdue University Interdisciplinary Life Science Program, Purdue University, West Lafayette, IN 47907, USA
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Sarah N. Lipp
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- The Indiana University Medical Scientist/Engineer Training Program, Indiana University, Indianapolis, IN 46202, USA
| | - Chengzhe Tian
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Research Center for Molecular Medicine (CEMM) of the Austrian Academy of Sciences, Vienna, Austria
| | - Audrey R. Watson
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Callan M. Luetkemeyer
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Alexander R. Ocken
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Sabrina L. Spencer
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Tamara L. Kinzer-Ursem
- Purdue University Interdisciplinary Life Science Program, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Sarah Calve
- Purdue University Interdisciplinary Life Science Program, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO 80309, USA
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9
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Albert-Gasco H, Smith HL, Alvarez-Castelao B, Swinden D, Halliday M, Janaki-Raman S, Butcher AJ, Mallucci GR. Trazodone rescues dysregulated synaptic and mitochondrial nascent proteomes in prion neurodegeneration. Brain 2024; 147:649-664. [PMID: 37703312 PMCID: PMC10834243 DOI: 10.1093/brain/awad313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/15/2023] Open
Abstract
The unfolded protein response (UPR) is rapidly gaining momentum as a therapeutic target for protein misfolding neurodegenerative diseases, in which its overactivation results in sustained translational repression leading to synapse loss and neurodegeneration. In mouse models of these disorders, from Alzheimer's to prion disease, modulation of the pathway-including by the licensed drug, trazodone-restores global protein synthesis rates with profound neuroprotective effects. However, the precise nature of the translational impairment, in particular the specific proteins affected in disease, and their response to therapeutic UPR modulation are poorly understood. We used non-canonical amino acid tagging (NCAT) to measure de novo protein synthesis in the brains of prion-diseased mice with and without trazodone treatment, in both whole hippocampus and cell-specifically. During disease the predominant nascent proteome changes occur in synaptic, cytoskeletal and mitochondrial proteins in both hippocampal neurons and astrocytes. Remarkably, trazodone treatment for just 2 weeks largely restored the whole disease nascent proteome in the hippocampus to that of healthy, uninfected mice, predominantly with recovery of proteins involved in synaptic and mitochondrial function. In parallel, trazodone treatment restored the disease-associated decline in synapses and mitochondria and their function to wild-type levels. In conclusion, this study increases our understanding of how translational repression contributes to neurodegeneration through synaptic and mitochondrial toxicity via depletion of key proteins essential for their function. Further, it provides new insights into the neuroprotective mechanisms of trazodone through reversal of this toxicity, relevant for the treatment of neurodegenerative diseases via translational modulation.
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Affiliation(s)
- Hector Albert-Gasco
- UK Dementia Research Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, UK
- Cambridge Institute of Science, Altos Labs, Great Abington CB21 6GP, UK
| | - Heather L Smith
- UK Dementia Research Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, UK
- Cambridge Institute of Science, Altos Labs, Great Abington CB21 6GP, UK
| | - Beatriz Alvarez-Castelao
- Department of Biochemistry and Molecular Biology, Veterinary School, Complutense University of Madrid, 28040 Madrid, Spain
- The San Carlos Hospital Health Research Institute, IdISSC, 28040 Madrid, Spain
| | - Dean Swinden
- UK Dementia Research Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, UK
- Cambridge Institute of Science, Altos Labs, Great Abington CB21 6GP, UK
| | - Mark Halliday
- Cambridge Institute of Science, Altos Labs, Great Abington CB21 6GP, UK
| | | | - Adrian J Butcher
- UK Dementia Research Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, UK
- Cambridge Institute of Science, Altos Labs, Great Abington CB21 6GP, UK
| | - Giovanna R Mallucci
- UK Dementia Research Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, UK
- Cambridge Institute of Science, Altos Labs, Great Abington CB21 6GP, UK
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10
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Zhang D, Gao Y, Zhu L, Wang Y, Li P. Advances and opportunities in methods to study protein translation - A review. Int J Biol Macromol 2024; 259:129150. [PMID: 38171441 DOI: 10.1016/j.ijbiomac.2023.129150] [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: 08/02/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024]
Abstract
It is generally believed that the regulation of gene expression involves protein translation occurring before RNA transcription. Therefore, it is crucial to investigate protein translation and its regulation. Recent advancements in biological sciences, particularly in the field of omics, have revolutionized protein translation research. These studies not only help characterize changes in protein translation during specific biological or pathological processes but also have significant implications in disease prevention and treatment. In this review, we summarize the latest methods in ribosome-based translation omics. We specifically focus on the application of fluorescence imaging technology and omics technology in studying overall protein translation. Additionally, we analyze the advantages, disadvantages, and application of these experimental methods, aiming to provide valuable insights and references to researchers studying translation.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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11
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Kiessling P, Kuppe C. Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases. Genome Med 2024; 16:14. [PMID: 38238823 PMCID: PMC10795303 DOI: 10.1186/s13073-024-01282-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same tissue section. This review focuses on the recent advancements in spatial multi-omics technologies, including novel data modalities and computational approaches. We discuss the advancements in low-resolution and high-resolution spatial multi-omics methods which can resolve up to 10,000 of individual molecules at subcellular level. By applying and integrating these techniques, researchers have recently gained valuable insights into the molecular circuits and mechanisms which govern cell biology along the cardiovascular disease spectrum. We provide an overview of current data analysis approaches, with a focus on data integration of multi-omic datasets, highlighting strengths and weaknesses of various computational pipelines. These tools play a crucial role in analyzing and interpreting spatial multi-omics datasets, facilitating the discovery of new findings, and enhancing translational cardiovascular research. Despite nontrivial challenges, such as the need for standardization of experimental setups, data analysis, and improved computational tools, the application of spatial multi-omics holds tremendous potential in revolutionizing our understanding of human disease processes and the identification of novel biomarkers and therapeutic targets. Exciting opportunities lie ahead for the spatial multi-omics field and will likely contribute to the advancement of personalized medicine for cardiovascular diseases.
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Affiliation(s)
- Paul Kiessling
- Department of Nephrology, Rheumatology, and Clinical Immunology, University Hospital RWTH Aachen, Aachen, Germany
| | - Christoph Kuppe
- Department of Nephrology, Rheumatology, and Clinical Immunology, University Hospital RWTH Aachen, Aachen, Germany.
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12
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Gazestani V, Kamath T, Nadaf NM, Dougalis A, Burris SJ, Rooney B, Junkkari A, Vanderburg C, Pelkonen A, Gomez-Budia M, Välimäki NN, Rauramaa T, Therrien M, Koivisto AM, Tegtmeyer M, Herukka SK, Abdulraouf A, Marsh SE, Hiltunen M, Nehme R, Malm T, Stevens B, Leinonen V, Macosko EZ. Early Alzheimer's disease pathology in human cortex involves transient cell states. Cell 2023; 186:4438-4453.e23. [PMID: 37774681 PMCID: PMC11107481 DOI: 10.1016/j.cell.2023.08.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/31/2023] [Accepted: 08/03/2023] [Indexed: 10/01/2023]
Abstract
Cellular perturbations underlying Alzheimer's disease (AD) are primarily studied in human postmortem samples and model organisms. Here, we generated a single-nucleus atlas from a rare cohort of cortical biopsies from living individuals with varying degrees of AD pathology. We next performed a systematic cross-disease and cross-species integrative analysis to identify a set of cell states that are specific to early AD pathology. These changes-which we refer to as the early cortical amyloid response-were prominent in neurons, wherein we identified a transitional hyperactive state preceding the loss of excitatory neurons, which we confirmed by acute slice physiology on independent biopsy specimens. Microglia overexpressing neuroinflammatory-related processes also expanded as AD pathology increased. Finally, both oligodendrocytes and pyramidal neurons upregulated genes associated with β-amyloid production and processing during this early hyperactive phase. Our integrative analysis provides an organizing framework for targeting circuit dysfunction, neuroinflammation, and amyloid production early in AD pathogenesis.
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Affiliation(s)
- Vahid Gazestani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tushar Kamath
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Graduate Program in Biophysics and Harvard/MIT MD-PhD Program, Harvard University, Cambridge, MA 02139, USA
| | - Naeem M Nadaf
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Antonios Dougalis
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - S J Burris
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brendan Rooney
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Antti Junkkari
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; Department of Neurosurgery, Kuopio University Hospital, Kuopio, Finland
| | | | - Anssi Pelkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mireia Gomez-Budia
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nelli-Noora Välimäki
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tuomas Rauramaa
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; Department of Pathology, Kuopio University Hospital, Kuopio, Finland
| | | | - Anne M Koivisto
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; Department of Neurology, Kuopio University Hospital, Kuopio, Finland; Department of Neurosciences, University of Helsinki, Helsinki, Finland; Department of Geriatrics, Helsinki University Hospital, Helsinki, Finland
| | | | - Sanna-Kaisa Herukka
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | | | - Samuel E Marsh
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Ralda Nehme
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Beth Stevens
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Boston, MA 02115, USA
| | - Ville Leinonen
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; Department of Neurosurgery, Kuopio University Hospital, Kuopio, Finland
| | - Evan Z Macosko
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Massachusetts General Hospital, Department of Psychiatry, Boston, MA 02114, USA.
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13
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Carlisle AK, Götz J, Bodea LG. Three methods for examining the de novo proteome of microglia using BONCAT bioorthogonal labeling and FUNCAT click chemistry. STAR Protoc 2023; 4:102418. [PMID: 37432857 PMCID: PMC10511912 DOI: 10.1016/j.xpro.2023.102418] [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: 03/01/2023] [Revised: 05/04/2023] [Accepted: 06/08/2023] [Indexed: 07/13/2023] Open
Abstract
Bioorthogonal labeling and click chemistry techniques allow the detailed examination of cellular physiology through tagging and visualizing newly synthesized proteins. Here, we describe three methods applying bioorthogonal non-canonical amino acid tagging and fluorescent non-canonical amino acid tagging to quantify protein synthesis in microglia. We describe steps for cell seeding and labeling. We then detail microscopy, flow cytometry, and Western blotting techniques. These methods can be easily adapted for other cell types to explore cellular physiology in health and disease. For complete details on the use and execution of this protocol, please refer to Evans et al. (2021).1.
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Affiliation(s)
- Alison Keolani Carlisle
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Jürgen Götz
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Liviu-Gabriel Bodea
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia.
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14
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Cabrera-Cabrera F, Tull H, Capuana R, Kasvandik S, Timmusk T, Koppel I. Cell type-specific labeling of newly synthesized proteins by puromycin inactivation. J Biol Chem 2023; 299:105129. [PMID: 37543363 PMCID: PMC10497999 DOI: 10.1016/j.jbc.2023.105129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023] Open
Abstract
Puromycin and its derivative O-propargyl puromycin (OPP) have recently found widespread use in detecting nascent proteins. Use of these metabolic labels in complex mixtures of cells leads to indiscriminate tagging of nascent proteomes independent of cell type. Here, we show how a widely used mammalian selection marker, puromycin N-acetyltransferase, can be repurposed for cell-specific metabolic labeling. This approach, which we named puromycin inactivation for cell-selective proteome labeling (PICSL), is based on efficient inactivation of puromycin or OPP in cells expressing puromycin N-acetyltransferase and detection of translation in other cell types. Using cocultures of neurons and glial cells from the rat brain cortex, we show the application of PICSL for puromycin immunostaining, Western blot, and mass spectrometric identification of nascent proteins. By combining PICSL and OPP-mediated proteomics, cell type-enriched proteins can be identified based on reduced OPP labeling in the cell type of interest.
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Affiliation(s)
| | - Helena Tull
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Roberta Capuana
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Sergo Kasvandik
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Tõnis Timmusk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia; Protobios Llc, Tallinn, Estonia
| | - Indrek Koppel
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.
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15
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Pérez-Garza J, Orea J, Ostroff L. Click Chemistry for Visualization of Newly Synthesized RNA and Antibody Labeling on Ultrathin Tissue Sections. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1075-1076. [PMID: 37613354 PMCID: PMC10637261 DOI: 10.1093/micmic/ozad067.552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Janeth Pérez-Garza
- Department of Physiology and Neurobiology. University of Connecticut, Storrs, CT
| | - Jairo Orea
- Department of Physiology and Neurobiology. University of Connecticut, Storrs, CT
| | - Linnaea Ostroff
- Department of Physiology and Neurobiology. University of Connecticut, Storrs, CT
- Connecticut Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, CT
- Institute of Materials Science, University of Connecticut, Storrs, CT
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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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de Mello NP, Fecher C, Pastor AM, Perocchi F, Misgeld T. Ex vivo immunocapture and functional characterization of cell-type-specific mitochondria using MitoTag mice. Nat Protoc 2023:10.1038/s41596-023-00831-w. [PMID: 37328604 DOI: 10.1038/s41596-023-00831-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Mitochondria are key bioenergetic organelles involved in many biosynthetic and signaling pathways. However, their differential contribution to specific functions of cells within complex tissues is difficult to dissect with current methods. The present protocol addresses this need by enabling the ex vivo immunocapture of cell-type-specific mitochondria directly from their tissue context through a MitoTag reporter mouse. While other available methods were developed for bulk mitochondria isolation or more abundant cell-type-specific mitochondria, this protocol was optimized for the selective isolation of functional mitochondria from medium-to-low-abundant cell types in a heterogeneous tissue, such as the central nervous system. The protocol has three major parts: First, mitochondria of a cell type of interest are tagged via an outer mitochondrial membrane eGFP by crossing MitoTag mice to a cell-type-specific Cre-driver line or by delivery of viral vectors for Cre expression. Second, homogenates are prepared from relevant tissues by nitrogen cavitation, from which tagged organelles are immunocaptured using magnetic microbeads. Third, immunocaptured mitochondria are used for downstream assays, e.g., to probe respiratory capacity or calcium handling, revealing cell-type-specific mitochondrial diversity in molecular composition and function. The MitoTag approach enables the identification of marker proteins to label cell-type-specific organelle populations in situ, elucidates cell-type-enriched mitochondrial metabolic and signaling pathways, and reveals functional mitochondrial diversity between adjacent cell types in complex tissues, such as the brain. Apart from establishing the mouse colony (6-8 weeks without import), the immunocapture protocol takes 2 h and functional assays require 1-2 h.
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Affiliation(s)
- Natalia Prudente de Mello
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians Universität München, Munich, Germany
| | - Caroline Fecher
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians Universität München, Munich, Germany
- Department of Cell Biology & Physiology, School of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Adrian Marti Pastor
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
| | - Fabiana Perocchi
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany.
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich, Germany.
- Munich Cluster for Systems Neurology, Munich, Germany.
| | - Thomas Misgeld
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany.
- Munich Cluster for Systems Neurology, Munich, Germany.
- German Center for Neurodegenerative Diseases, Munich, Germany.
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18
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Kumar P, Goettemoeller AM, Espinosa-Garcia C, Tobin BR, Tfaily A, Nelson RS, Natu A, Dammer EB, Santiago JV, Malepati S, Cheng L, Xiao H, Duong D, Seyfried NT, Wood LB, Rowan MJ, Rangaraju S. Native-state proteomics of Parvalbumin interneurons identifies novel molecular signatures and metabolic vulnerabilities to early Alzheimer's disease pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541038. [PMID: 37292756 PMCID: PMC10245729 DOI: 10.1101/2023.05.17.541038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
One of the earliest pathophysiological perturbations in Alzheimer's Disease (AD) may arise from dysfunction of fast-spiking parvalbumin (PV) interneurons (PV-INs). Defining early protein-level (proteomic) alterations in PV-INs can provide key biological and translationally relevant insights. Here, we use cell-type-specific in vivo biotinylation of proteins (CIBOP) coupled with mass spectrometry to obtain native-state proteomes of PV interneurons. PV-INs exhibited proteomic signatures of high metabolic, mitochondrial, and translational activity, with over-representation of causally linked AD genetic risk factors. Analyses of bulk brain proteomes indicated strong correlations between PV-IN proteins with cognitive decline in humans, and with progressive neuropathology in humans and mouse models of Aβ pathology. Furthermore, PV-IN-specific proteomes revealed unique signatures of increased mitochondrial and metabolic proteins, but decreased synaptic and mTOR signaling proteins in response to early Aβ pathology. PV-specific changes were not apparent in whole-brain proteomes. These findings showcase the first native state PV-IN proteomes in mammalian brain, revealing a molecular basis for their unique vulnerabilities in AD.
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19
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Swietlik JJ, Bärthel S, Falcomatà C, Fink D, Sinha A, Cheng J, Ebner S, Landgraf P, Dieterich DC, Daub H, Saur D, Meissner F. Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation. Nat Commun 2023; 14:2642. [PMID: 37156840 PMCID: PMC10167354 DOI: 10.1038/s41467-023-38171-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Cell-selective proteomics is a powerful emerging concept to study heterocellular processes in tissues. However, its high potential to identify non-cell-autonomous disease mechanisms and biomarkers has been hindered by low proteome coverage. Here, we address this limitation and devise a comprehensive azidonorleucine labeling, click chemistry enrichment, and mass spectrometry-based proteomics and secretomics strategy to dissect aberrant signals in pancreatic ductal adenocarcinoma (PDAC). Our in-depth co-culture and in vivo analyses cover more than 10,000 cancer cell-derived proteins and reveal systematic differences between molecular PDAC subtypes. Secreted proteins, such as chemokines and EMT-promoting matrisome proteins, associated with distinct macrophage polarization and tumor stromal composition, differentiate classical and mesenchymal PDAC. Intriguingly, more than 1,600 cancer cell-derived proteins including cytokines and pre-metastatic niche formation-associated factors in mouse serum reflect tumor activity in circulation. Our findings highlight how cell-selective proteomics can accelerate the discovery of diagnostic markers and therapeutic targets in cancer.
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Affiliation(s)
- Jonathan J Swietlik
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefanie Bärthel
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Chiara Falcomatà
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Diana Fink
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Ankit Sinha
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jingyuan Cheng
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefan Ebner
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Peter Landgraf
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Daniela C Dieterich
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Henrik Daub
- NEOsphere Biotechnologies GmbH, Martinsried, Germany
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.
| | - Felix Meissner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany.
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20
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Piol D, Robberechts T, Da Cruz S. Lost in local translation: TDP-43 and FUS in axonal/neuromuscular junction maintenance and dysregulation in amyotrophic lateral sclerosis. Neuron 2023; 111:1355-1380. [PMID: 36963381 DOI: 10.1016/j.neuron.2023.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/21/2022] [Accepted: 02/16/2023] [Indexed: 03/26/2023]
Abstract
Key early features of amyotrophic lateral sclerosis (ALS) are denervation of neuromuscular junctions and axonal degeneration. Motor neuron homeostasis relies on local translation through controlled regulation of axonal mRNA localization, transport, and stability. Yet the composition of the local transcriptome, translatome (mRNAs locally translated), and proteome during health and disease remains largely unexplored. This review covers recent discoveries on axonal translation as a critical mechanism for neuronal maintenance/survival. We focus on two RNA binding proteins, transactive response DNA binding protein-43 (TDP-43) and fused in sarcoma (FUS), whose mutations cause ALS and frontotemporal dementia (FTD). Emerging evidence points to their essential role in the maintenance of axons and synapses, including mRNA localization, transport, and local translation, and whose dysfunction may contribute to ALS. Finally, we describe recent advances in omics-based approaches mapping compartment-specific local RNA and protein compositions, which will be invaluable to elucidate fundamental local processes and identify key targets for therapy development.
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Affiliation(s)
- Diana Piol
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Tessa Robberechts
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Sandrine Da Cruz
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium.
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21
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Schiapparelli LM, Xie Y, Sharma P, McClatchy DB, Ma Y, Yates JR, Maximov A, Cline HT. Activity-Induced Cortical Glutamatergic Neuron Nascent Proteins. J Neurosci 2022; 42:7900-7920. [PMID: 36261270 PMCID: PMC9617616 DOI: 10.1523/jneurosci.0707-22.2022] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Neuronal activity initiates signaling cascades that culminate in diverse outcomes including structural and functional neuronal plasticity, and metabolic changes. While studies have revealed activity-dependent neuronal cell type-specific transcriptional changes, unbiased quantitative analysis of cell-specific activity-induced dynamics in newly synthesized proteins (NSPs) synthesis in vivo has been complicated by cellular heterogeneity and a relatively low abundance of NSPs within the proteome in the brain. Here we combined targeted expression of mutant MetRS (methionine tRNA synthetase) in genetically defined cortical glutamatergic neurons with tight temporal control of treatment with the noncanonical amino acid, azidonorleucine, to biotinylate NSPs within a short period after pharmacologically induced seizure in male and female mice. By purifying peptides tagged with heavy or light biotin-alkynes and using direct tandem mass spectrometry detection of biotinylated peptides, we quantified activity-induced changes in cortical glutamatergic neuron NSPs. Seizure triggered significant changes in ∼300 NSPs, 33% of which were decreased by seizure. Proteins mediating excitatory and inhibitory synaptic plasticity, including SynGAP1, Pak3, GEPH1, Copine-6, and collybistin, and DNA and chromatin remodeling proteins, including Rad21, Smarca2, and Ddb1, are differentially synthesized in response to activity. Proteins likely to play homeostatic roles in response to activity, such as regulators of proteastasis, intracellular ion control, and cytoskeleton remodeling proteins, are activity induced. Conversely, seizure decreased newly synthetized NCAM, among others, suggesting that seizure induced degradation. Overall, we identified quantitative changes in the activity-induced nascent proteome from genetically defined cortical glutamatergic neurons as a strategy to discover downstream mediators of neuronal plasticity and generate hypotheses regarding their function.SIGNIFICANCE STATEMENT Activity-induced neuronal and synaptic plasticity are mediated by changes in the protein landscape, including changes in the activity-induced newly synthesized proteins; however, identifying neuronal cell type-specific nascent proteome dynamics in the intact brain has been technically challenging. We conducted an unbiased proteomic screen from which we identified significant activity-induced changes in ∼300 newly synthesized proteins in genetically defined cortical glutamatergic neurons within 20 h after pharmacologically induced seizure. Bioinformatic analysis of the dynamic nascent proteome indicates that the newly synthesized proteins play diverse roles in excitatory and inhibitory synaptic plasticity, chromatin remodeling, homeostatic mechanisms, and proteasomal and metabolic functions, extending our understanding of the diversity of plasticity mechanisms.
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Affiliation(s)
- Lucio M Schiapparelli
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research Institute, La Jolla, California 92037
| | - Yi Xie
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research Institute, La Jolla, California 92037
- Skaggs Graduate School, Scripps Research Institute, La Jolla, California 92037
| | - Pranav Sharma
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research Institute, La Jolla, California 92037
- Xosomix, San Diego, California 92121
| | - Daniel B McClatchy
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, California 92037
| | - Yuanhui Ma
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, California 92037
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, California 92037
| | - Anton Maximov
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research Institute, La Jolla, California 92037
| | - Hollis T Cline
- Neuroscience Department and Dorris Neuroscience Center, Scripps Research Institute, La Jolla, California 92037
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22
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Sharifi Tabar M, Parsania C, Chen H, Su XD, Bailey CG, Rasko JE. Illuminating the dark protein-protein interactome. CELL REPORTS METHODS 2022; 2:100275. [PMID: 36046620 PMCID: PMC9421580 DOI: 10.1016/j.crmeth.2022.100275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In living systems, a complex network of protein-protein interactions (PPIs) underlies most biochemical events. The human protein-protein interactome has been surveyed using yeast two-hybrid (Y2H)- and mass spectrometry (MS)-based approaches such as affinity purification coupled to MS (AP-MS). Despite decades of systematic investigations and collaborative multi-disciplinary efforts, there is no "gold standard" for documenting PPIs. A surprisingly large fraction of the human interactome remains uncharted, which we refer to as the "dark interactome." In this review, we highlight the complexity of the human interactome and discuss the current status of the human reference interactome maps. We discuss why a large proportion of the human interactome has remained refractory to traditional approaches. We propose an experimental model that can enable the identification of the dark interactome in a cell-type-specific manner. We also propose a framework to implement when embarking on studies designed to rigorously identify and characterize protein interactions.
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Affiliation(s)
- Mehdi Sharifi Tabar
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chirag Parsania
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Hong Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Charles G. Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - John E.J. Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW 2006, Australia
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
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23
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Han C, Qin G. Reporter Systems for Assessments of Extracellular Vesicle Transfer. Front Cardiovasc Med 2022; 9:922420. [PMID: 35722089 PMCID: PMC9198260 DOI: 10.3389/fcvm.2022.922420] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/06/2022] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) are lipid bilayer particles naturally released from most if not all cell types to mediate inter-cellular exchange of bioactive molecules. Mounting evidence suggest their important role in diverse pathophysiological processes in the development, growth, homeostasis, and disease. Thus, sensitive and reliable assessments of functional EV cargo transfer from donor to acceptor cells are extremely important. Here, we summarize the methods EV are labeled and their functional transfer in acceptor cells are evaluated by various reporter systems.
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Affiliation(s)
- Chaoshan Han
- Department of Biomedical Engineering, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Biomedical Engineering, School of Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gangjian Qin
- Department of Biomedical Engineering, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Biomedical Engineering, School of Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Gangjian Qin,
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24
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Rayaprolu S, Bitarafan S, Santiago JV, Betarbet R, Sunna S, Cheng L, Xiao H, Nelson RS, Kumar P, Bagchi P, Duong DM, Goettemoeller AM, Oláh VJ, Rowan M, Levey AI, Wood LB, Seyfried NT, Rangaraju S. Cell type-specific biotin labeling in vivo resolves regional neuronal and astrocyte proteomic differences in mouse brain. Nat Commun 2022; 13:2927. [PMID: 35614064 PMCID: PMC9132937 DOI: 10.1038/s41467-022-30623-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 05/06/2022] [Indexed: 01/19/2023] Open
Abstract
Proteomic profiling of brain cell types using isolation-based strategies pose limitations in resolving cellular phenotypes representative of their native state. We describe a mouse line for cell type-specific expression of biotin ligase TurboID, for in vivo biotinylation of proteins. Using adenoviral and transgenic approaches to label neurons, we show robust protein biotinylation in neuronal soma and axons throughout the brain, allowing quantitation of over 2000 neuron-derived proteins spanning synaptic proteins, transporters, ion channels and disease-relevant druggable targets. Next, we contrast Camk2a-neuron and Aldh1l1-astrocyte proteomes and identify brain region-specific proteomic differences within both cell types, some of which might potentially underlie the selective vulnerability to neurological diseases. Leveraging the cellular specificity of proteomic labeling, we apply an antibody-based approach to uncover differences in neuron and astrocyte-derived signaling phospho-proteins and cytokines. This approach will facilitate the characterization of cell-type specific proteomes in a diverse number of tissues under both physiological and pathological states.
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Affiliation(s)
- Sruti Rayaprolu
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Sara Bitarafan
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Juliet V Santiago
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Ranjita Betarbet
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Sydney Sunna
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Lihong Cheng
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Hailian Xiao
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Ruth S Nelson
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Prateek Kumar
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Pritha Bagchi
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, 30322, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Duc M Duong
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, 30322, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | | | - Viktor János Oláh
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - Matt Rowan
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - Allan I Levey
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Levi B Wood
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA.
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, 30322, USA.
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA.
| | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA.
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25
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Liu C, Wong N, Watanabe E, Hou W, Biral L, DeCastro J, Mehdipour M, Aran K, Conboy M, Conboy I. Mechanisms and minimization of false discovery of metabolic bio-orthogonal non-canonical amino acid proteomics. Rejuvenation Res 2022; 25:95-109. [PMID: 35323026 PMCID: PMC9063144 DOI: 10.1089/rej.2022.0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Metabolic proteomics has been widely used to characterize dynamic protein networks in many areas of biomedicine, including in the arena of tissue aging and rejuvenation. Bio-orthogonal non-canonical amino acid tagging (BONCAT) is based on mutant methionine-tRNA synthases (MetRS) that incorporates metabolic tags, e.g., azido-nor leucine, ANL, into newly synthesized proteins. BONCAT revolutionizes metabolic proteomics, because mutant MetRS transgene allows one to identify cell type specific proteomes in mixed biological environments. This is not possible with other methods, such as stable isotope labeling with amino acids in cell culture (SILAC), isobaric tags for relative and absolute quantitation (iTRAQ) and tandem mass tags (TMT). At the same time, an inherent weakness of BONCAT is that after click chemistry-based enrichment, all identified proteins are assumed to have been metabolically tagged, but there is no confirmation in Mass Spectrometry data that only tagged proteins are detected. As we show here, such assumption is incorrect and accurate negative controls uncover a surprisingly high degree of false positives in BONCAT proteomics. We show not only how to reveal the false discovery and thus improve the accuracy of the analyses and conclusions but also approaches for avoiding it through minimizing non-specific detection of biotin, biotin-independent direct detection of metabolic tags, and improvement of signal to noise ratio through machine learning algorithms.
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Affiliation(s)
- Chao Liu
- University of California Berkeley, 1438, Stanley Hall B104, Berkeley, Berkeley, California, United States, 94720;
| | - Nathan Wong
- University of California Berkeley, 1438, Berkeley, California, United States;
| | - Etsuko Watanabe
- University of California Berkeley, 1438, Berkeley, California, United States;
| | - William Hou
- University of California Berkeley, 1438, Berkeley, California, United States;
| | - Leonardo Biral
- University of California Berkeley, 1438, Berkeley, California, United States;
| | - Jonalyn DeCastro
- Keck Graduate Institute, 48927, Claremont, California, United States;
| | - Melod Mehdipour
- University of California Berkeley, 1438, Berkeley, California, United States;
| | - Kiana Aran
- Keck Graduate Institute, 48927, Claremont, California, United States;
| | - Michael Conboy
- University of California Berkeley, 1438, Berkeley, California, United States;
| | - Irina Conboy
- UC Berkeley, 1438, Bioengineering and QB3, 174, Stanley Hall, Berkeley, California, United States, 94720;
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26
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Desch K, Schuman EM, Langer JD. Quantifying phosphorylation dynamics in primary neuronal cultures using LC-MS/MS. STAR Protoc 2022; 3:101063. [PMID: 35005645 PMCID: PMC8715330 DOI: 10.1016/j.xpro.2021.101063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cellular processes require tight and coordinated control of protein abundance, localization, and activity. One of the core mechanisms to achieve specific regulation of proteins is protein phosphorylation. Here we present a workflow to monitor protein abundance and phosphorylation in primary cultured neurons using liquid chromatography-coupled mass spectrometry. Our protocol provides a detailed guide on all steps for detection and label-free-quantification of phosphorylated and unmodified proteins of primary cortical neurons, including primary cell culture, phosphoproteomic sample preparation and data-processing, and evaluation. For complete details on the use and execution of this protocol, please refer to Desch et al. (2021).
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Affiliation(s)
- Kristina Desch
- Max Planck Institute for Brain Research, Max von Laue Strasse 4, 60438 Frankfurt, Germany
| | - Erin M. Schuman
- Max Planck Institute for Brain Research, Max von Laue Strasse 4, 60438 Frankfurt, Germany
| | - Julian D. Langer
- Max Planck Institute for Brain Research, Max von Laue Strasse 4, 60438 Frankfurt, Germany
- Max Planck Institute of Biophysics, Max von Laue Strasse 3, 60438 Frankfurt, Germany
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27
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Metabolic labeling of secreted matrix to investigate cell-material interactions in tissue engineering and mechanobiology. Nat Protoc 2022; 17:618-648. [PMID: 35140408 PMCID: PMC8985381 DOI: 10.1038/s41596-021-00652-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/25/2021] [Indexed: 12/19/2022]
Abstract
Re-creating features of the native extracellular matrix (ECM) with engineered biomaterials has become a valuable tool to probe the influence of ECM properties on cellular functions (e.g., differentiation) and toward the engineering of tissues. However, characterization of newly secreted (nascent) matrix and turnover, which are important in the context of cells interacting with these biomaterials, has been limited by a lack of tools. We developed a protocol to visualize and quantify the spatiotemporal evolution of newly synthesized and deposited matrix by cells that are either cultured atop (2D) or embedded within (3D) biomaterial systems (e.g., hydrogels, fibrous matrices). This technique relies on the incorporation of a noncanonical amino acid (azidohomoalanine) into proteins as they are synthesized. Deposited nascent ECM components are then visualized with fluorescent cyclooctynes via copper-free cycloaddition for spatiotemporal analysis or modified with cleavable biotin probes for identification. Here we describe the preparation of hyaluronic acid hydrogels through ultraviolet or visible light induced cross-linking for 2D and 3D cell culture, as well as the fluorescent labeling of nascent ECM deposited by cells during culture. We also provide protocols for secondary immunofluorescence of specific ECM components and ImageJ-based ECM quantification methods. Hyaluronic acid polymer synthesis takes 2 weeks to complete, and hydrogel formation for 2D or 3D cell culture is performed in 2-3 h. Lastly, we detail the identification of nascent proteins, including enrichment, preparation and analysis with mass spectrometry, which can be completed in 10 d.
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28
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Panariello BHD, Klein MI, Dias LM, Bellini A, Costa VB, Barbugli PA, Pavarina AC. Lactobacillus casei reduces the extracellular matrix components of fluconazole-susceptible Candida albicans biofilms. BIOFOULING 2021; 37:1006-1021. [PMID: 34789040 DOI: 10.1080/08927014.2021.2001645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/27/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Fluconazole-sensitive (CaS) and -resistant (CaR) C. albicans were grown as single-species and dual-species biofilms with Lactobacillus casei (Lc) and Lactobacillus rhamnosus (Lr). Single-species Lc and Lr were also evaluated. Biofilm analysis included viable plate counts, the extracellular matrix components, biomass, and structural organization. Lc reduced the viability of CaS, water-soluble polysaccharides, and eDNA in CaS + Lc biofilm. Lc biofilm presented more eDNA than CaS. The total biomass of CaS + Lc biofilm was higher than the single-species biofilms. The viability of Lc and Lr was reduced by CaR dual-species biofilms. The total and insoluble biomass in CaS + Lr was higher than in single-species CaS biofilms. Lc hindered the growth of CaS, and their association hampered matrix components linked to the structural integrity of the biofilm. These findings allow understanding of how the implementation of probiotics influences the growth of C. albicans biofilms and thereby helps with the development of novel approaches to control these biofilms.
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Affiliation(s)
- Beatriz H D Panariello
- Department of Dental Materials and Prosthodontics, São Paulo State University (UNESP), School of Dentistry, Araraquara, Brazil
- Department of Cariology, Operative Dentistry & Dental Public Health, Indiana University School of Dentistry, Indianapolis, IN, USA
| | - Marlise Inez Klein
- Department of Dental Materials and Prosthodontics, São Paulo State University (UNESP), School of Dentistry, Araraquara, Brazil
| | - Luana Mendonça Dias
- Department of Dental Materials and Prosthodontics, São Paulo State University (UNESP), School of Dentistry, Araraquara, Brazil
| | - Amanda Bellini
- Department of Dental Materials and Prosthodontics, São Paulo State University (UNESP), School of Dentistry, Araraquara, Brazil
| | - Vitoria Bonan Costa
- Department of Dental Materials and Prosthodontics, São Paulo State University (UNESP), School of Dentistry, Araraquara, Brazil
- Department of Surgery and Diagnosis, São Paulo State University (Unesp), School of Dentistry, Araraquara, Brazil
| | - Paula Aboud Barbugli
- Department of Dental Materials and Prosthodontics, São Paulo State University (UNESP), School of Dentistry, Araraquara, Brazil
| | - Ana Claudia Pavarina
- Department of Dental Materials and Prosthodontics, São Paulo State University (UNESP), School of Dentistry, Araraquara, Brazil
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29
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Current tools to interrogate microglial biology. Neuron 2021; 109:2805-2819. [PMID: 34390649 DOI: 10.1016/j.neuron.2021.07.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/23/2021] [Accepted: 07/06/2021] [Indexed: 12/26/2022]
Abstract
Microglial cells perform a plethora of functions in the central nervous system (CNS), involving them in brain development, maintenance of homeostasis in adulthood, and CNS diseases. Significant technical advancements have prompted the development of novel systems adapted to analyze microglia with increasing specificity and intricacy. The advent of single-cell technologies combined with targeted mouse models has been decisive in deciphering microglia heterogeneity and dissecting microglial functions. However sophisticated these tools have become, clear limitations remain. Understanding their pitfalls and advantages ensures their correct application. Therefore, we provide a guide to the cutting-edge methods currently available to dissect microglial biology.
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30
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van Bergen W, Heck AJR, Baggelaar MP. Recent advancements in mass spectrometry-based tools to investigate newly synthesized proteins. Curr Opin Chem Biol 2021; 66:102074. [PMID: 34364788 PMCID: PMC9548413 DOI: 10.1016/j.cbpa.2021.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/28/2021] [Accepted: 07/03/2021] [Indexed: 02/08/2023]
Abstract
Tight regulation of protein translation drives the proteome to undergo changes under influence of extracellular or intracellular signals. Despite mass spectrometry–based proteomics being an excellent method to study differences in protein abundance in complex proteomes, analyzing minute or rapid changes in protein synthesis and abundance remains challenging. Therefore, several dedicated techniques to directly detect and quantify newly synthesized proteins have been developed, notably puromycin-based, bio-orthogonal noncanonical amino acid tagging–based, and stable isotope labeling by amino acids in cell culture–based methods, combined with mass spectrometry. These techniques have enabled the investigation of perturbations, stress, or stimuli on protein synthesis. Improvements of these methods are still necessary to overcome various remaining limitations. Recent improvements include enhanced enrichment approaches and combinations with various stable isotope labeling techniques, which allow for more accurate analysis and comparison between conditions on shorter timeframes and in more challenging systems. Here, we aim to review the current state in this field.
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Affiliation(s)
- Wouter van Bergen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Marc P Baggelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
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31
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Du Y, Li X, Yan W, Zeng Z, Han D, Ouyang H, Pan X, Luo B, Zhou B, Fu Q, Lu D, Huang Z, Li Z. Deciphering the in vivo Dynamic Proteomics of Mesenchymal Stem Cells in Critical Limb Ischemia. Front Cell Dev Biol 2021; 9:682476. [PMID: 34277623 PMCID: PMC8278824 DOI: 10.3389/fcell.2021.682476] [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: 03/18/2021] [Accepted: 04/13/2021] [Indexed: 12/30/2022] Open
Abstract
Objective Regenerative therapy using mesenchymal stem cells (MSC) is a promising therapeutic method for critical limb ischemia (CLI). To understand how the cells are involved in the regenerative process of limb ischemia locally, we proposed a metabolic protein labeling method to label cell proteomes in situ and then decipher the proteome dynamics of MSCs in ischemic hind limb. Methods and Results In this study, we overexpressed mutant methionyl-tRNA synthetase (MetRS), which could utilize azidonorleucine (ANL) instead of methionine (Met) during protein synthesis in MSCs. Fluorescent non-canonical amino-acid tagging (FUNCAT) was performed to detect the utilization of ANL in mutant MSCs. Mice with hindlimb ischemia (HLI) or Sham surgery were treated with MetRSmut MSCs or PBS, followed by i.p. administration of ANL at days 0, 2 6, and 13 after surgery. FUNCAT was also performed in hindlimb tissue sections to demonstrate the incorporation of ANL in transplanted cells in situ. At days 1, 3, 7, and 14 after the surgery, laser doppler imaging were performed to detect the blood reperfusion of ischemic limbs. Ischemic tissues were also collected at these four time points for histological analysis including HE staining and vessel staining, and processed for click reaction based protein enrichment followed by mass spectrometry and bioinformatics analysis. The MetRSmut MSCs showed strong green signal in cell culture and in HLI muscles as well, indicating efficient incorporation of ANL in nascent protein synthesis. By 14 days post-treatment, MSCs significantly increased blood reperfusion and vessel density, while reducing inflammation in HLI model compared to PBS. Proteins enriched by click reaction were distinctive in the HLI group vs. the Sham group. 34, 31, 49, and 26 proteins were significantly up-regulated whereas 28, 32, 62, and 27 proteins were significantly down-regulated in HLI vs. Sham at days 1, 3, 7, and 14, respectively. The differentially expressed proteins were more pronounced in the pathways of apoptosis and energy metabolism. Conclusion In conclusion, mutant MetRS allows efficient and specific identification of dynamic cell proteomics in situ, which reflect the functions and adaptive changes of MSCs that may be leveraged to understand and improve stem cell therapy in critical limb ischemia.
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Affiliation(s)
- Yipeng Du
- Department of Cardiology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Department of Cardiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaoting Li
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Wenying Yan
- Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Zhaohua Zeng
- Department of Cardiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dunzheng Han
- Department of Cardiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hong Ouyang
- Department of Cardiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiudi Pan
- Department of Cardiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bihui Luo
- Department of Cardiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bohua Zhou
- Department of Cardiology, Pinghu Hospital, Health Science Center, Shenzhen University, Shenzhen, China
| | - Qiang Fu
- Department of Cardiology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Dongfeng Lu
- Department of Cardiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zheng Huang
- Department of Cardiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhiliang Li
- Department of Cardiology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Department of Cardiology, Pinghu Hospital, Health Science Center, Shenzhen University, Shenzhen, China
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Delikoyun K, Yaman S, Yilmaz E, Sarigil O, Anil-Inevi M, Telli K, Yalcin-Ozuysal O, Ozcivici E, Tekin HC. HologLev: A Hybrid Magnetic Levitation Platform Integrated with Lensless Holographic Microscopy for Density-Based Cell Analysis. ACS Sens 2021; 6:2191-2201. [PMID: 34124887 DOI: 10.1021/acssensors.0c02587] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In clinical practice, a variety of diagnostic applications require the identification of target cells. Density has been used as a physical marker to distinguish cell populations since metabolic activities could alter the cell densities. Magnetic levitation offers great promise for separating cells at the single cell level within heterogeneous populations with respect to cell densities. Traditional magnetic levitation platforms need bulky and precise optical microscopes to visualize levitated cells. Moreover, the evaluation process of cell densities is cumbersome, which also requires trained personnel for operation. In this work, we introduce a device (HologLev) as a fusion of the magnetic levitation principle and lensless digital inline holographic microscopy (LDIHM). LDIHM provides ease of use by getting rid of bulky and expensive optics. By placing an imaging sensor just beneath the microcapillary channel without any lenses, recorded holograms are processed for determining cell densities through a fully automated digital image processing scheme. The device costs less than $100 and has a compact design that can fit into a pocket. We perform viability tests on the device by levitating three different cell lines (MDA-MB-231, U937, D1 ORL UVA) and comparing them against their dead correspondents. We also tested the differentiation of mouse osteoblastic (7F2) cells by monitoring characteristic variations in their density. Last, the response of MDA-MB-231 cancer cells to a chemotherapy drug was demonstrated in our platform. HologLev provides cost-effective, label-free, fully automated cell analysis in a compact design that could be highly desirable for laboratory and point-of-care testing applications.
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Affiliation(s)
- Kerem Delikoyun
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Sena Yaman
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Esra Yilmaz
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Oyku Sarigil
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Muge Anil-Inevi
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Kubra Telli
- Faculty of Science, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Ozden Yalcin-Ozuysal
- Faculty of Science, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Engin Ozcivici
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - H. Cumhur Tekin
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
- METU MEMS Center, Ankara 06520, Turkey
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Timonidis N, Tiesinga PHE. Progress towards a cellularly resolved mouse mesoconnectome is empowered by data fusion and new neuroanatomy techniques. Neurosci Biobehav Rev 2021; 128:569-591. [PMID: 34119523 DOI: 10.1016/j.neubiorev.2021.06.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/02/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
Over the past decade there has been a rapid improvement in techniques for obtaining large-scale cellular level data related to the mouse brain connectome. However, a detailed mapping of cell-type-specific projection patterns is lacking, which would, for instance, allow us to study the role of circuit motifs in cognitive processes. In this work, we review advanced neuroanatomical and data fusion techniques within the context of a proposed Multimodal Connectomic Integration Framework for augmenting the cellularly resolved mouse mesoconnectome. First, we emphasize the importance of registering data modalities to a common reference atlas. We then review a number of novel experimental techniques that can provide data for characterizing cell-types in the mouse brain. Furthermore, we examine a number of data integration strategies, which involve fine-grained cell-type classification, spatial inference of cell densities, latent variable models for the mesoconnectome and multi-modal factorisation. Finally, we discuss a number of use cases which depend on connectome augmentation techniques, such as model simulations of functional connectivity and generating mechanistic hypotheses for animal disease models.
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Affiliation(s)
- Nestor Timonidis
- Neuroinformatics department, Donders Centre for Neuroscience, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Paul H E Tiesinga
- Neuroinformatics department, Donders Centre for Neuroscience, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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34
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Local Protein Translation and RNA Processing of Synaptic Proteins in Autism Spectrum Disorder. Int J Mol Sci 2021; 22:ijms22062811. [PMID: 33802132 PMCID: PMC8001067 DOI: 10.3390/ijms22062811] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a heritable neurodevelopmental condition associated with impairments in social interaction, communication and repetitive behaviors. While the underlying disease mechanisms remain to be fully elucidated, dysfunction of neuronal plasticity and local translation control have emerged as key points of interest. Translation of mRNAs for critical synaptic proteins are negatively regulated by Fragile X mental retardation protein (FMRP), which is lost in the most common single-gene disorder associated with ASD. Numerous studies have shown that mRNA transport, RNA metabolism, and translation of synaptic proteins are important for neuronal health, synaptic plasticity, and learning and memory. Accordingly, dysfunction of these mechanisms may contribute to the abnormal brain function observed in individuals with autism spectrum disorder (ASD). In this review, we summarize recent studies about local translation and mRNA processing of synaptic proteins and discuss how perturbations of these processes may be related to the pathophysiology of ASD.
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35
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Yu D, Liu C, Zhang H, Ren J, Qu X. Glycoengineering artificial receptors for microglia to phagocytose Aβ aggregates. Chem Sci 2021; 12:4963-4969. [PMID: 34163743 PMCID: PMC8179537 DOI: 10.1039/d0sc07067j] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
Oligomeric and fibrillar amyloid-β (Aβ) are principally internalized via receptor-mediated endocytosis (RME) by microglia, the main scavenger of Aβ in the brain. Nevertheless, the inflammatory cascade will be evoked after vast Aβ aggregate binding to pattern recognition receptors on the cell membrane, which then significantly decreases the expression of these receptors and further deteriorate Aβ deposition. This vicious circle will weaken the ability of microglia for Aβ elimination. Herein, a combination of metabolic glycoengineering and self-triggered click chemistry is utilized to engineer microglial membranes with ThS as artificial Aβ receptors to promote microglia to phagocytose Aβ aggregates. Additionally, to circumvent the undesirable immune response during the process of the bioorthogonal chemistry reaction and Aβ-microglial interaction, Mn-porphyrin metal-organic frameworks (Mn-MOFs) with superoxide dismutase (SOD) and catalase (CAT) mimic activity are employed to carry N-azidoacetylmannosamine (AcManNAz) and eradicate over-expressed reactive oxygen species (ROSs). The artificial Aβ receptors independent of a signal pathway involved in immunomodulation as well as Mn-MOFs with antioxidant properties can synergistically promote the phagocytosis and clearance of Aβ with significantly enhanced activity and negligible adverse effects. The present study will not only provide valuable insight into the rational design of the microglial surface engineering strategy via bioorthogonal chemistry, but also hold great potential for other disease intervention associated with receptor starvation.
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Affiliation(s)
- Dongqin Yu
- Laboratory of Chemical Biology, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Chun Liu
- Laboratory of Chemical Biology, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Haochen Zhang
- Laboratory of Chemical Biology, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
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36
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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: 18] [Impact Index Per Article: 6.0] [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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37
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Evans HT, Blackmore D, Götz J, Bodea LG. De novo proteomic methods for examining the molecular mechanisms underpinning long-term memory. Brain Res Bull 2021; 169:94-103. [PMID: 33465403 DOI: 10.1016/j.brainresbull.2020.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/07/2020] [Accepted: 12/21/2020] [Indexed: 01/19/2023]
Abstract
Memory formation is a fundamental function of the nervous system that enables the experience-based adaptation of behaviour. The formation, recall and updating of long-term memory (LTM) requires new protein synthesis through its direct involvement in neuronal processes, such as long-term potentiation (LTP), long-term depression (LTD) and synaptic scaling. We discuss the advantages and limitations of several emerging techniques which enable the tagging of newly synthesised proteins, including stable isotope labelling with amino acids in cell culture (SILAC), puromycin labelling, and non-canonical amino acid (NCAA) labelling. We further present how these methods allow for the identification and visualisation of proteins which are newly synthesised during different stages of memory formation. These emerging techniques will continue to expand our understanding of how memories are formed, consolidated and retrieved.
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Affiliation(s)
- Harrison Tudor Evans
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia
| | - Daniel Blackmore
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia.
| | - Liviu-Gabriel Bodea
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia.
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38
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Perez JD, Dieck ST, Alvarez-Castelao B, Tushev G, Chan IC, Schuman EM. Subcellular sequencing of single neurons reveals the dendritic transcriptome of GABAergic interneurons. eLife 2021; 10:63092. [PMID: 33404500 PMCID: PMC7819707 DOI: 10.7554/elife.63092] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/05/2021] [Indexed: 12/23/2022] Open
Abstract
Although mRNAs are localized in the processes of excitatory neurons, it is still unclear whether interneurons also localize a large population of mRNAs. In addition, the variability in the localized mRNA population within and between cell types is unknown. Here we describe the unbiased transcriptomic characterization of the subcellular compartments of hundreds of single neurons. We separately profiled the dendritic and somatic transcriptomes of individual rat hippocampal neurons and investigated mRNA abundances in the soma and dendrites of single glutamatergic and GABAergic neurons. We found that, like their excitatory counterparts, interneurons contain a rich repertoire of ~4000 mRNAs. We observed more cell type-specific features among somatic transcriptomes than their associated dendritic transcriptomes. Finally, using celltype-specific metabolic labeling of isolated neurites, we demonstrated that the processes of glutamatergic and, notably, GABAergic neurons were capable of local translation, suggesting mRNA localization and local translation are general properties of neurons.
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Affiliation(s)
- Julio D Perez
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | | | - Beatriz Alvarez-Castelao
- Department of Biochemistry and Molecular Biology, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Georgi Tushev
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Ivy Cw Chan
- Department of Behavior and Brain Organization, Center of Advanced European Studies and Research, Bonn, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
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39
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Rayaprolu S, Higginbotham L, Bagchi P, Watson CM, Zhang T, Levey AI, Rangaraju S, Seyfried NT. Systems-based proteomics to resolve the biology of Alzheimer's disease beyond amyloid and tau. Neuropsychopharmacology 2021; 46:98-115. [PMID: 32898852 PMCID: PMC7689445 DOI: 10.1038/s41386-020-00840-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/05/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
The repeated failures of amyloid-targeting therapies have challenged our narrow understanding of Alzheimer's disease (AD) pathogenesis and inspired wide-ranging investigations into the underlying mechanisms of disease. Increasing evidence indicates that AD develops from an intricate web of biochemical and cellular processes that extend far beyond amyloid and tau accumulation. This growing recognition surrounding the diversity of AD pathophysiology underscores the need for holistic systems-based approaches to explore AD pathogenesis. Here we describe how network-based proteomics has emerged as a powerful tool and how its application to the AD brain has provided an informative framework for the complex protein pathophysiology underlying the disease. Furthermore, we outline how the AD brain network proteome can be leveraged to advance additional scientific and translational efforts, including the discovery of novel protein biomarkers of disease.
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Affiliation(s)
- Sruti Rayaprolu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lenora Higginbotham
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Pritha Bagchi
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Caroline M Watson
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Tian Zhang
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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40
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Ross AB, Langer JD, Jovanovic M. Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives. Mol Cell Proteomics 2020; 20:100016. [PMID: 33556866 PMCID: PMC7950106 DOI: 10.1074/mcp.r120.002190] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/17/2023] Open
Abstract
In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At a steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here, we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.
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Affiliation(s)
- Alison Barbara Ross
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Julian David Langer
- Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany; Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, New York, USA.
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41
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Pino LK, Rose J, O'Broin A, Shah S, Schilling B. Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications. Biochem Soc Trans 2020; 48:1953-1966. [PMID: 33079175 PMCID: PMC7609030 DOI: 10.1042/bst20191091] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022]
Abstract
Research into the basic biology of human health and disease, as well as translational human research and clinical applications, all benefit from the growing accessibility and versatility of mass spectrometry (MS)-based proteomics. Although once limited in throughput and sensitivity, proteomic studies have quickly grown in scope and scale over the last decade due to significant advances in instrumentation, computational approaches, and bio-sample preparation. Here, we review these latest developments in MS and highlight how these techniques are used to study the mechanisms, diagnosis, and treatment of human diseases. We first describe recent groundbreaking technological advancements for MS-based proteomics, including novel data acquisition techniques and protein quantification approaches. Next, we describe innovations that enable the unprecedented depth of coverage in protein signaling and spatiotemporal protein distributions, including studies of post-translational modifications, protein turnover, and single-cell proteomics. Finally, we explore new workflows to investigate protein complexes and structures, and we present new approaches for protein-protein interaction studies and intact protein or top-down MS. While these approaches are only recently incipient, we anticipate that their use in biomedical MS proteomics research will offer actionable discoveries for the improvement of human health.
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Affiliation(s)
- Lindsay K. Pino
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Jacob Rose
- Buck Institute for Research on Aging, Novato, CA, U.S.A
| | - Amy O'Broin
- Buck Institute for Research on Aging, Novato, CA, U.S.A
| | - Samah Shah
- Buck Institute for Research on Aging, Novato, CA, U.S.A
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42
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Chung CZ, Amikura K, Söll D. Using Genetic Code Expansion for Protein Biochemical Studies. Front Bioeng Biotechnol 2020; 8:598577. [PMID: 33195171 PMCID: PMC7604363 DOI: 10.3389/fbioe.2020.598577] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/29/2020] [Indexed: 01/31/2023] Open
Abstract
Protein identification has gone beyond simply using protein/peptide tags and labeling canonical amino acids. Genetic code expansion has allowed residue- or site-specific incorporation of non-canonical amino acids into proteins. By taking advantage of the unique properties of non-canonical amino acids, we can identify spatiotemporal-specific protein states within living cells. Insertion of more than one non-canonical amino acid allows for selective labeling that can aid in the identification of weak or transient protein-protein interactions. This review will discuss recent studies applying genetic code expansion for protein labeling and identifying protein-protein interactions and offer considerations for future work in expanding genetic code expansion methods.
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Affiliation(s)
- Christina Z. Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
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43
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Abstract
It is increasingly recognized that local protein synthesis (LPS) contributes to fundamental aspects of axon biology, in both developing and mature neurons. Mutations in RNA-binding proteins (RBPs), as central players in LPS, and other proteins affecting RNA localization and translation are associated with a range of neurological disorders, suggesting disruption of LPS may be of pathological significance. In this review, we substantiate this hypothesis by examining the link between LPS and key axonal processes, and the implicated pathophysiological consequences of dysregulated LPS. First, we describe how the length and autonomy of axons result in an exceptional reliance on LPS. We next discuss the roles of LPS in maintaining axonal structural and functional polarity and axonal trafficking. We then consider how LPS facilitates the establishment of neuronal connectivity through regulation of axonal branching and pruning, how it mediates axonal survival into adulthood and its involvement in neuronal stress responses.
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Affiliation(s)
- Julie Qiaojin Lin
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Christine E Holt
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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Radziwon K, Weeks AM. Protein engineering for selective proteomics. Curr Opin Chem Biol 2020; 60:10-19. [PMID: 32768891 DOI: 10.1016/j.cbpa.2020.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/02/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022]
Abstract
Post-translational modifications, complex formation, subcellular localization, and cell-type-specific expression create functionally distinct protein subpopulations that enable living systems to execute rapid and precise responses to changing conditions. Systems-level analysis of these subproteomes remains challenging, requiring preservation of spatial information or enrichment of species that are transient and present at low abundance. Engineered proteins have emerged as important tools for selective proteomics based on their capacity for highly specific molecular recognition and their genetic targetability. Here, we focus on new developments in protein engineering for selective proteomics of post-translational modifications, protein complexes, subcellular compartments, and cell types. We also address remaining challenges and future opportunities to integrate engineered protein tools across different subproteome scales to map the proteome with unprecedented depth and detail.
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Affiliation(s)
- Katarzyna Radziwon
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Amy M Weeks
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Kallabis S, Abraham L, Müller S, Dzialas V, Türk C, Wiederstein JL, Bock T, Nolte H, Nogara L, Blaauw B, Braun T, Krüger M. High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers. Skelet Muscle 2020; 10:7. [PMID: 32293536 PMCID: PMC7087369 DOI: 10.1186/s13395-020-00226-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/04/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Skeletal muscles are composed of a heterogeneous collection of fiber types with different physiological adaption in response to a stimulus and disease-related conditions. Each fiber has a specific molecular expression of myosin heavy chain molecules (MyHC). So far, MyHCs are currently the best marker proteins for characterization of individual fiber types, and several proteome profiling studies have helped to dissect the molecular signature of whole muscles and individual fibers. METHODS Herein, we describe a mass spectrometric workflow to measure skeletal muscle fiber type-specific proteomes. To bypass the limited quantities of protein in single fibers, we developed a Proteomics high-throughput fiber typing (ProFiT) approach enabling profiling of MyHC in single fibers. Aliquots of protein extracts from separated muscle fibers were subjected to capillary LC-MS gradients to profile MyHC isoforms in a 96-well format. Muscle fibers with the same MyHC protein expression were pooled and subjected to proteomic, pulsed-SILAC, and phosphoproteomic analysis. RESULTS Our fiber type-specific quantitative proteome analysis confirmed the distribution of fiber types in the soleus muscle, substantiates metabolic adaptions in oxidative and glycolytic fibers, and highlighted significant differences between the proteomes of type IIb fibers from different muscle groups, including a differential expression of desmin and actinin-3. A detailed map of the Lys-6 incorporation rates in muscle fibers showed an increased turnover of slow fibers compared to fast fibers. In addition, labeling of mitochondrial respiratory chain complexes revealed a broad range of Lys-6 incorporation rates, depending on the localization of the subunits within distinct complexes. CONCLUSION Overall, the ProFiT approach provides a versatile tool to rapidly characterize muscle fibers and obtain fiber-specific proteomes for different muscle groups.
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Affiliation(s)
- Sebastian Kallabis
- CECAD Research Center, Institute for Genetics, University of Cologne, 50931, Cologne, Germany
| | - Lena Abraham
- CECAD Research Center, Institute for Genetics, University of Cologne, 50931, Cologne, Germany
| | - Stefan Müller
- CECAD Research Center, Institute for Genetics, University of Cologne, 50931, Cologne, Germany
| | - Verena Dzialas
- CECAD Research Center, Institute for Genetics, University of Cologne, 50931, Cologne, Germany
| | - Clara Türk
- CECAD Research Center, Institute for Genetics, University of Cologne, 50931, Cologne, Germany
| | - Janica Lea Wiederstein
- CECAD Research Center, Institute for Genetics, University of Cologne, 50931, Cologne, Germany
| | - Theresa Bock
- CECAD Research Center, Institute for Genetics, University of Cologne, 50931, Cologne, Germany
| | - Hendrik Nolte
- Max Planck Institute for the Biology of Aging, 50931, Cologne, Germany
| | - Leonardo Nogara
- Venetian Institute of Molecular Medicine (VIMM), Via Orus 2, 35129, Padova, Italy
| | - Bert Blaauw
- Venetian Institute of Molecular Medicine (VIMM), Via Orus 2, 35129, Padova, Italy
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Marcus Krüger
- CECAD Research Center, Institute for Genetics, University of Cologne, 50931, Cologne, Germany. .,Center for Molecular Medicine (CMMC), University of Cologne, 50931, Cologne, Germany.
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Denninger JK, Chen X, Turkoglu AM, Sarchet P, Volk AR, Rieskamp JD, Yan P, Kirby ED. Defining the adult hippocampal neural stem cell secretome: In vivo versus in vitro transcriptomic differences and their correlation to secreted protein levels. Brain Res 2020; 1735:146717. [PMID: 32035887 DOI: 10.1016/j.brainres.2020.146717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 01/08/2023]
Abstract
Adult hippocampal neural stem and progenitor cells (NSPCs) secrete a variety of proteins that affect tissue function. Though several individual NSPC-derived proteins have been shown to impact key cellular processes, a broad characterization is lacking. Secretome profiling of low abundance stem cell populations is typically achieved via proteomic characterization of in vitro, isolated cells. Here, we identified hundreds of secreted proteins in conditioned media from in vitro adult mouse hippocampal NSPCs using an antibody array and mass spectrometry. Comparison of protein abundance between antibody array and mass spectrometry plus quantification of several key secreted proteins by ELISA revealed notable disconnect between methods in what proteins were identified as being high versus low abundance, suggesting that data from antibody arrays in particular should be approached with caution. We next assessed the NSPC secretome on a transcriptional level with single cell and bulk RNA sequencing (RNAseq) of cultured NSPCs. Comparison of RNAseq transcript levels of highly secreted proteins revealed that quantification of gene expression did not necessarily predict relative protein abundance. Interestingly, comparing our in vitro NSPC gene expression data with similar data from freshly isolated, in vivo hippocampal NSPCs revealed strong correlations in global gene expression between in vitro and in vivo NSPCs. Understanding the components and functions of the NSPC secretome is essential to understanding how these cells may modulate the hippocampal neurogenic niche. Cumulatively, our data emphasize the importance of using proteomics in conjunction with transcriptomics and highlights the need for better methods of unbiased secretome profiling.
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Affiliation(s)
- Jiyeon K Denninger
- Department of Psychology, College of Arts and Sciences, The Ohio State University, United States
| | - Xi Chen
- Comprehensive Cancer Center, The Ohio State University, United States
| | - Altan M Turkoglu
- College of Arts and Sciences, The Ohio State University, United States
| | - Patricia Sarchet
- Comprehensive Cancer Center, The Ohio State University, United States
| | - Abby R Volk
- College of Arts and Sciences, The Ohio State University, United States
| | - Joshua D Rieskamp
- Neuroscience Graduate Program, The Ohio State University, United States
| | - Pearlly Yan
- Comprehensive Cancer Center, The Ohio State University, United States; Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, United States
| | - Elizabeth D Kirby
- Department of Psychology, College of Arts and Sciences, The Ohio State University, United States; Department of Neuroscience, The Ohio State University, United States; Chronic Brain Injury Initiative, The Ohio State University, United States.
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Evans HT, Bodea LG, Götz J. Cell-specific non-canonical amino acid labelling identifies changes in the de novo proteome during memory formation. eLife 2020; 9:e52990. [PMID: 31904341 PMCID: PMC6944461 DOI: 10.7554/elife.52990] [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: 10/23/2019] [Accepted: 12/13/2019] [Indexed: 12/15/2022] Open
Abstract
The formation of spatial long-term memory (LTM) requires the de novo synthesis of distinct sets of proteins; however, a non-biased examination of the de novo proteome in this process is lacking. Here, we generated a novel mouse strain, which enables cell-type-specific labelling of newly synthesised proteins with non-canonical amino acids (NCAAs) by genetically restricting the expression of the mutant tRNA synthetase, NLL-MetRS, to hippocampal neurons. By combining this labelling technique with an accelerated version of the active place avoidance task and bio-orthogonal non-canonical amino acid tagging (BONCAT) followed by SWATH quantitative mass spectrometry, we identified 156 proteins that were altered in synthesis in hippocampal neurons during spatial memory formation. In addition to observing increased synthesis of known proteins important in memory-related processes, such as glutamate receptor recycling, we also identified altered synthesis of proteins associated with mRNA splicing as a potential mechanism involved in spatial LTM formation.
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Affiliation(s)
- Harrison Tudor Evans
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Liviu-Gabriel Bodea
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
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Alevra M, Mandad S, Ischebeck T, Urlaub H, Rizzoli SO, Fornasiero EF. A mass spectrometry workflow for measuring protein turnover rates in vivo. Nat Protoc 2019; 14:3333-3365. [PMID: 31685960 DOI: 10.1038/s41596-019-0222-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022]
Abstract
Proteins are continually produced and degraded, to avoid the accumulation of old or damaged molecules and to maintain the efficiency of physiological processes. Despite its importance, protein turnover has been difficult to measure in vivo. Previous approaches to evaluating turnover in vivo have required custom labeling approaches, involved complex mass spectrometry (MS) analyses, or used comparative strategies that do not allow direct quantitative measurements. Here, we describe a robust protocol for quantitative proteome turnover analysis in mice that is based on a commercially available diet for stable isotope labeling of amino acids in mammals (SILAM). We start by discussing fundamental concepts of protein turnover, including different methodological approaches. We then cover in detail the practical aspects of metabolic labeling and explain both the experimental and computational steps that must be taken to obtain accurate in vivo results. Finally, we present a simple experimental workflow that enables measurement of precise turnover rates in a time frame of ~4-5 weeks, including the labeling time. We also provide all the scripts needed for the interpretation of the MS results and for comparing turnover across different conditions. Overall, the workflow presented here comprises several improvements in the determination of protein lifetimes with respect to other available methods, including a minimally invasive labeling strategy and a robust interpretation of MS results, thus enhancing reproducibility across laboratories.
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Affiliation(s)
- Mihai Alevra
- Department of Neuro- and Sensory Physiology & Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Göttingen, Germany
| | - Sunit Mandad
- Department of Neuro- and Sensory Physiology & Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Göttingen, Germany.,Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute of Biophysical Chemistry, Göttingen, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute of Biophysical Chemistry, Göttingen, Germany
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology & Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Göttingen, Germany.
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology & Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Göttingen, Germany.
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Koren SA, Gillett DA, D'Alton SV, Hamm MJ, Abisambra JF. Proteomic Techniques to Examine Neuronal Translational Dynamics. Int J Mol Sci 2019; 20:ijms20143524. [PMID: 31323794 PMCID: PMC6678648 DOI: 10.3390/ijms20143524] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/08/2019] [Accepted: 07/15/2019] [Indexed: 01/30/2023] Open
Abstract
Impairments in translation have been increasingly implicated in the pathogenesis and progression of multiple neurodegenerative diseases. Assessing the spatiotemporal dynamics of translation in the context of disease is a major challenge. Recent developments in proteomic analyses have enabled the resolution of nascent peptides in a short timescale on the order of minutes. In addition, a quantitative analysis of translation has progressed in vivo, showing remarkable potential for coupling these techniques with cognitive and behavioral outcomes. Here, we review these modern approaches to measure changes in translation and ribosomal function with a specific focus on current applications in the mammalian brain and in the study of neurodegenerative diseases.
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Affiliation(s)
- Shon A Koren
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32601, USA
| | - Drew A Gillett
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32601, USA
| | - Simon V D'Alton
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32601, USA
| | - Matthew J Hamm
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32601, USA
| | - Jose F Abisambra
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32601, USA.
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