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Lu H, Zhu Z, Fields L, Zhang H, Li L. Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross-Linking. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39300771 DOI: 10.1002/mas.21908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/31/2024] [Accepted: 09/02/2024] [Indexed: 09/22/2024]
Abstract
The exploration of protein structure and function stands at the forefront of life science and represents an ever-expanding focus in the development of proteomics. As mass spectrometry (MS) offers readout of protein conformational changes at both the protein and peptide levels, MS-based structural proteomics is making significant strides in the realms of structural and molecular biology, complementing traditional structural biology techniques. This review focuses on two powerful MS-based techniques for peptide-level readout, namely limited proteolysis-mass spectrometry (LiP-MS) and cross-linking mass spectrometry (XL-MS). First, we discuss the principles, features, and different workflows of these two methods. Subsequently, we delve into the bioinformatics strategies and software tools used for interpreting data associated with these protein conformation readouts and how the data can be integrated with other computational tools. Furthermore, we provide a comprehensive summary of the noteworthy applications of LiP-MS and XL-MS in diverse areas including neurodegenerative diseases, interactome studies, membrane proteins, and artificial intelligence-based structural analysis. Finally, we discuss the factors that modulate protein conformational changes. We also highlight the remaining challenges in understanding the intricacies of protein conformational changes by LiP-MS and XL-MS technologies.
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Affiliation(s)
- Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Zexin Zhu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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Krsek A, Ostojic L, Zivalj D, Baticic L. Navigating the Neuroimmunomodulation Frontier: Pioneering Approaches and Promising Horizons-A Comprehensive Review. Int J Mol Sci 2024; 25:9695. [PMID: 39273641 PMCID: PMC11396210 DOI: 10.3390/ijms25179695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/30/2024] [Accepted: 09/03/2024] [Indexed: 09/15/2024] Open
Abstract
The research in neuroimmunomodulation aims to shed light on the complex relationships that exist between the immune and neurological systems and how they affect the human body. This multidisciplinary field focuses on the way immune responses are influenced by brain activity and how neural function is impacted by immunological signaling. This provides important insights into a range of medical disorders. Targeting both brain and immunological pathways, neuroimmunomodulatory approaches are used in clinical pain management to address chronic pain. Pharmacological therapies aim to modulate neuroimmune interactions and reduce inflammation. Furthermore, bioelectronic techniques like vagus nerve stimulation offer non-invasive control of these systems, while neuromodulation techniques like transcranial magnetic stimulation modify immunological and neuronal responses to reduce pain. Within the context of aging, neuroimmunomodulation analyzes the ways in which immunological and neurological alterations brought on by aging contribute to cognitive decline and neurodegenerative illnesses. Restoring neuroimmune homeostasis through strategies shows promise in reducing age-related cognitive decline. Research into mood disorders focuses on how immunological dysregulation relates to illnesses including anxiety and depression. Immune system fluctuations are increasingly recognized for their impact on brain function, leading to novel treatments that target these interactions. This review emphasizes how interdisciplinary cooperation and continuous research are necessary to better understand the complex relationship between the neurological and immune systems.
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Affiliation(s)
- Antea Krsek
- Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Leona Ostojic
- Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Dorotea Zivalj
- Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Lara Baticic
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
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3
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Kim D, Nita-Lazar A. Progress in mass spectrometry approaches to profiling protein-protein interactions in the studies of the innate immune system. JOURNAL OF PROTEINS AND PROTEOMICS 2024; 15:545-559. [PMID: 39380887 PMCID: PMC11460538 DOI: 10.1007/s42485-024-00156-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/04/2024] [Accepted: 06/24/2024] [Indexed: 10/10/2024]
Abstract
Understanding protein-protein interactions (PPIs) is pivotal for deciphering the intricacies of biological processes. Dysregulation of PPIs underlies a spectrum of diseases, including cancer, neurodegenerative disorders, and autoimmune conditions, highlighting the imperative of investigating these interactions for therapeutic advancements. This review delves into the realm of mass spectrometry-based techniques for elucidating PPIs and their profound implications in biological research. Mass spectrometry in the PPI research field not only facilitates the evaluation of protein-protein interaction modulators but also discovers unclear molecular mechanisms and sheds light on both on- and off-target effects, thus aiding in drug development. Our discussion navigates through six pivotal techniques: affinity purification mass spectrometry (AP-MS), proximity labeling mass spectrometry (PL-MS), cross-linking mass spectrometry (XL-MS), size exclusion chromatography coupled with mass spectrometry (SEC-MS), limited proteolysis-coupled mass spectrometry (LiP-MS), and thermal proteome profiling (TPP).
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Affiliation(s)
- Doeun Kim
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA
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4
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Taranov A, Bedolla A, Iwasawa E, Brown FN, Baumgartner S, Fugate EM, Levoy J, Crone SA, Goto J, Luo Y. The choroid plexus maintains adult brain ventricles and subventricular zone neuroblast pool, which facilitates poststroke neurogenesis. Proc Natl Acad Sci U S A 2024; 121:e2400213121. [PMID: 38954546 PMCID: PMC11252789 DOI: 10.1073/pnas.2400213121] [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: 01/10/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
The brain's neuroreparative capacity after injuries such as ischemic stroke is partly contained in the brain's neurogenic niches, primarily the subventricular zone (SVZ), which lies in close contact with the cerebrospinal fluid (CSF) produced by the choroid plexus (ChP). Despite the wide range of their proposed functions, the ChP/CSF remain among the most understudied compartments of the central nervous system (CNS). Here, we report a mouse genetic tool (the ROSA26iDTR mouse line) for noninvasive, specific, and temporally controllable ablation of CSF-producing ChP epithelial cells to assess the roles of the ChP and CSF in brain homeostasis and injury. Using this model, we demonstrate that ChP ablation causes rapid and permanent CSF volume loss in both aged and young adult brains, accompanied by disruption of ependymal cilia bundles. Surprisingly, ChP ablation did not result in overt neurological deficits at 1 mo postablation. However, we observed a pronounced decrease in the pool of SVZ neuroblasts (NBs) following ChP ablation, which occurs due to their enhanced migration into the olfactory bulb. In the middle cerebral artery occlusion model of ischemic stroke, NB migration into the lesion site was also reduced in the CSF-depleted mice. Thus, our study establishes an important role of ChP/CSF in regulating the regenerative capacity of the adult brain under normal conditions and after ischemic stroke.
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Affiliation(s)
- Aleksandr Taranov
- Department of Molecular and Cellular Biosciences, College of Medicine, University of Cincinnati, Cincinnati, OH45229
| | - Alicia Bedolla
- Department of Molecular and Cellular Biosciences, College of Medicine, University of Cincinnati, Cincinnati, OH45229
| | - Eri Iwasawa
- Division of Pediatric Neurosurgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH45229
| | - Farrah N. Brown
- Division of Pediatric Neurosurgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH45229
| | - Sarah Baumgartner
- Division of Pediatric Neurosurgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH45229
| | - Elizabeth M. Fugate
- Imaging Research Center, Department of Radiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH45229
| | - Joel Levoy
- Imaging Research Center, Department of Radiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH45229
| | - Steven A. Crone
- Division of Pediatric Neurosurgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH45229
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH45229
- Department of Neurosurgery, College of Medicine, University of Cincinnati, Cincinnati, OH45267
| | - June Goto
- Division of Pediatric Neurosurgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH45229
- Department of Neurosurgery, College of Medicine, University of Cincinnati, Cincinnati, OH45267
| | - Yu Luo
- Department of Molecular and Cellular Biosciences, College of Medicine, University of Cincinnati, Cincinnati, OH45229
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5
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Manriquez-Sandoval E, Brewer J, Lule G, Lopez S, Fried SD. FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Data Sets Built on FragPipe. J Proteome Res 2024; 23:2332-2342. [PMID: 38787630 DOI: 10.1021/acs.jproteome.3c00887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Here, we present FLiPPR, or FragPipe LiP (limited proteolysis) Processor, a tool that facilitates the analysis of data from limited proteolysis mass spectrometry (LiP-MS) experiments following primary search and quantification in FragPipe. LiP-MS has emerged as a method that can provide proteome-wide information on protein structure and has been applied to a range of biological and biophysical questions. Although LiP-MS can be carried out with standard laboratory reagents and mass spectrometers, analyzing the data can be slow and poses unique challenges compared to typical quantitative proteomics workflows. To address this, we leverage FragPipe and then process its output in FLiPPR. FLiPPR formalizes a specific data imputation heuristic that carefully uses missing data in LiP-MS experiments to report on the most significant structural changes. Moreover, FLiPPR introduces a data merging scheme and a protein-centric multiple hypothesis correction scheme, enabling processed LiP-MS data sets to be more robust and less redundant. These improvements strengthen statistical trends when previously published data are reanalyzed with the FragPipe/FLiPPR workflow. We hope that FLiPPR will lower the barrier for more users to adopt LiP-MS, standardize statistical procedures for LiP-MS data analysis, and systematize output to facilitate eventual larger-scale integration of LiP-MS data.
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Affiliation(s)
- Edgar Manriquez-Sandoval
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joy Brewer
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Gabriela Lule
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Samanta Lopez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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6
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Bjørkum AA, Griebel L, Birkeland E. Human serum proteomics reveals a molecular signature after one night of sleep deprivation. SLEEP ADVANCES : A JOURNAL OF THE SLEEP RESEARCH SOCIETY 2024; 5:zpae042. [PMID: 39131770 PMCID: PMC11310596 DOI: 10.1093/sleepadvances/zpae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 05/31/2024] [Indexed: 08/13/2024]
Abstract
Study Objectives Sleep deprivation is highly prevalent and caused by conditions such as night shift work or illnesses like obstructive sleep apnea. Compromised sleep affects cardiovascular-, immune-, and neuronal systems. Recently, we published human serum proteome changes after a simulated night shift. This pilot proteomic study aimed to further explore changes in human blood serum after 6 hours of sleep deprivation at night. Methods Human blood serum samples from eight self-declared healthy females were analyzed using Orbitrap Eclipse mass spectrometry (MS-MS) and high-pressure liquid chromatography. We used a within-participant design, in which the samples were taken after 6 hours of sleep at night and after 6 hours of sleep deprivation the following night. Systems biological databases and bioinformatic software were used to analyze the data and comparative analysis were done with other published sleep-related proteomic datasets. Results Out of 494 proteins, 66 were found to be differentially expressed proteins (DEPs) after 6 hours of sleep deprivation. Functional enrichment analysis revealed the associations of these DEPs with several biological functions related to the altered regulation of cellular processes such as platelet degranulation and blood coagulation, as well as associations with different curated gene sets. Conclusions This study presents serum proteomic changes after 6 hours of sleep deprivation, supports previous findings showing that short sleep deprivation affects several biological processes, and reveals a molecular signature of proteins related to pathological conditions such as altered coagulation and platelet function, impaired lipid and immune function, and cell proliferation. Data are available via ProteomeXchange with identifier PXD045729. This paper is part of the Genetic and other molecular underpinnings of sleep, sleep disorders, and circadian rhythms including translational approaches Collection.
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Affiliation(s)
- Alvhild Alette Bjørkum
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Leandra Griebel
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Bergen, Norway
- Department of Health Sciences and Technology, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Even Birkeland
- The Proteomics Unit at The Department of Biomedicine, University of Bergen, Bergen, Norway
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7
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Dormann D, Lemke EA. Adding intrinsically disordered proteins to biological ageing clocks. Nat Cell Biol 2024; 26:851-858. [PMID: 38783141 DOI: 10.1038/s41556-024-01423-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024]
Abstract
Research into how the young and old differ, and which biomarkers reflect the diverse biological processes underlying ageing, is a current and fast-growing field. Biological clocks provide a means to evaluate whether a molecule, cell, tissue or even an entire organism is old or young. Here we summarize established and emerging molecular clocks as timepieces. We emphasize that intrinsically disordered proteins (IDPs) tend to transform into a β-sheet-rich aggregated state and accumulate in non-dividing or slowly dividing cells as they age. We hypothesize that understanding these protein-based molecular ageing mechanisms might provide a conceptual pathway to determining a cell's health age by probing the aggregation state of IDPs, which we term the IDP clock.
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Affiliation(s)
- Dorothee Dormann
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
| | - Edward Anton Lemke
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg University, Mainz, Germany.
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8
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Shuken SR, Yu Q, Gygi SP. Inserting Pre-analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics with Sample Multiplexing. J Proteome Res 2024; 23:1834-1843. [PMID: 38594897 PMCID: PMC11068481 DOI: 10.1021/acs.jproteome.4c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
GoDig, a platform for targeted pathway proteomics without the need for manual assay scheduling or synthetic standards, is a powerful, flexible, and easy-to-use method that uses tandem mass tags to increase sample throughput up to 18-fold relative to label-free methods. Though the protein-level success rates of GoDig are high, the peptide-level success rates are more limited, hampering assays of harder-to-quantify proteins and site-specific phenomena. To guide the optimization of GoDig assays as well as improvements to the GoDig platform, we created GoDigViewer, a new stand-alone software that provides detailed visualizations of GoDig runs. GoDigViewer guided the implementation of "priming runs," an acquisition mode with significantly higher success rates. In this mode, two or more chromatographic priming runs are automatically performed to improve the accuracy and precision of target elution orders, followed by analytical runs which quantify targets. Using priming runs, success rates exceeded 97% for a list of 400 peptide targets and 95% for a list of 200 targets that are usually not quantified using untargeted mass spectrometry. We used priming runs to establish a quantitative assay of 125 macroautophagy proteins that had a >95% success rate and revealed differences in macroautophagy expression profiles across four human cell lines.
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Affiliation(s)
- Steven R Shuken
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
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9
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Lozinski BM, Ghorbani S, Yong VW. Biology of neurofibrosis with focus on multiple sclerosis. Front Immunol 2024; 15:1370107. [PMID: 38596673 PMCID: PMC11002094 DOI: 10.3389/fimmu.2024.1370107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024] Open
Abstract
Tissue damage elicits a wound healing response of inflammation and remodeling aimed at restoring homeostasis. Dysregulation of wound healing leads to accumulation of effector cells and extracellular matrix (ECM) components, collectively termed fibrosis, which impairs organ functions. Fibrosis of the central nervous system, neurofibrosis, is a major contributor to the lack of neural regeneration and it involves fibroblasts, microglia/macrophages and astrocytes, and their deposited ECM. Neurofibrosis occurs commonly across neurological conditions. This review describes processes of wound healing and fibrosis in tissues in general, and in multiple sclerosis in particular, and considers approaches to ameliorate neurofibrosis to enhance neural recovery.
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Affiliation(s)
| | | | - V. Wee Yong
- Hotchkiss Brain Institute and the Department of Clinical Neuroscience, University of Calgary, Calgary, AB, Canada
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10
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Feng J, Li Y, Li Y, Yin Q, Li H, Li J, Zhou B, Meng J, Lian H, Wu M, Li Y, Dou K, Song W, Lu B, Liu L, Hu S, Nie Y. Versican Promotes Cardiomyocyte Proliferation and Cardiac Repair. Circulation 2024; 149:1004-1015. [PMID: 37886839 DOI: 10.1161/circulationaha.123.066298] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND The adult mammalian heart is incapable of regeneration, whereas a transient regenerative capacity is maintained in the neonatal heart, primarily through the proliferation of preexisting cardiomyocytes. Neonatal heart regeneration after myocardial injury is accompanied by an expansion of cardiac fibroblasts and compositional changes in the extracellular matrix. Whether and how these changes influence cardiomyocyte proliferation and heart regeneration remains to be investigated. METHODS We used apical resection and myocardial infarction surgical models in neonatal and adult mice to investigate extracellular matrix components involved in heart regeneration after injury. Single-cell RNA sequencing and liquid chromatography-mass spectrometry analyses were used for versican identification. Cardiac fibroblast-specific Vcan deletion was achieved using the mouse strains Col1a2-2A-CreER and Vcanfl/fl. Molecular signaling pathways related to the effects of versican were assessed through Western blot, immunostaining, and quantitative reverse transcription polymerase chain reaction. Cardiac fibrosis and heart function were evaluated by Masson trichrome staining and echocardiography, respectively. RESULTS Versican, a cardiac fibroblast-derived extracellular matrix component, was upregulated after neonatal myocardial injury and promoted cardiomyocyte proliferation. Conditional knockout of Vcan in cardiac fibroblasts decreased cardiomyocyte proliferation and impaired neonatal heart regeneration. In adult mice, intramyocardial injection of versican after myocardial infarction enhanced cardiomyocyte proliferation, reduced fibrosis, and improved cardiac function. Furthermore, versican augmented the proliferation of human induced pluripotent stem cell-derived cardiomyocytes. Mechanistically, versican activated integrin β1 and downstream signaling molecules, including ERK1/2 and Akt, thereby promoting cardiomyocyte proliferation and cardiac repair. CONCLUSIONS Our study identifies versican as a cardiac fibroblast-derived pro-proliferative proteoglycan and clarifies the role of versican in promoting adult cardiac repair. These findings highlight its potential as a therapeutic factor for ischemic heart diseases.
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Affiliation(s)
- Jie Feng
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Yandong Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Yan Li
- State Key Laboratory of Tribology, Tsinghua University, Beijing, China (Y.L.)
| | - Qianqian Yin
- Institute of Medical Innovation and Research, Peking University Third Hospital, Peking University, Beijing, China (Q.Q.Y.)
| | - Haotong Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Jun Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Bin Zhou
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academic of Sciences, Shanghai (B.Z.)
| | - Jian Meng
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Hong Lian
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Mengge Wu
- Experimental Animal Center, Fuwai Central-China Hospital, Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou (M.G.W.)
| | - Yahuan Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Kefei Dou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Weihua Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Bin Lu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Lihui Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Shengshou Hu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences (Y.N.)
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Fuwai Central-China Hospital, Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou (Y.N.)
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11
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Abiose O, Rutledge J, Moran‐Losada P, Belloy ME, Wilson EN, He Z, Trelle AN, Channappa D, Romero A, Park J, Yutsis MV, Sha SJ, Andreasson KI, Poston KL, Henderson VW, Wagner AD, Wyss‐Coray T, Mormino EC. Post-translational modifications linked to preclinical Alzheimer's disease-related pathological and cognitive changes. Alzheimers Dement 2024; 20:1851-1867. [PMID: 38146099 PMCID: PMC10984434 DOI: 10.1002/alz.13576] [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: 08/01/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 12/27/2023]
Abstract
INTRODUCTION In this study, we leverage proteomic techniques to identify communities of proteins underlying Alzheimer's disease (AD) risk among clinically unimpaired (CU) older adults. METHODS We constructed a protein co-expression network using 3869 cerebrospinal fluid (CSF) proteins quantified by SomaLogic, Inc., in a cohort of participants along the AD clinical spectrum. We then replicated this network in an independent cohort of CU older adults and related these modules to clinically-relevant outcomes. RESULTS We discovered modules enriched for phosphorylation and ubiquitination that were associated with abnormal amyloid status, as well as p-tau181 (M4: β = 2.44, p < 0.001, M7: β = 2.57, p < 0.001) and executive function performance (M4: β = -2.00, p = 0.005, M7: β = -2.39, p < 0.001). DISCUSSION In leveraging CSF proteomic data from individuals spanning the clinical spectrum of AD, we highlight the importance of post-translational modifications for early cognitive and pathological changes.
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Affiliation(s)
- Olamide Abiose
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
- Wu Tsai Neurosciences InstituteStanford University School of MedicineStanfordCaliforniaUSA
| | - Jarod Rutledge
- The Phil and Penny Knight Initiative for Brain ResilienceStanford UniversityStanfordCaliforniaUSA
- Department of GeneticsStanford UniversityStanfordCaliforniaUSA
| | - Patricia Moran‐Losada
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
- Wu Tsai Neurosciences InstituteStanford University School of MedicineStanfordCaliforniaUSA
- The Phil and Penny Knight Initiative for Brain ResilienceStanford UniversityStanfordCaliforniaUSA
| | - Michael E. Belloy
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
| | - Edward N. Wilson
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
- Wu Tsai Neurosciences InstituteStanford University School of MedicineStanfordCaliforniaUSA
| | - Zihuai He
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
- Center for Biomedical Informatics ResearchStanford University School of MedicineStanfordCaliforniaUSA
| | - Alexandra N. Trelle
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
| | - Divya Channappa
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
| | - America Romero
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
| | - Jennifer Park
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
| | - Maya V. Yutsis
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
| | - Sharon J. Sha
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
| | - Katrin I. Andreasson
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
- Wu Tsai Neurosciences InstituteStanford University School of MedicineStanfordCaliforniaUSA
- Chan Zuckerberg BiohubSan FranciscoCaliforniaUSA
| | - Kathleen L. Poston
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
- Wu Tsai Neurosciences InstituteStanford University School of MedicineStanfordCaliforniaUSA
- The Phil and Penny Knight Initiative for Brain ResilienceStanford UniversityStanfordCaliforniaUSA
| | - Victor W. Henderson
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
- Department of Epidemiology & Population HealthStanford University School of MedicineStanfordCaliforniaUSA
| | - Anthony D. Wagner
- Wu Tsai Neurosciences InstituteStanford University School of MedicineStanfordCaliforniaUSA
- Department of PsychologyStanford UniversityStanfordCaliforniaUSA
| | - Tony Wyss‐Coray
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
- Wu Tsai Neurosciences InstituteStanford University School of MedicineStanfordCaliforniaUSA
- The Phil and Penny Knight Initiative for Brain ResilienceStanford UniversityStanfordCaliforniaUSA
| | - Elizabeth C. Mormino
- Department of Neurology and Neurological SciencesStanford University School of MedicinePalo AltoCaliforniaUSA
- Wu Tsai Neurosciences InstituteStanford University School of MedicineStanfordCaliforniaUSA
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12
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Shuken SR, Yu Q, Gygi SP. Inserting Pre-Analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics With Sample Multiplexing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.579551. [PMID: 38370708 PMCID: PMC10871336 DOI: 10.1101/2024.02.08.579551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
GoDig, a recent platform for targeted pathway proteomics without the need for manual assay scheduling or synthetic standard peptides, is a relatively flexible and easy-to-use method that uses tandem mass tags (TMT) to increase sample throughput up to 18-fold relative to label-free targeted proteomics. Though the protein quantification success rate of GoDig is generally high, the peptide-level success rate is more limited, hampering the extension of GoDig to assays of harder-to-quantify proteins and site-specific phenomena. In order to guide the optimization of GoDig assays as well as improvements to the GoDig platform, we created GoDigViewer, a new stand-alone software that provides detailed visualizations of GoDig runs. GoDigViewer guided the implementation of "priming runs," an acquisition mode with significantly higher success rates due to improved elution order calibration. In this mode, one or more chromatographic priming runs are automatically performed to determine accurate and precise target elution orders, followed by analytical runs which quantify targets. Using priming runs, peptide-level quantification success rates exceeded 97% for a list of 400 peptide targets and 95% for a list of 200 targets that are usually not quantified using untargeted mass spectrometry. We used priming runs to establish a quantitative assay of 125 macroautophagy proteins that had a >95% success rate and revealed differences in macroautophagy protein expression profiles across four human cell lines.
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Affiliation(s)
- Steven R. Shuken
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
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13
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Taranov A, Bedolla A, Iwasawa E, Brown FN, Baumgartner S, Fugate EM, Levoy J, Crone SA, Goto J, Luo Y. The choroid plexus maintains ventricle volume and adult subventricular zone neuroblast pool, which facilitates post-stroke neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.575277. [PMID: 38328050 PMCID: PMC10849542 DOI: 10.1101/2024.01.22.575277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The brain's neuroreparative capacity after injuries such as ischemic stroke is contained in the brain's neurogenic niches, primarily the subventricular zone (SVZ), which lies in close contact with the cerebrospinal fluid (CSF) produced by the choroid plexus (ChP). Despite the wide range of their proposed functions, the ChP/CSF remain among the most understudied compartments of the central nervous system (CNS). Here we report a mouse genetic tool (the ROSA26iDTR mouse line) for non-invasive, specific, and temporally controllable ablation of CSF-producing ChP epithelial cells to assess the roles of the ChP and CSF in brain homeostasis and injury. Using this model, we demonstrate that ChP ablation causes rapid and permanent CSF volume loss accompanied by disruption of ependymal cilia bundles. Surprisingly, ChP ablation did not result in overt neurological deficits at one-month post-ablation. However, we observed a pronounced decrease in the pool of SVZ neuroblasts following ChP ablation, which occurs due to their enhanced migration into the olfactory bulb. In the MCAo model of ischemic stroke, neuroblast migration into the lesion site was also reduced in the CSF-depleted mice. Thus, our study establishes an important and novel role of ChP/CSF in regulating the regenerative capacity of the adult brain under normal conditions and after ischemic stroke.
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Affiliation(s)
- Aleksandr Taranov
- Department of Molecular and Cellular Biosciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Alicia Bedolla
- Department of Molecular and Cellular Biosciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Eri Iwasawa
- Division of Pediatric Neurosurgery, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Farrah N. Brown
- Division of Pediatric Neurosurgery, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Sarah Baumgartner
- Division of Pediatric Neurosurgery, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Elizabeth M. Fugate
- Imaging Research Center, Cincinnati Children’s Hospital Medical Center, Department of Radiology, University of Cincinnati, Cincinnati, USA
| | - Joel Levoy
- Imaging Research Center, Cincinnati Children’s Hospital Medical Center, Department of Radiology, University of Cincinnati, Cincinnati, USA
| | - Steven A. Crone
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
- Division of Pediatric Neurosurgery, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
- Department of Neurosurgery, College of Medicine, University of Cincinnati, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
| | - June Goto
- Division of Pediatric Neurosurgery, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
- Department of Neurosurgery, College of Medicine, University of Cincinnati, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
| | - Yu Luo
- Department of Molecular and Cellular Biosciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
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14
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Manriquez-Sandoval E, Brewer J, Lule G, Lopez S, Fried SD. FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569947. [PMID: 38106106 PMCID: PMC10723326 DOI: 10.1101/2023.12.04.569947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Here, we present FLiPPR, or FragPipe LiP (limited proteolysis) Processor, a tool that facilitates the analysis of data from limited proteolysis mass spectrometry (LiP-MS) experiments following primary search and quantification in FragPipe. LiP-MS has emerged as a method that can provide proteome-wide information on protein structure and has been applied to a range of biological and biophysical questions. Although LiP-MS can be carried out with standard laboratory reagents and mass spectrometers, analyzing the data can be slow and poses unique challenges compared to typical quantitative proteomics workflows. To address this, we leverage the fast, sensitive, and accurate search and label-free quantification algorithms in FragPipe and then process its output in FLiPPR. FLiPPR formalizes a specific data imputation heuristic that carefully uses missing data in LiP-MS experiments to report on the most significant structural changes. Moreover, FLiPPR introduces a new data merging scheme (from ions to cut-sites) and a protein-centric multiple hypothesis correction scheme, collectively enabling processed LiP-MS datasets to be more robust and less redundant. These improvements substantially strengthen statistical trends when previously published data are reanalyzed with the FragPipe/FLiPPR workflow. As a final feature, FLiPPR facilitates the collection of structural metadata to identify correlations between experiments and structural features. We hope that FLiPPR will lower the barrier for more users to adopt LiP-MS, standardize statistical procedures for LiP-MS data analysis, and systematize output to facilitate eventual larger-scale integration of LiP-MS data.
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Affiliation(s)
- Edgar Manriquez-Sandoval
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Joy Brewer
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA
| | - Gabriela Lule
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Samanta Lopez
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Stephen D. Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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15
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Paukštytė J, López Cabezas RM, Feng Y, Tong K, Schnyder D, Elomaa E, Gregorova P, Doudin M, Särkkä M, Sarameri J, Lippi A, Vihinen H, Juutila J, Nieminen A, Törönen P, Holm L, Jokitalo E, Krisko A, Huiskonen J, Sarin LP, Hietakangas V, Picotti P, Barral Y, Saarikangas J. Global analysis of aging-related protein structural changes uncovers enzyme-polymerization-based control of longevity. Mol Cell 2023; 83:3360-3376.e11. [PMID: 37699397 DOI: 10.1016/j.molcel.2023.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/18/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023]
Abstract
Aging is associated with progressive phenotypic changes. Virtually all cellular phenotypes are produced by proteins, and their structural alterations can lead to age-related diseases. However, we still lack comprehensive knowledge of proteins undergoing structural-functional changes during cellular aging and their contributions to age-related phenotypes. Here, we conducted proteome-wide analysis of early age-related protein structural changes in budding yeast using limited proteolysis-mass spectrometry (LiP-MS). The results, compiled in online ProtAge catalog, unraveled age-related functional changes in regulators of translation, protein folding, and amino acid metabolism. Mechanistically, we found that folded glutamate synthase Glt1 polymerizes into supramolecular self-assemblies during aging, causing breakdown of cellular amino acid homeostasis. Inhibiting Glt1 polymerization by mutating the polymerization interface restored amino acid levels in aged cells, attenuated mitochondrial dysfunction, and led to lifespan extension. Altogether, this comprehensive map of protein structural changes enables identifying mechanisms of age-related phenotypes and offers opportunities for their reversal.
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Affiliation(s)
- Jurgita Paukštytė
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Rosa María López Cabezas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Yuehan Feng
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Kai Tong
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Ellinoora Elomaa
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Pavlina Gregorova
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Matteo Doudin
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Meeri Särkkä
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Jesse Sarameri
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Alice Lippi
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helena Vihinen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Juhana Juutila
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Anni Nieminen
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Petri Törönen
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Liisa Holm
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Anita Krisko
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Juha Huiskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - L Peter Sarin
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Ville Hietakangas
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Paola Picotti
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland; Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Juha Saarikangas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland.
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16
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Lee S, Devanney NA, Golden LR, Smith CT, Schwartz JL, Walsh AE, Clarke HA, Goulding DS, Allenger EJ, Morillo-Segovia G, Friday CM, Gorman AA, Hawkinson TR, MacLean SM, Williams HC, Sun RC, Morganti JM, Johnson LA. APOE modulates microglial immunometabolism in response to age, amyloid pathology, and inflammatory challenge. Cell Rep 2023; 42:112196. [PMID: 36871219 PMCID: PMC10117631 DOI: 10.1016/j.celrep.2023.112196] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/29/2022] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
The E4 allele of Apolipoprotein E (APOE) is associated with both metabolic dysfunction and a heightened pro-inflammatory response: two findings that may be intrinsically linked through the concept of immunometabolism. Here, we combined bulk, single-cell, and spatial transcriptomics with cell-specific and spatially resolved metabolic analyses in mice expressing human APOE to systematically address the role of APOE across age, neuroinflammation, and AD pathology. RNA sequencing (RNA-seq) highlighted immunometabolic changes across the APOE4 glial transcriptome, specifically in subsets of metabolically distinct microglia enriched in the E4 brain during aging or following an inflammatory challenge. E4 microglia display increased Hif1α expression and a disrupted tricarboxylic acid (TCA) cycle and are inherently pro-glycolytic, while spatial transcriptomics and mass spectrometry imaging highlight an E4-specific response to amyloid that is characterized by widespread alterations in lipid metabolism. Taken together, our findings emphasize a central role for APOE in regulating microglial immunometabolism and provide valuable, interactive resources for discovery and validation research.
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Affiliation(s)
- Sangderk Lee
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
| | - Nicholas A Devanney
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA; Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
| | - Lesley R Golden
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA
| | - Cathryn T Smith
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA
| | - James L Schwartz
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
| | - Adeline E Walsh
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA
| | - Harrison A Clarke
- Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA; Department of Biochemistry & Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA; Center for Advanced Spatial Biomolecule Research, University of Florida, Gainesville, FL, USA
| | - Danielle S Goulding
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
| | | | | | - Cassi M Friday
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA
| | - Amy A Gorman
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
| | - Tara R Hawkinson
- Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA; Department of Biochemistry & Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA; Center for Advanced Spatial Biomolecule Research, University of Florida, Gainesville, FL, USA
| | - Steven M MacLean
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA
| | - Holden C Williams
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA
| | - Ramon C Sun
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Biochemistry & Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA; Center for Advanced Spatial Biomolecule Research, University of Florida, Gainesville, FL, USA
| | - Josh M Morganti
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA.
| | - Lance A Johnson
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA; Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA.
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17
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Kaur A, Shuken S, Yang AC, Iram T. A protocol for collection and infusion of cerebrospinal fluid in mice. STAR Protoc 2023; 4:102015. [PMID: 36638015 PMCID: PMC9852694 DOI: 10.1016/j.xpro.2022.102015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/21/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Here, we provide a step-by-step protocol for the collection and intracerebroventricular infusion of cerebrospinal fluid (CSF) in mice. We describe steps to withdraw CSF quickly and abundantly while avoiding blood contamination. Using the Lynch coil technique, we gain functional insights into the collected CSF by slowly infusing minimal amounts of CSF directly to the lateral ventricles of aged mice. This protocol is versatile and can be used to infuse drugs, antibodies, or scarce biological compounds. For complete details on the use and execution of this protocol, please refer to Iram et al. (2022).1.
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Affiliation(s)
- Achint Kaur
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven Shuken
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Chris Yang
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Bakar Aging Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tal Iram
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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18
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Wang B, Zhong X, Fields L, Lu H, Zhu Z, Li L. Structural Proteomic Profiling of Cerebrospinal Fluids to Reveal Novel Conformational Biomarkers for Alzheimer's Disease. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:459-471. [PMID: 36745855 PMCID: PMC10276618 DOI: 10.1021/jasms.2c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Alzheimer's disease (AD) is the most common representation of dementia, with brain pathological hallmarks of protein abnormal aggregation, such as with amyloid beta and tau protein. It is well established that posttranslational modifications on tau protein, particularly phosphorylation, increase the likelihood of its aggregation and subsequent formation of neurofibrillary tangles, another hallmark of AD. As additional misfolded proteins presumably exist distinctly in AD disease states, which would serve as potential source of AD biomarkers, we used limited proteolysis-coupled with mass spectrometry (LiP-MS) to probe protein structural changes. After optimizing the LiP-MS conditions, we further applied this method to human cerebrospinal fluid specimens collected from healthy control, mild cognitive impairment (MCI), and AD subject groups to characterize proteome-wide misfolding tendencies as a result of disease progression. The fully tryptic peptides embedding LiP sites were compared with the half-tryptic peptides generated from internal cleavage of the same region to determine any structural unfolding or misfolding. We discovered hundreds of significantly up- and down-regulated peptides associated with MCI and AD indicating their potential structural changes in AD progression. Moreover, we detected 53 structurally changed regions in 12 proteins with high confidence between the healthy control and disease groups, illustrating the functional relevance of these proteins with AD progression. These newly discovered conformational biomarker candidates establish valuable future directions for exploring the molecular mechanism of designing therapeutic targets for AD.
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Affiliation(s)
- Bin Wang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Xiaofang Zhong
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Zexin Zhu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
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19
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Shuken SR, McNerney MW. Costs and Benefits of Popular P-Value Correction Methods in Three Models of Quantitative Omic Experiments. Anal Chem 2023; 95:2732-2740. [PMID: 36693222 PMCID: PMC10653731 DOI: 10.1021/acs.analchem.2c03719] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The multiple hypothesis testing problem is inherent in large-scale quantitative "omic" experiments such as mass spectrometry-based proteomics. Yet, tools for comparing the costs and benefits of different p-value correction methods under different experimental conditions are lacking. We performed thousands of simulations of omic experiments under a range of experimental conditions and applied correction using the Benjamini-Hochberg (BH), Bonferroni, and permutation-based false discovery proportion (FDP) estimation methods. The tremendous false discovery rate (FDR) benefit of correction was confirmed in a range of different contexts. No correction method can guarantee a low FDP in a single experiment, but the probability of a high FDP is small when a high number and proportion of corrected p-values are significant. On average, correction decreased sensitivity, but the sensitivity costs of BH and permutation were generally modest compared to the FDR benefits. In a given experiment, observed sensitivity was always maintained or decreased by BH and Bonferroni, whereas it was often increased by permutation. Overall, permutation had better FDR and sensitivity than BH. We show how increasing sample size, decreasing variability, or increasing effect size can enable the detection of all true changes while still correcting p-values, and we present basic guidelines for omic experimental design. Analysis of an experimental proteomic data set with defined changes corroborated these trends. We developed an R Shiny web application for further exploration and visualization of these models, which we call the Simulator of P-value Multiple Hypothesis Correction (SIMPLYCORRECT) and a high-performance R package, permFDP, for easy use of the permutation-based FDP estimation method.
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Affiliation(s)
- Steven R Shuken
- Department of Chemistry, Stanford University, 364 Lomita Dr., Stanford, California94305, United States
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, 291 Campus Dr., Stanford, California94305, United States
- Wu Tsai Neurosciences Institute, Stanford University, 290 Jane Stanford Way, Stanford, California94305, United States
| | - M Windy McNerney
- Mental Illness Research Education and Clinical Center (MIRECC), Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, California94304, United States
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 291 Campus Dr., Stanford, California94305, United States
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Fonken LK, Gaudet AD. Neuroimmunology of healthy brain aging. Curr Opin Neurobiol 2022; 77:102649. [PMID: 36368270 PMCID: PMC9826730 DOI: 10.1016/j.conb.2022.102649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/10/2022]
Abstract
Aging involves progressive deterioration away from homeostasis. Whereas the healthy adult brain maintains neuroimmune cells in a surveillant and homeostatic state, aged glial cells have a hyperreactive phenotype. These age-related pro-inflammatory biases are driven in part by cell-intrinsic factors, including increased cell priming and pro-inflammatory cell states. In addition, the aged inflammatory milieu is shaped by an altered environment, such as amplified danger signals and cytokines and dysregulated glymphatic function. These cell-instrinsic and environmental factors conspire to heighten the age-related risk for neuroimmune activation and associated pathology. In this review, we discuss cellular and molecular neuroimmune shifts with "healthy" aging; how these age-related changes affect physiology and behavior; and how recent research has revealed neuroimmune pathways and targets for improving health span.
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Affiliation(s)
- Laura K Fonken
- Division of Pharmacology and Toxicology, College of Pharmacy, University of Texas at Austin, Austin, TX, USA.
| | - Andrew D Gaudet
- Department of Psychology, College of Liberal Arts, University of Texas at Austin, Austin, TX, USA; Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, TX, USA. https://twitter.com/Gaudet_91
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