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Mathisen AF, Legøy TA, Larsen U, Unger L, Abadpour S, Paulo JA, Scholz H, Ghila L, Chera S. The age-dependent regulation of pancreatic islet landscape is fueled by a HNF1a-immune signaling loop. Mech Ageing Dev 2024; 220:111951. [PMID: 38825059 DOI: 10.1016/j.mad.2024.111951] [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: 01/09/2024] [Revised: 04/30/2024] [Accepted: 05/21/2024] [Indexed: 06/04/2024]
Abstract
Animal longevity is a function of global vital organ functionality and, consequently, a complex polygenic trait. Yet, monogenic regulators controlling overall or organ-specific ageing exist, owing their conservation to their function in growth and development. Here, by using pathway analysis combined with wet-biology methods on several dynamic timelines, we identified Hnf1a as a novel master regulator of the maturation and ageing in the adult pancreatic islet during the first year of life. Conditional transgenic mice bearing suboptimal levels of this transcription factor in the pancreatic islets displayed age-dependent changes, with a profile echoing precocious maturation. Additionally, the comparative pathway analysis revealed a link between Hnf1a age-dependent regulation and immune signaling, which was confirmed in the ageing timeline of an overly immunodeficient mouse model. Last, the global proteome analysis of human islets spanning three decades of life largely backed the age-specific regulation observed in mice. Collectively, our results suggest a novel role of Hnf1a as a monogenic regulator of the maturation and ageing process in the pancreatic islet via a direct or indirect regulatory loop with immune signaling.
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Affiliation(s)
- Andreas Frøslev Mathisen
- Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Thomas Aga Legøy
- Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ulrik Larsen
- Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Lucas Unger
- Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Shadab Abadpour
- Hybrid Technology Hub-Centre of Excellence, Faculty of Medicine, University of Oslo, Norway; Institute for Surgical Research, Department of Transplant Medicine, Oslo University Hospital, Oslo, Norway
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Hanne Scholz
- Hybrid Technology Hub-Centre of Excellence, Faculty of Medicine, University of Oslo, Norway; Institute for Surgical Research, Department of Transplant Medicine, Oslo University Hospital, Oslo, Norway
| | - Luiza Ghila
- Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Simona Chera
- Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway.
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2
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Wang X, Ding L, Zhao Y, Gao X. 6-Plex Tandem Phosphorus Tags (TPT) for Accurate Quantitative Proteomics. Anal Chem 2024. [PMID: 38991974 DOI: 10.1021/acs.analchem.4c01865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Isobaric chemical labeling is a widely used strategy for high-throughput quantitative proteomics based on mass spectrometry. However, commercially available reagents have high costs in applications as well as the sensitivity limitations for detection of the trace protein samples. Previously, we developed a 2-plex isobaric labeling strategy based on phosphorus chemistry for ultrasensitive proteome quantification with high accuracy. In this work, 6-plex tandem phosphorus tags (TPT) were developed with 3-fold increase in the multiplexing quantitative capacity compared to the 2-plex isobaric phosphorus reagents introduced previously. High isotope enrichment of 18O labeling was incorporated into the phosphoryl group with three exchangeable oxygen atoms by using commercially available H218O. The combinational incorporations of 18O atom in reporter ions and balance group set up the low-cost foundation for development of multiplex TPT reagents. The novel 6-plex TPT reagents could produce phosphoramidate as unique reporter ions with approximately 1 Da mass difference and thus enable 6-plex quantitative analysis in high-resolution ESI-MS/MS analysis. Using HeLa cell tryptic peptides, we concluded that 6-plex TPT reagents could facilitate large-scale accurate quantitative proteomics with very high labeling efficiency.
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Affiliation(s)
- Xiaoyu Wang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- State Key Laboratory of Cellular Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Lianshuai Ding
- State Key Laboratory of Cellular Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361102, China
- School of life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yufen Zhao
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Xiang Gao
- State Key Laboratory of Cellular Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361102, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Xiamen, Fujian 361102, China
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3
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Li J, Zhan X. Mass spectrometry analysis of phosphotyrosine-containing proteins. MASS SPECTROMETRY REVIEWS 2024; 43:857-887. [PMID: 36789499 DOI: 10.1002/mas.21836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.
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Affiliation(s)
- Jiajia Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
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4
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Wozniak JM, Li W, Governa P, Chen LY, Jadhav A, Dongre A, Forli S, Parker CG. Enhanced mapping of small-molecule binding sites in cells. Nat Chem Biol 2024; 20:823-834. [PMID: 38167919 PMCID: PMC11213684 DOI: 10.1038/s41589-023-01514-z] [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: 12/05/2022] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Photoaffinity probes are routinely utilized to identify proteins that interact with small molecules. However, despite this common usage, resolving the specific sites of these interactions remains a challenge. Here we developed a chemoproteomic workflow to determine precise protein binding sites of photoaffinity probes in cells. Deconvolution of features unique to probe-modified peptides, such as their tendency to produce chimeric spectra, facilitated the development of predictive models to confidently determine labeled sites. This yielded an expansive map of small-molecule binding sites on endogenous proteins and enabled the integration with multiplexed quantitation, increasing the throughput and dimensionality of experiments. Finally, using structural information, we characterized diverse binding sites across the proteome, providing direct evidence of their tractability to small molecules. Together, our findings reveal new knowledge for the analysis of photoaffinity probes and provide a robust method for high-resolution mapping of reversible small-molecule interactions en masse in native systems.
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Affiliation(s)
- Jacob M Wozniak
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Weichao Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Paolo Governa
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Li-Yun Chen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Appaso Jadhav
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashok Dongre
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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5
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Kagiou C, Cisneros JA, Farnung J, Liwocha J, Offensperger F, Dong K, Yang K, Tin G, Horstmann CS, Hinterndorfer M, Paulo JA, Scholes NS, Sanchez Avila J, Fellner M, Andersch F, Hannich JT, Zuber J, Kubicek S, Gygi SP, Schulman BA, Winter GE. Alkylamine-tethered molecules recruit FBXO22 for targeted protein degradation. Nat Commun 2024; 15:5409. [PMID: 38926334 PMCID: PMC11208438 DOI: 10.1038/s41467-024-49739-3] [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: 01/29/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Targeted protein degradation (TPD) relies on small molecules to recruit proteins to E3 ligases to induce their ubiquitylation and degradation by the proteasome. Only a few of the approximately 600 human E3 ligases are currently amenable to this strategy. This limits the actionable target space and clinical opportunities and thus establishes the necessity to expand to additional ligases. Here we identify and characterize SP3N, a specific degrader of the prolyl isomerase FKBP12. SP3N features a minimal design, where a known FKBP12 ligand is appended with a flexible alkylamine tail that conveys degradation properties. We found that SP3N is a precursor and that the alkylamine is metabolized to an active aldehyde species that recruits the SCFFBXO22 ligase for FKBP12 degradation. Target engagement occurs via covalent adduction of Cys326 in the FBXO22 C-terminal domain, which is critical for ternary complex formation, ubiquitylation and degradation. This mechanism is conserved for two recently reported alkylamine-based degraders of NSD2 and XIAP, thus establishing alkylamine tethering and covalent hijacking of FBXO22 as a generalizable TPD strategy.
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Affiliation(s)
- Chrysanthi Kagiou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Jose A Cisneros
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Jakob Farnung
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Joanna Liwocha
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Fabian Offensperger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Kevin Dong
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ka Yang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Gary Tin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Christina S Horstmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Natalie S Scholes
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Juan Sanchez Avila
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Michaela Fellner
- Research Institute of Molecular Pathology, Vienna BioCenter, 1030, Vienna, Austria
| | - Florian Andersch
- Research Institute of Molecular Pathology, Vienna BioCenter, 1030, Vienna, Austria
| | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna BioCenter, 1030, Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria.
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6
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Rossio V, Paulo JA, Liu X, Gygi SP, King RW. Specificity profiling of deubiquitylases against endogenously generated ubiquitin-protein conjugates. Cell Chem Biol 2024:S2451-9456(24)00180-6. [PMID: 38810651 DOI: 10.1016/j.chembiol.2024.05.001] [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: 02/05/2024] [Revised: 03/15/2024] [Accepted: 05/01/2024] [Indexed: 05/31/2024]
Abstract
Deubiquitylating enzymes (DUBs) remove ubiquitin from proteins thereby regulating their stability or activity. Our understanding of DUB-substrate specificity is limited because DUBs are typically not compared to each other against many physiological substrates. By broadly inhibiting DUBs in Xenopus egg extract, we generated hundreds of ubiquitylated proteins and compared the ability of 30 DUBs to deubiquitylate them using quantitative proteomics. We identified five high-impact DUBs (USP7, USP9X, USP36, USP15, and USP24) that each reduced ubiquitylation of over 10% of the isolated proteins. Candidate substrates of high-impact DUBs showed substantial overlap and were enriched for disordered regions, suggesting this feature may promote substrate recognition. Other DUBs showed lower impact and non-overlapping specificity, targeting distinct non-disordered proteins including complexes such as the ribosome or the proteasome. Altogether our study identifies candidate DUB substrates and defines patterns of functional redundancy and specificity, revealing substrate characteristics that may influence DUB-substrate recognition.
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Affiliation(s)
- Valentina Rossio
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Xinyue Liu
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Randall W King
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA.
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7
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Cai Y, Chang C, Liao R. Overcoming the detrimental O-acylation in TMTpro labeling improves the proteome depth and quantification precision. Anal Chim Acta 2024; 1304:342538. [PMID: 38637049 DOI: 10.1016/j.aca.2024.342538] [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: 12/25/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND With the advent of proline-based reporter isobaric Tandem Mass Tag (TMTpro) reagents, the sample multiplexing capacity of tandem mass tags (TMTs) has been expanded, and up to 18 samples can be quantified in a multiplexed manner. Like classic TMT reagents, TMTpro reagents contain a tertiary amine group, which markedly enhances their reactivity toward hydroxyl groups and results in O-acylation of serine, threonine and tyrosine residues. This overlabeling significantly compromises proteome analysis in terms of depth and precision. In particular, the reactivity of hydroxyl-containing residues can be dramatically enhanced when coexisting with a histidine in the same peptides, leading to a severe systematic bias against the analysis of these peptides. Although some protocols using a reduced molar excess of TMT under alkaline conditions can alleviate overlabeling of histidine-free peptides to some extent, they have a limited effect on histidyl- and hydroxyl-containing peptides. RESULTS Here, we report a novel TMTpro labeling method that overcomes detrimental overlabeling while providing high labeling efficiency of amines. Additionally, our method is cost-effective, as it requires only half the amount of TMTpro reagents recommended by the reagent manufacturer. In a deep-scale analysis of a yeast/human two-proteome model sample, we compared our method with a typical alkaline labeling method using a reduced molar excess of TMTpro. Even at a depth of over 10,000 proteins, our method detected 23.7% more unique peptides and 8.7% more protein groups compared to the alkaline labeling method. Moreover, our method significantly improved the quantitative precision due to the reduced variability in labeling and increased protein sequence coverage. This substantially enhanced the statistical power of our method for detecting differentially abundant proteins, providing an average of 13% more yeast proteins that reached statistical significance. SIGNIFCANCE We presented a novel TMTpro labeling method that overcomes the detrimental O-acylation and thus significantly improves the depth and quantitative precision for proteome analysis.
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Affiliation(s)
- Yan Cai
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Chenchen Chang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Rijing Liao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China.
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8
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Lumpkin CJ, Patel H, Potts GK, Chaurasia S, Gibilisco L, Srivastava GP, Lee JY, Brown NJ, Amarante P, Williams JD, Karran E, Townsend M, Woods D, Ravikumar B. Broad proteomics analysis of seeding-induced aggregation of α-synuclein in M83 neurons reveals remodeling of proteostasis mechanisms that might contribute to Parkinson's disease pathogenesis. Mol Brain 2024; 17:26. [PMID: 38778381 PMCID: PMC11110445 DOI: 10.1186/s13041-024-01099-1] [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: 07/03/2023] [Accepted: 05/11/2024] [Indexed: 05/25/2024] Open
Abstract
Aggregation of misfolded α-synuclein (α-syn) is a key characteristic feature of Parkinson's disease (PD) and related synucleinopathies. The nature of these aggregates and their contribution to cellular dysfunction is still not clearly elucidated. We employed mass spectrometry-based total and phospho-proteomics to characterize the underlying molecular and biological changes due to α-syn aggregation using the M83 mouse primary neuronal model of PD. We identified gross changes in the proteome that coincided with the formation of large Lewy body-like α-syn aggregates in these neurons. We used protein-protein interaction (PPI)-based network analysis to identify key protein clusters modulating specific biological pathways that may be dysregulated and identified several mechanisms that regulate protein homeostasis (proteostasis). The observed changes in the proteome may include both homeostatic compensation and dysregulation due to α-syn aggregation and a greater understanding of both processes and their role in α-syn-related proteostasis may lead to improved therapeutic options for patients with PD and related disorders.
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Affiliation(s)
- Casey J Lumpkin
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
- Laboratory of Aging and Infertility Research, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Hiral Patel
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
| | - Gregory K Potts
- Discovery Research, AbbVie Inc, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Shilpi Chaurasia
- Excelra Knowledge Solutions Pvt Ltd, Uppal, Hyderabad, India, 500039
| | - Lauren Gibilisco
- Genomics Research Center, Computational Biology Neuroscience, AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Gyan P Srivastava
- Data & Statistical Sciences, AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Janice Y Lee
- Discovery Research, AbbVie Inc, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Nathan J Brown
- Biotherapeutics, AbbVie Bioresearch Center, 100 Research Drive, Worcester, MA, 01605, USA
| | - Patricia Amarante
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
| | - Jon D Williams
- Discovery Research, AbbVie Inc, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Eric Karran
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
| | - Matthew Townsend
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
| | - Dori Woods
- Laboratory of Aging and Infertility Research, Department of Biology, Northeastern University, Boston, Massachusetts, USA.
| | - Brinda Ravikumar
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA.
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9
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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10
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Peters-Clarke TM, Liang Y, Mertz KL, Lee KW, Westphall MS, Hinkle JD, McAlister GC, Syka JEP, Kelly RT, Coon JJ. Boosting the Sensitivity of Quantitative Single-Cell Proteomics with Infrared-Tandem Mass Tags. J Proteome Res 2024. [PMID: 38713017 DOI: 10.1021/acs.jproteome.4c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Single-cell proteomics is a powerful approach to precisely profile protein landscapes within individual cells toward a comprehensive understanding of proteomic functions and tissue and cellular states. The inherent challenges associated with limited starting material demand heightened analytical sensitivity. Just as advances in sample preparation maximize the amount of material that makes it from the cell to the mass spectrometer, we strive to maximize the number of ions that make it from ion source to the detector. In isobaric tagging experiments, limited reporter ion generation limits quantitative accuracy and precision. The combination of infrared photoactivation and ion parking circumvents the m/z dependence inherent in HCD, maximizing reporter generation and avoiding unintended degradation of TMT reporter molecules in infrared-tandem mass tags (IR-TMT). The method was applied to single-cell human proteomes using 18-plex TMTpro, resulting in 4-5-fold increases in reporter signal compared to conventional SPS-MS3 approaches. IR-TMT enables faster duty cycles, higher throughput, and increased peptide identification and quantification. Comparative experiments showcase 4-5-fold lower injection times for IR-TMT, providing superior sensitivity without compromising accuracy. In all, IR-TMT enhances the dynamic range of proteomic experiments and is compatible with gas-phase fractionation and real-time searching, promising increased gains in the study of cellular heterogeneity.
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Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Yiran Liang
- Department of Chemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Keaton L Mertz
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Kenneth W Lee
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua D Hinkle
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - John E P Syka
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Ryan T Kelly
- Department of Chemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53515, United States
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11
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Foltz L, Avabhrath N, Lanchy JM, Levy T, Possemato A, Ariss M, Peterson B, Grimes M. Craniofacial chondrogenesis in organoids from human stem cell-derived neural crest cells. iScience 2024; 27:109585. [PMID: 38623327 PMCID: PMC11016914 DOI: 10.1016/j.isci.2024.109585] [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: 07/14/2023] [Revised: 02/27/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Knowledge of cell signaling pathways that drive human neural crest differentiation into craniofacial chondrocytes is incomplete, yet essential for using stem cells to regenerate craniomaxillofacial structures. To accelerate translational progress, we developed a differentiation protocol that generated self-organizing craniofacial cartilage organoids from human embryonic stem cell-derived neural crest stem cells. Histological staining of cartilage organoids revealed tissue architecture and staining typical of elastic cartilage. Protein and post-translational modification (PTM) mass spectrometry and snRNA-seq data showed that chondrocyte organoids expressed robust levels of cartilage extracellular matrix (ECM) components: many collagens, aggrecan, perlecan, proteoglycans, and elastic fibers. We identified two populations of chondroprogenitor cells, mesenchyme cells and nascent chondrocytes, and the growth factors involved in paracrine signaling between them. We show that ECM components secreted by chondrocytes not only create a structurally resilient matrix that defines cartilage, but also play a pivotal autocrine cell signaling role in determining chondrocyte fate.
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Affiliation(s)
- Lauren Foltz
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, Center for Structural and Functional Neuroscience, The University of Montana, Missoula, MT 59812, USA
| | - Nagashree Avabhrath
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, Center for Structural and Functional Neuroscience, The University of Montana, Missoula, MT 59812, USA
| | - Jean-Marc Lanchy
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, Center for Structural and Functional Neuroscience, The University of Montana, Missoula, MT 59812, USA
| | - Tyler Levy
- Cell Signaling Technology, Danvers, MA 01923, USA
| | | | - Majd Ariss
- Cell Signaling Technology, Danvers, MA 01923, USA
| | | | - Mark Grimes
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, Center for Structural and Functional Neuroscience, The University of Montana, Missoula, MT 59812, USA
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12
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Li H, Fletcher-Etherington A, Hunter LM, Keshri S, Fielding CA, Nightingale K, Ravenhill B, Nobre L, Potts M, Antrobus R, Crump CM, Rubinsztein DC, Stanton RJ, Weekes MP. Human cytomegalovirus degrades DMXL1 to inhibit autophagy, lysosomal acidification, and viral assembly. Cell Host Microbe 2024; 32:466-478.e11. [PMID: 38479395 DOI: 10.1016/j.chom.2024.02.013] [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: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 04/13/2024]
Abstract
Human cytomegalovirus (HCMV) is an important human pathogen that regulates host immunity and hijacks host compartments, including lysosomes, to assemble virions. We combined a quantitative proteomic analysis of HCMV infection with a database of proteins involved in vacuolar acidification, revealing Dmx-like protein-1 (DMXL1) as the only protein that acidifies vacuoles yet is degraded by HCMV. Systematic comparison of viral deletion mutants reveals the uncharacterized 7 kDa US33A protein as necessary and sufficient for DMXL1 degradation, which occurs via recruitment of the E3 ubiquitin ligase Kip1 ubiquitination-promoting complex (KPC). US33A-mediated DMXL1 degradation inhibits lysosome acidification and autophagic cargo degradation. Formation of the virion assembly compartment, which requires lysosomes, occurs significantly later with US33A-expressing virus infection, with reduced viral replication. These data thus identify a viral strategy for cellular remodeling, with the potential to employ US33A in therapies for viral infection or rheumatic conditions, in which inhibition of lysosome acidification can attenuate disease.
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Affiliation(s)
- Hanqi Li
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
| | - Alice Fletcher-Etherington
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
| | - Leah M Hunter
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
| | - Swati Keshri
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; UK Dementia Institute, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Ceri A Fielding
- Cardiff University School of Medicine, Division of Infection and Immunity, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK
| | - Katie Nightingale
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
| | - Benjamin Ravenhill
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
| | - Luis Nobre
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
| | - Martin Potts
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
| | - Colin M Crump
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - David C Rubinsztein
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK; UK Dementia Institute, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Richard J Stanton
- Cardiff University School of Medicine, Division of Infection and Immunity, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.
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13
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Mitchell W, Goeminne LJE, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. eLife 2024; 12:RP90579. [PMID: 38517750 PMCID: PMC10959535 DOI: 10.7554/elife.90579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
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Affiliation(s)
- Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Ludger JE Goeminne
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Sirui Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Julie Y Chen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Kerry A Pierce
- Broad Institute of MIT and HarvardCambridgeUnited States
| | | | - Clary B Clish
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
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14
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DaRosa PA, Penchev I, Gumbin SC, Scavone F, Wąchalska M, Paulo JA, Ordureau A, Peter JJ, Kulathu Y, Harper JW, Becker T, Beckmann R, Kopito RR. UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. Nature 2024; 627:445-452. [PMID: 38383785 DOI: 10.1038/s41586-024-07073-0] [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: 03/13/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024]
Abstract
Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour1. UFM1 is a UBL that predominantly modifies a single lysine residue on a single ribosomal protein, uL24 (also called RPL26), on ribosomes at the cytoplasmic surface of the endoplasmic reticulum (ER)2,3. UFM1 conjugation (UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER3,4. Neither the molecular mechanism by which the UFMylation machinery achieves such precise target selection nor how this ribosomal modification promotes 60S rescue is known. Here we show that ribosome UFMylation in vivo occurs on free 60S and we present sequential cryo-electron microscopy snapshots of the heterotrimeric UFM1 E3 ligase (E3(UFM1)) engaging its substrate uL24. E3(UFM1) binds the L1 stalk, empty transfer RNA-binding sites and the peptidyl transferase centre through carboxy-terminal domains of UFL1, which results in uL24 modification more than 150 Å away. After catalysing UFM1 transfer, E3(UFM1) remains stably bound to its product, UFMylated 60S, forming a C-shaped clamp that extends all the way around the 60S from the transfer RNA-binding sites to the polypeptide tunnel exit. Our structural and biochemical analyses suggest a role for E3(UFM1) in post-termination release and recycling of the large ribosomal subunit from the ER membrane.
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Affiliation(s)
- Paul A DaRosa
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Ivan Penchev
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany
| | | | | | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joshua J Peter
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas Becker
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany
| | - Roland Beckmann
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany.
| | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, CA, USA.
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15
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Watkins JM, Montes C, Clark NM, Song G, Oliveira CC, Mishra B, Brachova L, Seifert CM, Mitchell MS, Yang J, Braga Dos Reis PA, Urano D, Muktar MS, Walley JW, Jones AM. Phosphorylation Dynamics in a flg22-Induced, G Protein-Dependent Network Reveals the AtRGS1 Phosphatase. Mol Cell Proteomics 2024; 23:100705. [PMID: 38135118 PMCID: PMC10837098 DOI: 10.1016/j.mcpro.2023.100705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 11/22/2023] [Accepted: 12/19/2023] [Indexed: 12/24/2023] Open
Abstract
The microbe-associated molecular pattern flg22 is recognized in a flagellin-sensitive 2-dependent manner in root tip cells. Here, we show a rapid and massive change in protein abundance and phosphorylation state of the Arabidopsis root cell proteome in WT and a mutant deficient in heterotrimeric G-protein-coupled signaling. flg22-induced changes fall on proteins comprising a subset of this proteome, the heterotrimeric G protein interactome, and on highly-populated hubs of the immunity network. Approximately 95% of the phosphorylation changes in the heterotrimeric G-protein interactome depend, at least partially, on a functional G protein complex. One member of this interactome is ATBα, a substrate-recognition subunit of a protein phosphatase 2A complex and an interactor to Arabidopsis thaliana Regulator of G Signaling 1 protein (AtRGS1), a flg22-phosphorylated, 7-transmembrane spanning modulator of the nucleotide-binding state of the core G-protein complex. A null mutation of ATBα strongly increases basal endocytosis of AtRGS1. AtRGS1 steady-state protein level is lower in the atbα mutant in a proteasome-dependent manner. We propose that phosphorylation-dependent endocytosis of AtRGS1 is part of the mechanism to degrade AtRGS1, thus sustaining activation of the heterotrimeric G protein complex required for the regulation of system dynamics in innate immunity. The PP2A(ATBα) complex is a critical regulator of this signaling pathway.
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Affiliation(s)
- Justin M Watkins
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Celio Cabral Oliveira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry and Molecular Biology/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Bharat Mishra
- Department of Biology, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Libuse Brachova
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Clara M Seifert
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Malek S Mitchell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jing Yang
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Daisuke Urano
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - M Shahid Muktar
- Department of Biology, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA.
| | - Alan M Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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16
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Ahlstedt BA, Ganji R, Mukkavalli S, Paulo JA, Gygi SP, Raman M. UBXN1 maintains ER proteostasis and represses UPR activation by modulating translation. EMBO Rep 2024; 25:672-703. [PMID: 38177917 PMCID: PMC10897191 DOI: 10.1038/s44319-023-00027-z] [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: 03/03/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
ER protein homeostasis (proteostasis) is essential for proper folding and maturation of proteins in the secretory pathway. Loss of ER proteostasis can lead to the accumulation of misfolded or aberrant proteins in the ER and triggers the unfolded protein response (UPR). In this study, we find that the p97 adaptor UBXN1 is an important negative regulator of the UPR. Loss of UBXN1 sensitizes cells to ER stress and activates the UPR. This leads to widespread upregulation of the ER stress transcriptional program. Using comparative, quantitative proteomics we show that deletion of UBXN1 results in a significant enrichment of proteins involved in ER-quality control processes including those involved in protein folding and import. Notably, we find that loss of UBXN1 does not perturb p97-dependent ER-associated degradation (ERAD). Our studies indicate that loss of UBXN1 increases translation in both resting and ER-stressed cells. Surprisingly, this process is independent of p97 function. Taken together, our studies have identified a new role for UBXN1 in repressing translation and maintaining ER proteostasis in a p97 independent manner.
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Affiliation(s)
- Brittany A Ahlstedt
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
- ALPCA diagnostics, Salem, NH, USA
| | - Rakesh Ganji
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Sirisha Mukkavalli
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
- Dana Farber Cancer Research Institute, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology Harvard Medical School, Boston, MA, USA
| | - Steve P Gygi
- Department of Cell Biology Harvard Medical School, Boston, MA, USA
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
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17
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Wu Z, Huang X, Huang L, Zhang X. 102-Plex Approach for Accurate and Multiplexed Proteome Quantification. Anal Chem 2024; 96:1402-1409. [PMID: 38215345 DOI: 10.1021/acs.analchem.3c03036] [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: 01/14/2024]
Abstract
Hyperplexing approaches have been aimed to meet the demand for large-scale proteomic analyses. Currently, the analysis capacity has expanded to up to 54 samples within a single experiment by utilizing different isotopic and isobaric reagent combinations. In this report, we propose a super multiplexed approach to enable the analysis of up to 102 samples in a single experiment, by the combination of our recently developed TAG-TMTpro and TAG-IBT16 labeling. We systematically investigated the identification and quantification performance of the 102-plex approach using the mixtures of E. coli and HeLa peptides. Our results revealed that all labeling series demonstrated accurate and reliable quantification performance. The combination of TAG-IBT16 and TAG-TMTpro approaches expands the multiplexing capacity to 102 plexes, providing a more multiplexed quantification method for even larger-scale proteomic analysis. Data are available via ProteomeXchange with the identifier PXD042398.
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Affiliation(s)
- Zhen Wu
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xirui Huang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lin Huang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
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18
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Amiri M, Kiniry SJ, Possemato AP, Mahmood N, Basiri T, Dufour CR, Tabatabaei N, Deng Q, Bellucci MA, Harwalkar K, Stokes MP, Giguère V, Kaufman RJ, Yamanaka Y, Baranov PV, Tahmasebi S, Sonenberg N. Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells. Cell Rep 2024; 43:113615. [PMID: 38159280 PMCID: PMC10962698 DOI: 10.1016/j.celrep.2023.113615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/24/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024] Open
Abstract
The integrated stress response (ISR) is critical for cell survival under stress. In response to diverse environmental cues, eIF2α becomes phosphorylated, engendering a dramatic change in mRNA translation. The activation of ISR plays a pivotal role in the early embryogenesis, but the eIF2-dependent translational landscape in pluripotent embryonic stem cells (ESCs) is largely unexplored. We employ a multi-omics approach consisting of ribosome profiling, proteomics, and metabolomics in wild-type (eIF2α+/+) and phosphorylation-deficient mutant eIF2α (eIF2αA/A) mouse ESCs (mESCs) to investigate phosphorylated (p)-eIF2α-dependent translational control of naive pluripotency. We show a transient increase in p-eIF2α in the naive epiblast layer of E4.5 embryos. Absence of eIF2α phosphorylation engenders an exit from naive pluripotency following 2i (two chemical inhibitors of MEK1/2 and GSK3α/β) withdrawal. p-eIF2α controls translation of mRNAs encoding proteins that govern pluripotency, chromatin organization, and glutathione synthesis. Thus, p-eIF2α acts as a key regulator of the naive pluripotency gene regulatory network.
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Affiliation(s)
- Mehdi Amiri
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, T12 XF62 Cork, Ireland
| | | | - Niaz Mahmood
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Tayebeh Basiri
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Catherine R Dufour
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Negar Tabatabaei
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Qiyun Deng
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Michael A Bellucci
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Keerthana Harwalkar
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Matthew P Stokes
- Cell Signaling Technology, Inc., 3 Trask Lane, Danvers, MA 01923, USA
| | - Vincent Giguère
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Randal J Kaufman
- Degenerative Diseases Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Yojiro Yamanaka
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, T12 XF62 Cork, Ireland
| | - Soroush Tahmasebi
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL 60612, USA.
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada.
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19
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Joshi SK, Piehowski P, Liu T, Gosline SJC, McDermott JE, Druker BJ, Traer E, Tyner JW, Agarwal A, Tognon CE, Rodland KD. Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine. Annu Rev Pharmacol Toxicol 2024; 64:455-479. [PMID: 37738504 PMCID: PMC10950354 DOI: 10.1146/annurev-pharmtox-022723-113921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools.
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Affiliation(s)
- Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Paul Piehowski
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sara J C Gosline
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jason E McDermott
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Karin D Rodland
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Pacific Northwest National Laboratory, Richland, Washington, USA
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20
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Kim C, Wang XD, Liu Z, Hao J, Wang S, Li P, Zi Z, Ding Q, Jang S, Kim J, Luo Y, Huffman KE, Pal Choudhuri S, del Rio S, Cai L, Liang H, Drapkin BJ, Minna JD, Yu Y. Induced degradation of lineage-specific oncoproteins drives the therapeutic vulnerability of small cell lung cancer to PARP inhibitors. SCIENCE ADVANCES 2024; 10:eadh2579. [PMID: 38241363 PMCID: PMC10798557 DOI: 10.1126/sciadv.adh2579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Although BRCA1/2 mutations are not commonly found in small cell lung cancer (SCLC), a substantial fraction of SCLC shows clinically relevant response to PARP inhibitors (PARPis). However, the underlying mechanism(s) of PARPi sensitivity in SCLC is poorly understood. We performed quantitative proteomic analyses and identified proteomic changes that signify PARPi responses in SCLC cells. We found that the vulnerability of SCLC to PARPi could be explained by the degradation of lineage-specific oncoproteins (e.g., ASCL1). PARPi-induced activation of the E3 ligase HUWE1 mediated the ubiquitin-proteasome system (UPS)-dependent ASCL1 degradation. Although PARPi induced a general DNA damage response in SCLC cells, this signal generated a cell-specific response in ASCL1 degradation, leading to the identification of HUWE1 expression as a predictive biomarker for PARPi. Combining PARPi with agents targeting these pathways markedly improved therapeutic response in SCLC. The degradation of lineage-specific oncoproteins therefore represents a previously unidentified mechanism for PARPi efficacy in SCLC.
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Affiliation(s)
- Chiho Kim
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Xu-Dong Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zhengshuai Liu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jianwei Hao
- Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shuai Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Peng Li
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhenzhen Zi
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qing Ding
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Seoyeon Jang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yikai Luo
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth E. Huffman
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shreoshi Pal Choudhuri
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sofia del Rio
- Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Ling Cai
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benjamin J. Drapkin
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yonghao Yu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
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21
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Dong KD, Schmid EW, Bomgarden RD, Choi JH, Gygi SP, Yu Q, Paulo JA. Adapting an Isobaric Tag-Labeled Yeast Peptide Standard to Develop Targeted Proteomics Assays. J Proteome Res 2024; 23:142-148. [PMID: 38009700 PMCID: PMC10777125 DOI: 10.1021/acs.jproteome.3c00493] [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: 11/29/2023]
Abstract
Targeted proteomics strategies present a streamlined hypothesis-driven approach to analyze specific sets of pathways or disease related proteins. goDig is a quantitative, targeted tandem mass tag (TMT)-based assay that can measure the relative abundance differences for hundreds of proteins directly from unfractionated mixtures. Specific protein groups or entire pathways of up to 200 proteins can be selected for quantitative profiling, while leveraging sample multiplexing permits the simultaneous analysis of up to 18 samples. Despite these benefits, implementing goDig is not without challenges, as it requires access to an instrument application programming interface (iAPI), an elution order and spectral library, a web-based method builder, and dedicated companion software. In addition, the absence of an example test assay may dissuade researchers from testing or implementing goDig. Here, we repurpose the TKO11 standard─which is commercially available but may also be assembled in-lab─and establish it as a de facto test assay for goDig. We build a proteome-wide goDig yeast library, quantify protein expression across several gene ontology (GO) categories, and compare these results to a fully fractionated yeast gold-standard data set. Essentially, we provide a guide detailing the goDig-based quantification of TKO11, which can also be used as a template for user-defined assays in other species.
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Affiliation(s)
- Kevin D Dong
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ernst W Schmid
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ryan D Bomgarden
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
| | - Jae H Choi
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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22
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Hasper J, Welle K, Swovick K, Hryhorenko J, Ghaemmaghami S, Buchwalter A. Long lifetime and tissue-specific accumulation of lamin A/C in Hutchinson-Gilford progeria syndrome. J Cell Biol 2024; 223:e202307049. [PMID: 37966721 PMCID: PMC10651395 DOI: 10.1083/jcb.202307049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/10/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
LMNA mutations cause laminopathies that afflict the cardiovascular system and include Hutchinson-Gilford progeria syndrome. The origins of tissue specificity in these diseases are unclear as the lamin A/C proteins are broadly expressed. We show that LMNA transcript levels are not predictive of lamin A/C protein levels across tissues and use quantitative proteomics to discover that tissue context and disease mutation each influence lamin A/C protein's lifetime. Lamin A/C's lifetime is an order of magnitude longer in the aorta, heart, and fat, where laminopathy pathology is apparent, than in the liver and intestine, which are spared from the disease. Lamin A/C is especially insoluble in cardiovascular tissues, which may limit degradation and promote protein stability. Progerin is even more long lived than lamin A/C in the cardiovascular system and accumulates there over time. Progerin accumulation is associated with impaired turnover of hundreds of abundant proteins in progeroid tissues. These findings identify impaired lamin A/C protein turnover as a novel feature of laminopathy syndromes.
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Affiliation(s)
- John Hasper
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Kevin Welle
- Mass Spectrometry Resource Laboratory, University of Rochester, Rochester, NY, USA
| | - Kyle Swovick
- Mass Spectrometry Resource Laboratory, University of Rochester, Rochester, NY, USA
| | - Jennifer Hryhorenko
- Mass Spectrometry Resource Laboratory, University of Rochester, Rochester, NY, USA
| | - Sina Ghaemmaghami
- Mass Spectrometry Resource Laboratory, University of Rochester, Rochester, NY, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Abigail Buchwalter
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Physiology, University of California, San Francisco, CA, USA
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23
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Li J. Proteomic Analyses of the Mouse Brain. Methods Mol Biol 2024; 2794:105-120. [PMID: 38630224 DOI: 10.1007/978-1-0716-3810-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Proteomics is a scientific field that aims to identify and characterize all proteins within a biological system, including their posttranslational modifications (PTMs), quantitative changes, and protein-protein interactions. Over the last two decades, proteomic approaches have been widely used in neuroscience research, providing multidimensional insights into the biology and pathology of the brain.Here, we present a basic protocol for profiling protein expression in the mouse brain, which involves total protein extraction, fractionation, digestion, and identification through liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). This method is compatible with many prevalent techniques used for protein quantitation, PTM analysis, and protein-protein interaction mapping.
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Affiliation(s)
- Jing Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, China.
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24
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Wu W, Fields L, DeLaney K, Buchberger AR, Li L. An Updated Guide to the Identification, Quantitation, and Imaging of the Crustacean Neuropeptidome. Methods Mol Biol 2024; 2758:255-289. [PMID: 38549019 PMCID: PMC11071638 DOI: 10.1007/978-1-0716-3646-6_14] [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: 04/02/2024]
Abstract
Crustaceans serve as a useful, simplified model for studying peptides and neuromodulation, as they contain numerous neuropeptide homologs to mammals and enable electrophysiological studies at the single-cell and neural circuit levels. Crustaceans contain well-defined neural networks, including the stomatogastric ganglion, oesophageal ganglion, commissural ganglia, and several neuropeptide-rich organs such as the brain, pericardial organs, and sinus glands. As existing mass spectrometry (MS) methods are not readily amenable to neuropeptide studies, there is a great need for optimized sample preparation, data acquisition, and data analysis methods. Herein, we present a general workflow and detailed methods for MS-based neuropeptidomic analysis of crustacean tissue samples and circulating fluids. In conjunction with profiling, quantitation can also be performed with isotopic or isobaric labeling. Information regarding the localization patterns and changes of peptides can be studied via mass spectrometry imaging. Combining these sample preparation strategies and MS analytical techniques allows for a multi-faceted approach to obtaining deep knowledge of crustacean peptidergic signaling pathways.
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Affiliation(s)
- Wenxin Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
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25
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Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. Cell Rep 2023; 42:113478. [PMID: 37991919 PMCID: PMC10785701 DOI: 10.1016/j.celrep.2023.113478] [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: 05/17/2023] [Revised: 09/13/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) remains a significant public health threat due to the ability of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and Middle East respiratory syndrome (MERS)-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here, we use our recently developed integrative DNA And Protein Tagging methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.
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Affiliation(s)
- Jonathan D Lee
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA.
| | - Bridget L Menasche
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Maria Mavrikaki
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Madison M Uyemura
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Su Min Hong
- Department of Genetics, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Nina Kozlova
- Department of Genetics, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mia M Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Arne Müller
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Tanvi Saxena
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan R Posey
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Priscilla Cheung
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Taru Muranen
- Department of Genetics, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Yujing J Heng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Frank J Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Department of Genetics, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
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26
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Rossio V, Paulo JA, Liu X, Gygi SP, King RW. Substrate identification and specificity profiling of deubiquitylases against endogenously-generated ubiquitin-protein conjugates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572581. [PMID: 38187689 PMCID: PMC10769257 DOI: 10.1101/2023.12.20.572581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Deubiquitylating enzymes (DUBs) remove ubiquitin from proteins thereby regulating their stability or activity. Our understanding of DUB-substrate specificity is limited because DUBs are typically not compared to each other against many physiological substrates. By broadly inhibiting DUBs in Xenopus egg extract, we generated hundreds of ubiquitylated proteins and compared the ability of 30 DUBs to deubiquitylate them using quantitative proteomics. We identified five high impact DUBs (USP7, USP9X, USP36, USP15 and USP24) that each reduced ubiquitylation of over ten percent of the isolated proteins. Candidate substrates of high impact DUBs showed substantial overlap and were enriched for disordered regions, suggesting this feature may promote substrate recognition. Other DUBs showed lower impact and non-overlapping specificity, targeting distinct non-disordered proteins including complexes such as the ribosome or the proteasome. Altogether our study identifies candidate DUB substrates and defines patterns of functional redundancy and specificity, revealing substrate characteristics that may influence DUB-substrate recognition.
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27
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Fisher AL, Wang CY, Xu Y, Phillips S, Paulo JA, Małachowska B, Xiao X, Fendler W, Mancias JD, Babitt JL. Quantitative proteomics and RNA-sequencing of mouse liver endothelial cells identify novel regulators of BMP6 by iron. iScience 2023; 26:108555. [PMID: 38125029 PMCID: PMC10730383 DOI: 10.1016/j.isci.2023.108555] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 09/29/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Hepcidin is the master hormone governing systemic iron homeostasis. Iron regulates hepcidin by activating bone morphogenetic protein (BMP)6 expression in liver endothelial cells (LECs), but the mechanisms are incompletely understood. To address this, we performed proteomics and RNA-sequencing on LECs from iron-adequate and iron-loaded mice. Gene set enrichment analysis identified transcription factors activated by high iron, including Nrf-2, which was previously reported to contribute to BMP6 regulation, and c-Jun. Jun (encoding c-Jun) knockdown blocked Bmp6 but not Nrf-2 pathway induction by iron in LEC cultures. Chromatin immunoprecipitation of mouse livers showed iron-dependent c-Jun binding to predicted sites in Bmp6 regulatory regions. Finally, c-Jun inhibitor blunted induction of Bmp6 and hepcidin, but not Nrf-2 activity, in iron-loaded mice. However, Bmp6 and iron parameters were unchanged in endothelial Jun knockout mice. Our data suggest that c-Jun participates in iron-mediated BMP6 regulation independent of Nrf-2, though the mechanisms may be redundant and/or multifactorial.
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Affiliation(s)
- Allison L. Fisher
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chia-Yu Wang
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yang Xu
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sydney Phillips
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Beata Małachowska
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
- Department of Radiation Oncology, Albert Einstein College of Medicine, NYC, NY, USA
| | - Xia Xiao
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joseph D. Mancias
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jodie L. Babitt
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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28
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Ctortecka C, Hartlmayr D, Seth A, Mendjan S, Tourniaire G, Udeshi ND, Carr SA, Mechtler K. An Automated Nanowell-Array Workflow for Quantitative Multiplexed Single-Cell Proteomics Sample Preparation at High Sensitivity. Mol Cell Proteomics 2023; 22:100665. [PMID: 37839701 PMCID: PMC10684380 DOI: 10.1016/j.mcpro.2023.100665] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023] Open
Abstract
Multiplexed and label-free mass spectrometry-based approaches with single-cell resolution have attributed surprising heterogeneity to presumed homogenous cell populations. Even though specialized experimental designs and instrumentation have demonstrated remarkable advances, the efficient sample preparation of single cells still lags. Here, we introduce the proteoCHIP, a universal option for single-cell proteomics sample preparation including multiplexed labeling up to 16-plex with high sensitivity and throughput. The automated processing using a commercial system combining single-cell isolation and picoliter dispensing, the cellenONE, reduces final sample volumes to low nanoliters submerged in a hexadecane layer simultaneously eliminating error-prone manual sample handling and overcoming evaporation. The specialized proteoCHIP design allows direct injection of single cells via a standard autosampler resulting in around 1500 protein groups per TMT10-plex with reduced or eliminated need for a carrier proteome. We evaluated the effect of wider precursor isolation windows at single-cell input levels and found that using 2 Da isolation windows increased overall sensitivity without significantly impacting interference. Using the dedicated mass spectrometry acquisition strategies detailed here, we identified on average close to 2000 proteins per TMT10-plex across 170 multiplexed single cells that readily distinguished human cell types. Overall, our workflow combines highly efficient sample preparation, chromatographic and ion mobility-based filtering, rapid wide-window data-dependent acquisition analysis, and intelligent data analysis for optimal multiplexed single-cell proteomics. This versatile and automated proteoCHIP-based sample preparation approach is sufficiently sensitive to drive biological applications of single-cell proteomics and can be readily adopted by proteomics laboratories.
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Affiliation(s)
- Claudia Ctortecka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
| | - David Hartlmayr
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria; Cellenion SASU, Lyon, France
| | | | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | | | - Namrata D Udeshi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria; Cellenion SASU, Lyon, France; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria; The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria.
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29
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Mitchell W, Goeminne LJ, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.546730. [PMID: 37425825 PMCID: PMC10327104 DOI: 10.1101/2023.06.30.546730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
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Affiliation(s)
- Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Ludger J.E. Goeminne
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Sirui Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Julie Y. Chen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115 United States
| | - Kerry A. Pierce
- Broad Institute of MIT and Harvard, Cambridge, MA 01241 United States
| | - Angelina H. Choy
- Broad Institute of MIT and Harvard, Cambridge, MA 01241 United States
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 01241 United States
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115 United States
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
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30
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Zhang T, Liu X, Rossio V, Dawson SL, Gygi SP, Paulo JA. Enhancing Proteome Coverage by Using Strong Anion-Exchange in Tandem with Basic-pH Reversed-Phase Chromatography for Sample Multiplexing-Based Proteomics. J Proteome Res 2023:10.1021/acs.jproteome.3c00492. [PMID: 37962907 PMCID: PMC11090996 DOI: 10.1021/acs.jproteome.3c00492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Sample multiplexing-based proteomic strategies rely on fractionation to improve proteome coverage. Tandem mass tag (TMT) experiments, for example, can currently accommodate up to 18 samples with proteins spanning several orders of magnitude, thus necessitating fractionation to achieve reasonable proteome coverage. Here, we present a simple yet effective peptide fractionation strategy that partitions a pooled TMT sample with a two-step elution using a strong anion-exchange (SAX) spin column prior to gradient-based basic pH reversed-phase (BPRP) fractionation. We highlight our strategy with a TMTpro18-plex experiment using nine diverse human cell lines in biological duplicate. We collected three data sets, one using only BPRP fractionation and two others of each SAX-partition followed by BPRP. The three data sets quantified a similar number of proteins and peptides, and the data highlight noticeable differences in the distribution of peptide charge and isoelectric point between the SAX partitions. The combined SAX partition data set contributed 10% more proteins and 20% more unique peptides that were not quantified by BPRP fractionation alone. In addition to this improved fractionation strategy, we provide an online resource of relative abundance profiles for over 11,000 proteins across the nine human cell lines, as well as two additional experiments using ovarian and pancreatic cancer cell lines.
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Affiliation(s)
- Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Valentina Rossio
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Shane L Dawson
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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31
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Hu Z, Zhang M, Fan J, Hu J, Lin G, Piao S, Liu P, Liu J, Fu S, Sun W, Gygi SP, Zhang J, Zhou C. High-Level Secretion of Pregnancy Zone Protein Is a Novel Biomarker of DNA Damage-Induced Senescence and Promotes Spontaneous Senescence. J Proteome Res 2023; 22:3570-3579. [PMID: 37831546 DOI: 10.1021/acs.jproteome.3c00403] [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: 10/15/2023]
Abstract
Identification of unique and specific biomarkers to better detect and quantify senescent cells remains challenging. By a global proteomic profiling of senescent human skin BJ fibroblasts induced by ionizing radiation (IR), the cellular level of pregnancy zone protein (PZP), a presumable pan-protease inhibitor never been linked to cellular senescence before, was found to be decreased by more than 10-fold, while the level of PZP in the conditioned medium was increased concomitantly. This observation was confirmed in a variety of senescent cells induced by IR or DNA-damaging drugs, indicating that high-level secretion of PZP is a novel senescence-associated secretory phenotype. RT-PCR examination verified that the transcription of the PZP gene is enhanced in various cells at senescence or upregulated following DNA damage treatment in a p53-independent manner. Moreover, pretreatment with late pregnancy serum containing a high level of PZP led to inhibition of doxorubicin-induced senescence in A549 cells, and depletion of PZP in the pregnancy serum could enhance such inhibition. Finally, the addition of immuno-precipitated PZP complexes into tissue culture attenuated the growth of A549 cells and promoted the spontaneous senescence. Therefore, we revealed that high-level secretion of PZP is a novel and unique feature associated with DNA damage-induced senescence, and secreted PZP is a positive regulator of cellular senescence, particularly during the late stage of gestation.
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Affiliation(s)
- Ziqi Hu
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Mingzhu Zhang
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Jiankun Fan
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Jiandong Hu
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Guochao Lin
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Shengwen Piao
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Peng Liu
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Jichao Liu
- The 2th Affiliated Hospital, Harbin Medical University, Harbin 150001, China
| | - Songbin Fu
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin150081, China
| | - Wenjing Sun
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin150081, China
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jinwei Zhang
- The 2th Affiliated Hospital, Harbin Medical University, Harbin 150001, China
| | - Chunshui Zhou
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin150081, China
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Lin D, Wu S, Cheng Y, Yan X, Liu Q, Ren T, Zhang J, Wang N. Early Proteomic Characteristics and Changes in the Optic Nerve Head, Optic Nerve, and Retina in a Rat Model of Ocular Hypertension. Mol Cell Proteomics 2023; 22:100654. [PMID: 37793503 PMCID: PMC10665672 DOI: 10.1016/j.mcpro.2023.100654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 07/18/2023] [Accepted: 08/23/2023] [Indexed: 10/06/2023] Open
Abstract
The pathogenesis of glaucoma is still unknown. There are few studies on the dynamic change of tissue-specific and time-specific molecular pathophysiology caused by ocular hypertension (OHT). This study aimed to identify the early proteomic alterations in the retina, optic nerve head (ONH), and optic nerve (ON). After establishing a rat model of OHT, we harvested the tissues from control and glaucomatous eyes and analyzed the changes in protein expression using a multiplexed quantitative proteomics approach (TMT-MS3). Our study identified 6403 proteins after 1-day OHT and 4399 proteins after 7-days OHT in the retina, 5493 proteins after 1-day OHT and 4544 proteins after 7-days OHT in ONH, and 5455 proteins after 1-day OHT and 3835 proteins after 7-days OHT in the ON. Of these, 560 and 489 differential proteins were identified on day 1 and 7 after OHT in the retina, 428 and 761 differential proteins were identified on day 1 and 7 after OHT in the ONH, and 257 and 205 differential proteins on days 1 and 7 after OHT in the ON. Computational analysis on day 1 and 7 of OHT revealed that alpha-2 macroglobulin was upregulated across two time points and three tissues stably. The differentially expressed proteins between day 1 and 7 after OHT in the retina, ONH, and ON were associated with glutathione metabolism, mitochondrial dysfunction/oxidative phosphorylation, oxidative stress, microtubule, and crystallin. And the most significant change in retina are crystallins. We validated this proteomic result with the Western blot of crystallin proteins and found that upregulated on day 1 but recovered on day 7 after OHT, which are promising as therapeutic targets. These findings provide insights into the time- and region-order mechanisms that are specifically affected in the retina, ONH, and ON in response to elevated IOP during the early stages.
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Affiliation(s)
- Danting Lin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Shen Wu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Ying Cheng
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Xuejing Yan
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Qian Liu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Tianmin Ren
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Jingxue Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China; Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China.
| | - Ningli Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China; Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China.
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33
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Pienkowski T, Kowalczyk T, Cysewski D, Kretowski A, Ciborowski M. Glioma and post-translational modifications: A complex relationship. Biochim Biophys Acta Rev Cancer 2023; 1878:189009. [PMID: 37913943 DOI: 10.1016/j.bbcan.2023.189009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023]
Abstract
Post-translational modifications (PTMs) are common covalent processes in biochemical pathways that alter protein function and activity. These modifications occur through proteolytic cleavage or attachment of modifying groups, such as phosphoryl, methyl, glycosyl, or acetyl groups, with one or more amino acid residues of a single protein. Some PTMs also present crosstalk abilities that affect both protein functionality and structure, creating new proteoforms. Any alteration in organism homeostasis may be a cancer hallmark. Cataloging PTMs and consequently, emerging proteoforms, present new therapeutic targets, approaches, and opportunities to discover additional discriminatory biomarkers in disease diagnostics. In this review, we focus on experimentally confirmed PTMs and their potential crosstalk in glioma research to introduce new opportunities for this tumor type, which emerge within the PTMomics area.
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Affiliation(s)
- Tomasz Pienkowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Tomasz Kowalczyk
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland; Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, Mickiewicza 2C, 15-222 Bialystok, Poland
| | - Dominik Cysewski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland; Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland.
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Bailey BL, Nguyen W, Cowman AF, Sleebs BE. Chemo-proteomics in antimalarial target identification and engagement. Med Res Rev 2023; 43:2303-2351. [PMID: 37232495 PMCID: PMC10947479 DOI: 10.1002/med.21975] [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: 06/22/2022] [Revised: 04/24/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
Humans have lived in tenuous battle with malaria over millennia. Today, while much of the world is free of the disease, areas of South America, Asia, and Africa still wage this war with substantial impacts on their social and economic development. The threat of widespread resistance to all currently available antimalarial therapies continues to raise concern. Therefore, it is imperative that novel antimalarial chemotypes be developed to populate the pipeline going forward. Phenotypic screening has been responsible for the majority of the new chemotypes emerging in the past few decades. However, this can result in limited information on the molecular target of these compounds which may serve as an unknown variable complicating their progression into clinical development. Target identification and validation is a process that incorporates techniques from a range of different disciplines. Chemical biology and more specifically chemo-proteomics have been heavily utilized for this purpose. This review provides an in-depth summary of the application of chemo-proteomics in antimalarial development. Here we focus particularly on the methodology, practicalities, merits, and limitations of designing these experiments. Together this provides learnings on the future use of chemo-proteomics in antimalarial development.
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Affiliation(s)
- Brodie L. Bailey
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - William Nguyen
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Alan F. Cowman
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
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35
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Adhikary U, Paulo JA, Godes M, Roychoudhury S, Prew MS, Ben-Nun Y, Yu EW, Budhraja A, Opferman JT, Chowdhury D, Gygi SP, Walensky LD. Targeting MCL-1 triggers DNA damage and an anti-proliferative response independent from apoptosis induction. Cell Rep 2023; 42:113176. [PMID: 37773750 PMCID: PMC10787359 DOI: 10.1016/j.celrep.2023.113176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 07/13/2023] [Accepted: 09/11/2023] [Indexed: 10/01/2023] Open
Abstract
MCL-1 is a high-priority target due to its dominant role in the pathogenesis and chemoresistance of cancer, yet clinical trials of MCL-1 inhibitors are revealing toxic side effects. MCL-1 biology is complex, extending beyond apoptotic regulation and confounded by its multiple isoforms, its domains of unresolved structure and function, and challenges in distinguishing noncanonical activities from the apoptotic response. We find that, in the presence or absence of an intact mitochondrial apoptotic pathway, genetic deletion or pharmacologic targeting of MCL-1 induces DNA damage and retards cell proliferation. Indeed, the cancer cell susceptibility profile of MCL-1 inhibitors better matches that of anti-proliferative than pro-apoptotic drugs, expanding their potential therapeutic applications, including synergistic combinations, but heightening therapeutic window concerns. Proteomic profiling provides a resource for mechanistic dissection and reveals the minichromosome maintenance DNA helicase as an interacting nuclear protein complex that links MCL-1 to the regulation of DNA integrity and cell-cycle progression.
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Affiliation(s)
- Utsarga Adhikary
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marina Godes
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Michelle S Prew
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yael Ben-Nun
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ellen W Yu
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Amit Budhraja
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Joseph T Opferman
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Loren D Walensky
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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36
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Gygi JS, Liu X, Levi BP, Paulo JA. Proteome-wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing. Proteomics 2023:e2300303. [PMID: 37882342 PMCID: PMC11045664 DOI: 10.1002/pmic.202300303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023]
Abstract
The GET pathway is associated with post-translational delivery of tail-anchored (TA) proteins to the endoplasmic reticulum (ER) in yeast, as well as other eukaryotes. Moreover, dysfunction of the GET pathway has been associated with various pathological conditions (i.e., neurodegenerative disorders, cardiovascular ailments, and protein misfolding diseases). In this study, we used yeast deletion strains of Get complex members (specifically, Get1, Get2, Get3, Get4, and Get5) coupled with sample multiplexing-based quantitative mass spectrometry to profile protein abundance on a proteome-wide scale across the five individual deletion strains. Our dataset consists of over 4500 proteins, which corresponds to >75% of the yeast proteome. The data reveal several dozen proteins that are differentially abundant in one or more deletion strains, some of which are membrane-associated, yet the abundance of many TA proteins remained unchanged. This study provides valuable insights into the roles of these Get genes, and the potential for alternative pathways which help maintain cellular function despite the disruption of the GET pathway.
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Affiliation(s)
- Joel S Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin P Levi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
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37
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Patil A, Strom AR, Paulo JA, Collings CK, Ruff KM, Shinn MK, Sankar A, Cervantes KS, Wauer T, St Laurent JD, Xu G, Becker LA, Gygi SP, Pappu RV, Brangwynne CP, Kadoch C. A disordered region controls cBAF activity via condensation and partner recruitment. Cell 2023; 186:4936-4955.e26. [PMID: 37788668 PMCID: PMC10792396 DOI: 10.1016/j.cell.2023.08.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/16/2023] [Accepted: 08/24/2023] [Indexed: 10/05/2023]
Abstract
Intrinsically disordered regions (IDRs) represent a large percentage of overall nuclear protein content. The prevailing dogma is that IDRs engage in non-specific interactions because they are poorly constrained by evolutionary selection. Here, we demonstrate that condensate formation and heterotypic interactions are distinct and separable features of an IDR within the ARID1A/B subunits of the mSWI/SNF chromatin remodeler, cBAF, and establish distinct "sequence grammars" underlying each contribution. Condensation is driven by uniformly distributed tyrosine residues, and partner interactions are mediated by non-random blocks rich in alanine, glycine, and glutamine residues. These features concentrate a specific cBAF protein-protein interaction network and are essential for chromatin localization and activity. Importantly, human disease-associated perturbations in ARID1B IDR sequence grammars disrupt cBAF function in cells. Together, these data identify IDR contributions to chromatin remodeling and explain how phase separation provides a mechanism through which both genomic localization and functional partner recruitment are achieved.
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Affiliation(s)
- Ajinkya Patil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy R Strom
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kiersten M Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Min Kyung Shinn
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Akshay Sankar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kasey S Cervantes
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tobias Wauer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
| | - Jessica D St Laurent
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Department of Obstetrics and Gynecology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Grace Xu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lindsay A Becker
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 21044, USA; Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA.
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 21044, USA.
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38
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Gourisankar S, Wenderski W, Paulo JA, Kim SH, Roepke K, Ellis C, Gygi SP, Crabtree GR. Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562244. [PMID: 37873481 PMCID: PMC10592824 DOI: 10.1101/2023.10.13.562244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Genes encoding subunits of the SWI/SNF or BAF ATP-dependent chromatin remodeling complex are among the most enriched for deleterious de novo mutations in intellectual disabilities and autism spectrum disorder, but the causative molecular pathways are not fully known 1,2 . Synaptic activity in neurons is critical for learning and memory and proper neural development 3 . Neural activity prompts calcium influx and transcription within minutes, facilitated in the nucleus by various transcription factors (TFs) and chromatin modifiers 4 . While BAF is required for activity-dependent developmental processes such as dendritic outgrowth 5-7 , the immediate molecular consequences of neural activity on BAF complexes and their functions are unknown. Here we mapped minute-scale biochemical consequences of neural activity, modeled by membrane depolarization of embryonic mouse primary cortical neurons, on BAF complexes. We used acute chemical perturbations of BAF ATPase activity and kinase signaling to define the activity-dependent effects on BAF complexes and activity-dependent BAF functions. Our studies found that BAF complexes change in subunit composition and are selectively phosphorylated within 10 minutes of depolarization. Increased levels of the core PBAF subunit Baf200/ Arid2 , uniquely containing an RFX-like DNA-binding domain, are concurrent with ATPase-dependent opening of chromatin at RFX/X-box motifs. Changes in BAF composition and phosphorylation lead to the regulation of chromatin accessibility for critical neurogenesis TFs. These biochemical effects are a convergent phenomenon downstream of multiple growth factor signaling pathways in mouse neurons and fibroblasts suggesting that BAF integrates signaling information from the membrane. In support of such a membrane-to-nucleus signaling cascade, we also identified a BAF-interacting kinase, Dclk2, whose inhibition attenuates BAF phosphorylation selectively. Our findings support a direct role of BAF complexes in responding to synaptic activity to regulate TF binding and transcription.
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Rossio V, Liu X, Paulo JA. Comparative Proteomic Analysis of Two Commonly Used Laboratory Yeast Strains: W303 and BY4742. Proteomes 2023; 11:30. [PMID: 37873872 PMCID: PMC10594481 DOI: 10.3390/proteomes11040030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is a powerful model system that is often used to expand our understanding of cellular processes and biological functions. Although many genetically well-characterized laboratory strains of S. cerevisiae are available, they may have different genetic backgrounds which can confound data interpretation. Here, we report a comparative whole-proteome analysis of two common laboratory yeast background strains, W303 and BY4742, in both exponential and stationary growth phases using isobaric-tag-based mass spectrometry to highlight differences in proteome complexity. We quantified over 4400 proteins, hundreds of which showed differences in abundance between strains and/or growth phases. Moreover, we used proteome-wide protein abundance to profile the mating type of the strains used in the experiment, the auxotrophic markers, and associated metabolic pathways, as well as to investigate differences in particular classes of proteins, such as the pleiotropic drug resistance (PDR) proteins. This study is a valuable resource that offers insight into mechanistic differences between two common yeast background strains and can be used as a guide to select a background that is best suited for addressing a particular biological question.
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Affiliation(s)
- Valentina Rossio
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA;
| | | | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA;
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40
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Burton NR, Polasky DA, Shikwana F, Ofori S, Yan T, Geiszler DJ, Veiga Leprevost FD, Nesvizhskii AI, Backus KM. Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics. J Am Chem Soc 2023; 145:21303-21318. [PMID: 37738129 DOI: 10.1021/jacs.3c05797] [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] [Indexed: 09/24/2023]
Abstract
Mass spectrometry-based chemoproteomics has emerged as an enabling technology for functional biology and drug discovery. To address limitations of established chemoproteomics workflows, including cumbersome reagent synthesis and low throughput sample preparation, here, we established the silane-based cleavable isotopically labeled proteomics (sCIP) method. The sCIP method is enabled by a high yielding and scalable route to dialkoxydiphenylsilane fluorenylmethyloxycarbonyl (DADPS-Fmoc)-protected amino acid building blocks, which enable the facile synthesis of customizable, isotopically labeled, and chemically cleavable biotin capture reagents. sCIP is compatible with both MS1- and MS2-based quantitation, and the sCIP-MS2 method is distinguished by its click-assembled isobaric tags in which the reporter group is encoded in the sCIP capture reagent and balancer in the pan cysteine-reactive probe. The sCIP-MS2 workflow streamlines sample preparation with early stage isobaric labeling and sample pooling, allowing for high coverage and increased sample throughput via customized low cost six-plex sample multiplexing. When paired with a custom FragPipe data analysis workflow and applied to cysteine-reactive fragment screens, sCIP proteomics revealed established and unprecedented cysteine-ligand pairs, including the discovery that mitochondrial uncoupling agent FCCP acts as a covalent-reversible cysteine-reactive electrophile.
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Affiliation(s)
- Nikolas R Burton
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Flowreen Shikwana
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Samuel Ofori
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Tianyang Yan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Keriann M Backus
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California 90095, United States
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41
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Rossio V, Paulo JA. Comparison of the Proteomes and Phosphoproteomes of S. cerevisiae Cells Harvested with Different Strategies. Proteomes 2023; 11:28. [PMID: 37873870 PMCID: PMC10594529 DOI: 10.3390/proteomes11040028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a powerful model system that is widely used to investigate many cellular processes. The harvesting of yeast cells is the first step in almost every experimental procedure. Here, yeast cells are isolated from their growth medium, collected, and used for successive experiments or analysis. The two most common methods to harvest S. cerevisiae are centrifugation and filtration. Understanding if and how centrifugation and filtration affect yeast physiology is essential with respect to downstream data interpretation. Here, we profile and compare the proteomes and the phosphoproteomes, using isobaric label-based quantitative mass spectrometry, of three common methods used to harvest S. cerevisiae cells: low-speed centrifugation, high-speed centrifugation, and filtration. Our data suggest that, while the proteome was stable across the tested conditions, hundreds of phosphorylation events were different between centrifugation and filtration. Our analysis shows that, under our experimental conditions, filtration may cause both cell wall and osmotic stress at higher levels compared to centrifugation, implying harvesting-method-specific stresses. Thus, considering that the basal activation levels of specific stresses may differ under certain harvesting conditions is an important, but often overlooked, aspect of experimental design.
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Affiliation(s)
- Valentina Rossio
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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42
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Chi B, Öztürk MM, Paraggio CL, Leonard CE, Sanita ME, Dastpak M, O’Connell JD, Coady JA, Zhang J, Gygi SP, Lopez-Gonzalez R, Yin S, Reed R. Causal ALS genes impact the MHC class II antigen presentation pathway. Proc Natl Acad Sci U S A 2023; 120:e2305756120. [PMID: 37722062 PMCID: PMC10523463 DOI: 10.1073/pnas.2305756120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/18/2023] [Indexed: 09/20/2023] Open
Abstract
Mutations in RNA/DNA-binding proteins cause amyotrophic lateral sclerosis (ALS), but the underlying disease mechanisms remain unclear. Here, we report that a set of ALS-associated proteins, namely FUS, EWSR1, TAF15, and MATR3, impact the expression of genes encoding the major histocompatibility complex II (MHC II) antigen presentation pathway. Both subunits of the MHC II heterodimer, HLA-DR, are down-regulated in ALS gene knockouts/knockdown in HeLa and human microglial cells, due to loss of the MHC II transcription factor CIITA. Importantly, hematopoietic progenitor cells (HPCs) derived from human embryonic stem cells bearing the FUSR495X mutation and HPCs derived from C9ORF72 ALS patient induced pluripotent stem cells also exhibit disrupted MHC II expression. Given that HPCs give rise to numerous immune cells, our data raise the possibility that loss of the MHC II pathway results in global failure of the immune system to protect motor neurons from damage that leads to ALS.
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Affiliation(s)
- Binkai Chi
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Muhammet M. Öztürk
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Christina L. Paraggio
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Claudia E. Leonard
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Maria E. Sanita
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Mahtab Dastpak
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Jeremy D. O’Connell
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Jordan A. Coady
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Jiuchun Zhang
- Harvard Medical School Cell Biology Initiative for Genome Editing and Neurodegeneration, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Steven P. Gygi
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Rodrigo Lopez-Gonzalez
- Department of Neurosciences Lerner Research Institute, Cleveland Clinic, Cleveland, OH44196
| | - Shanye Yin
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY10461
| | - Robin Reed
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
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43
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Cosarderelioglu C, Kreimer S, Plaza‐Rodriguez AI, Iglesias PA, Talbot CC, Siragy HM, Carey RM, Ubaida‐Mohien C, O'Rourke B, Ferrucci L, Bennett DA, Walston J, Abadir P. Decoding Angiotensin Receptors: TOMAHAQ-Based Detection and Quantification of Angiotensin Type-1 and Type-2 Receptors. J Am Heart Assoc 2023; 12:e030791. [PMID: 37681524 PMCID: PMC10547273 DOI: 10.1161/jaha.123.030791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/20/2023] [Indexed: 09/09/2023]
Abstract
Background The renin-angiotensin system plays a crucial role in human physiology, and its main hormone, angiotensin, activates 2 G-protein-coupled receptors, the angiotensin type-1 and type-2 receptors, in almost every organ. However, controversy exists about the location, distribution, and expression levels of these receptors. Concerns have been raised over the low sensitivity, low specificity, and large variability between lots of commercially available antibodies for angiotensin type-1 and type-2 receptors, which makes it difficult to reconciliate results of different studies. Here, we describe the first non-antibody-based sensitive and specific targeted quantitative mass spectrometry assay for angiotensin receptors. Methods and Results Using a technique that allows targeted analysis of multiple peptides across multiple samples in a single mass spectrometry analysis, known as TOMAHAQ (triggered by offset, multiplexed, accurate mass, high resolution, and absolute quantification), we have identified and validated specific human tryptic peptides that permit identification and quantification of angiotensin type-1 and type-2 receptors in biological samples. Several peptide sequences are conserved in rodents, making these mass spectrometry assays amenable to both preclinical and clinical studies. We have used this method to quantify angiotensin type-1 and type-2 receptors in postmortem frontal cortex samples of older adults (n=28) with Alzheimer dementia. We correlated levels of angiotensin receptors to biomarkers classically linked to renin-angiotensin system activation, including oxidative stress, inflammation, amyloid-β load, and paired helical filament-tau tangle burden. Conclusions These robust high-throughput assays will not only catalyze novel mechanistic studies in the angiotensin research field but may also help to identify patients with an unbalanced angiotensin receptor distribution who would benefit from angiotensin receptor blocker treatment.
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Affiliation(s)
- Caglar Cosarderelioglu
- Division of Geriatric Medicine and GerontologyJohns Hopkins University School of MedicineBaltimoreMD
- Division of Geriatrics, Department of Internal MedicineAnkara University School of MedicineAnkaraTurkey
| | - Simion Kreimer
- The Mass Spectrometry and Proteomics FacilityJohns Hopkins University School of MedicineBaltimoreMD
| | | | - Pablo A. Iglesias
- Department of Electrical and Computer Engineering, Whiting School of EngineeringJohns Hopkins UniversityBaltimoreMD
| | - C. Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of MedicineBaltimoreMD
| | - Helmy M. Siragy
- Division of Endocrinology and Metabolism, Department of MedicineUniversity of VirginiaCharlottesvilleVA
| | - Robert M. Carey
- Division of Endocrinology and Metabolism, Department of MedicineUniversity of VirginiaCharlottesvilleVA
| | | | - Brian O'Rourke
- Division of Cardiology, Department of MedicineJohns Hopkins UniversityBaltimoreMD
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of HealthBaltimoreMD
| | - David A. Bennett
- Rush Alzheimer’s Disease CenterRush University Medical CenterChicagoIL
| | - Jeremy Walston
- Division of Geriatric Medicine and GerontologyJohns Hopkins University School of MedicineBaltimoreMD
| | - Peter Abadir
- Division of Geriatric Medicine and GerontologyJohns Hopkins University School of MedicineBaltimoreMD
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Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555625. [PMID: 37693555 PMCID: PMC10491142 DOI: 10.1101/2023.08.31.555625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
COVID-19 remains a significant public health threat due to the ability of SARS-CoV-2 variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and MERS-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here we used our recently developed integrative DNA And Protein Tagging (iDAPT) methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.
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45
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Lapehn S, Colacino JA, Harris C. Spatiotemporal protein dynamics during early organogenesis in mouse conceptuses treated with valproic acid. Neurotoxicol Teratol 2023; 99:107286. [PMID: 37442398 PMCID: PMC10697214 DOI: 10.1016/j.ntt.2023.107286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/29/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Valproic acid (VPA) is an anti-epileptic medication that increases the risk of neural tube defect (NTD) outcomes in infants exposed during gestation. Previous studies into VPA's mechanism of action have focused on alterations in gene expression and metabolism but have failed to consider how exposure changes the abundance of critical developmental proteins over time. This study evaluates the effects of VPA on protein abundance in the developmentally distinct tissues of the mouse visceral yolk sac (VYS) and embryo proper (EMB) using mouse whole embryo culture. Embryos were exposed to 600 μM VPA at 2 h intervals over 10 h during early organogenesis with the aim of identifying protein pathways relevant to VPA's mechanism of action in failed NTC. Protein abundance was measured through tandem mass tag (TMT) labeling followed by liquid chromatography and mass spectrometry. Overall, there were over 1500 proteins with altered abundance after VPA exposure in the EMB or VYS with 428 of these proteins showing previous gene expression associations with VPA exposure. Limited overlap of significant proteins between tissues supported the conclusion of independent roles for the VYS and EMB in response to VPA. Pathway analysis of proteins with increased or decreased abundance identified multiple pathways with mechanistic relevance to NTC and embryonic development including convergent extension, Wnt Signaling/planar cell polarity, cellular migration, cellular proliferation, cell death, and cytoskeletal organization processes as targets of VPA. Clustering of co-regulated proteins to identify shared patterns of protein abundance over time highlighted 4 h and 6/10 h as periods of divergent protein abundance between control and VPA-treated samples in the VYS and EMB, respectively. Overall, this study demonstrated that VPA temporally alters protein content in critical developmental pathways in the VYS and the EMB during early organogenesis in mice.
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Affiliation(s)
- Samantha Lapehn
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States.
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Craig Harris
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
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46
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Wang N, Shibata Y, Paulo JA, Gygi SP, Rapoport TA. A conserved membrane curvature-generating protein is crucial for autophagosome formation in fission yeast. Nat Commun 2023; 14:4765. [PMID: 37553386 PMCID: PMC10409813 DOI: 10.1038/s41467-023-40530-4] [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: 09/22/2022] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
Organelles are shaped by curvature-generating proteins, which include the reticulons and REEPs that are involved in forming the endoplasmic reticulum (ER). A conserved REEP subfamily differs from the ER-shaping REEPs in abundance and membrane topology and has unidentified functions. Here, we show that Rop1, the single member of this family in the fission yeast Schizosacharomyces pombe, is crucial for the macroautophagy of organelles and cytosolic proteins. Rop1 is needed for the formation of phagophores, cup-like structures consisting of two closely apposed membrane sheets that encapsulate cargo. It is recruited at early stages to phagophores and is required for their maturation into autophagosomes. Rop1 function relies on its ability to generate high membrane curvature and on its colocalization with the autophagy component Atg2 that is thought to reside at the phagophore rim. We propose that Rop1 facilitates the formation and growth of the double-membrane structure of the autophagosome.
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Affiliation(s)
- Ning Wang
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Yoko Shibata
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
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47
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Gu L, Li X, Zhu W, Shen Y, Wang Q, Liu W, Zhang J, Zhang H, Li J, Li Z, Liu Z, Li C, Wang H. Ultrasensitive proteomics depicted an in-depth landscape for the very early stage of mouse maternal-to-zygotic transition. J Pharm Anal 2023; 13:942-954. [PMID: 37719194 PMCID: PMC10499587 DOI: 10.1016/j.jpha.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 09/19/2023] Open
Abstract
Single-cell or low-input multi-omics techniques have revolutionized the study of pre-implantation embryo development. However, the single-cell or low-input proteomic research in this field is relatively underdeveloped because of the higher threshold of the starting material for mammalian embryo samples and the lack of hypersensitive proteome technology. In this study, a comprehensive solution of ultrasensitive proteome technology (CS-UPT) was developed for single-cell or low-input mouse oocyte/embryo samples. The deep coverage and high-throughput routes significantly reduced the starting material and were selected by investigators based on their demands. Using the deep coverage route, we provided the first large-scale snapshot of the very early stage of mouse maternal-to-zygotic transition, including almost 5,500 protein groups from 20 mouse oocytes or zygotes for each sample. Moreover, significant protein regulatory networks centered on transcription factors and kinases between the MII oocyte and 1-cell embryo provided rich insights into minor zygotic genome activation.
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Affiliation(s)
- Lei Gu
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xumiao Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wencheng Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 200031, China
| | - Yi Shen
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Qinqin Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wenjun Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Junfeng Zhang
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Huiping Zhang
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Jingquan Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ziyi Li
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 200031, China
| | - Chen Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hui Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
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MacKenzie TMG, Cisneros R, Maynard RD, Snyder MP. Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome. Cells 2023; 12:1860. [PMID: 37508524 PMCID: PMC10377898 DOI: 10.3390/cells12141860] [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: 05/29/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
A phenotypic hallmark of cancer is aberrant transcriptional regulation. Transcriptional regulation is controlled by a complicated array of molecular factors, including the presence of transcription factors, the deposition of histone post-translational modifications, and long-range DNA interactions. Determining the molecular identity and function of these various factors is necessary to understand specific aspects of cancer biology and reveal potential therapeutic targets. Regulation of the genome by specific factors is typically studied using chromatin immunoprecipitation followed by sequencing (ChIP-Seq) that identifies genome-wide binding interactions through the use of factor-specific antibodies. A long-standing goal in many laboratories has been the development of a 'reverse-ChIP' approach to identify unknown binding partners at loci of interest. A variety of strategies have been employed to enable the selective biochemical purification of sequence-defined chromatin regions, including single-copy loci, and the subsequent analytical detection of associated proteins. This review covers mass spectrometry techniques that enable quantitative proteomics before providing a survey of approaches toward the development of strategies for the purification of sequence-specific chromatin as a 'reverse-ChIP' technique. A fully realized reverse-ChIP technique holds great potential for identifying cancer-specific targets and the development of personalized therapeutic regimens.
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Affiliation(s)
| | - Rocío Cisneros
- Sarafan ChEM-H/IMA Postbaccalaureate Fellow in Target Discovery, Stanford University, Stanford, CA 94305, USA
| | - Rajan D Maynard
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Genetics Department, Stanford University, Stanford, CA 94305, USA
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49
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Weiner S, Blennow K, Zetterberg H, Gobom J. Next-generation proteomics technologies in Alzheimer's disease: from clinical research to routine diagnostics. Expert Rev Proteomics 2023; 20:143-150. [PMID: 37701966 DOI: 10.1080/14789450.2023.2255752] [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: 05/21/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023]
Abstract
INTRODUCTION Clinical proteomics studies of Alzheimer's disease (AD) research aim to identify biomarkers useful for clinical research, diagnostics, and improve our understanding of the pathological processes involved in the disease. The rapidly increasing performance of proteomics technologies is likely to have great impact on AD research. AREAS COVERED We review recent proteomics approaches that have advanced the field of clinical AD research. Specifically, we discuss the application of targeted mass spectrometry (MS), labeling-based and label-free MS-based as well as affinity-based proteomics to AD biomarker development, underpinning their importance with the latest impactful clinical studies. We evaluate how proteomics technologies have been adapted to meet current challenges. Finally, we discuss the limitations and potential of proteomics techniques and whether their scope might extend beyond current research-based applications. EXPERT OPINION To date, proteomics technologies in the AD field have been largely limited to AD biomarker discovery. The recent development of the first successful disease-modifying treatments of AD will further increase the need for blood biomarkers for early, accurate diagnosis, and CSF biomarkers that reflect specific pathological processes. Proteomics has the potential to meet these requirements and to progress into clinical routine practice, provided that current limitations are overcome.
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Affiliation(s)
- Sophia Weiner
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Dementia Research Institute at UCL, London, UK
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
| | - Johan Gobom
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
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50
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Bowser BL, Robinson RAS. Enhanced Multiplexing Technology for Proteomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:379-400. [PMID: 36854207 DOI: 10.1146/annurev-anchem-091622-092353] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The identification of thousands of proteins and their relative levels of expression has furthered understanding of biological processes and disease and stimulated new systems biology hypotheses. Quantitative proteomics workflows that rely on analytical assays such as mass spectrometry have facilitated high-throughput measurements of proteins partially due to multiplexing. Multiplexing allows proteome differences across multiple samples to be measured simultaneously, resulting in more accurate quantitation, increased statistical robustness, reduced analysis times, and lower experimental costs. The number of samples that can be multiplexed has evolved from as few as two to more than 50, with studies involving more than 10 samples being denoted as enhanced multiplexing or hyperplexing. In this review, we give an update on emerging multiplexing proteomics techniques and highlight advantages and limitations for enhanced multiplexing strategies.
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Affiliation(s)
- Bailey L Bowser
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA;
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA;
- Department of Neurology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Memory and Alzheimer's Center, Nashville, Tennessee, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Brain Institute, Vanderbilt School of Medicine, Nashville, Tennessee, USA
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