1
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Soo PC, Lee CC, Shie MF, Patil AA, Descanzo MJN, Chin YC, Chen HA, Horng YT, Lin CB, Lee JJ, Chiang CK, Peng WP. Enhancing the sequence coverage of nanodiamond-extracted early secretory proteins from the Mycobacterium tuberculosis complex. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3464-3474. [PMID: 38804556 DOI: 10.1039/d4ay00314d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The unambiguous identification of protein species requires high sequence coverage. In this study, we successfully improved the sequence coverage of early secretory 10 kDa cell filtrate protein (CFP-10) and 6 kDa early secretory antigenic target (ESAT-6) proteins from the Mycobacterium tuberculosis complex (MTC) in broth culture media with the use of the 4-chloro-α-cyanocinnamic acid (Cl-CCA) matrix. Conventional matrices, α-cyano-hydroxy-cinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB), were also used for comparison. After nanodiamond (ND) extraction, the sequence coverage of the CFP-10 protein was 87% when CHCA and DHB matrices were used, and the ESAT-6 protein was not detected. On the other hand, the sequence coverage for ND-extracted CFP-10 and ESAT-6 could reach 94% and 100%, respectively, when the Cl-CCA matrix was used and with the removal of interference from bovine serum albumin (BSA) protein and α-crystallin (ACR) protein. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was also adopted to analyze the protein mass spectra. A total of 6 prominent ion signals were observed, including ESAT-6 protein peaks at mass-to-charge ratios (m/z) of ∼7931, ∼7974, ∼9768, and ∼9813 and CFP-10 protein peaks at m/z of ∼10 100 and ∼10 660. The ESAT-6 ion signals were always detected concurrently with CFP-10 ion signals, but CFP-10 ion signals could be detected alone without the ESAT-6 ion signals. Furthermore, the newly found ESAT-6 peaks were also confirmed using a Mag-Beads-Protein G kit with an ESAT-6 antibody to capture the ESAT-6 protein, which was also consistent with the sequence coverage analysis.
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Affiliation(s)
- Po-Chi Soo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Ching-Chieh Lee
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan.
| | - Meng-Fu Shie
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan.
| | - Avinash A Patil
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan.
| | | | - Ya-Ching Chin
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan.
| | - Hsi-An Chen
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan.
| | - Yu-Tze Horng
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Chih-Bin Lin
- Department of Internal Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
| | - Jen-Jyh Lee
- Department of Internal Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
| | - Cheng-Kang Chiang
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien, Taiwan
| | - Wen-Ping Peng
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan.
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2
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Felipe Fumero E, Walter C, Frenz JM, Seifert F, Alla V, Hennig T, Angenendt L, Hartmann W, Wolf S, Serve H, Oellerich T, Lenz G, Müller-Tidow C, Schliemann C, Huber O, Dugas M, Mann M, Jayavelu AK, Mikesch JH, Arteaga MF. Epigenetic control over the cell-intrinsic immune response antagonizes self-renewal in acute myeloid leukemia. Blood 2024; 143:2284-2299. [PMID: 38457355 DOI: 10.1182/blood.2023021640] [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: 06/29/2023] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 03/10/2024] Open
Abstract
ABSTRACT Epigenetic modulation of the cell-intrinsic immune response holds promise as a therapeutic approach for leukemia. However, current strategies designed for transcriptional activation of endogenous transposons and subsequent interferon type-I (IFN-I) response, show limited clinical efficacy. Histone lysine methylation is an epigenetic signature in IFN-I response associated with suppression of IFN-I and IFN-stimulated genes, suggesting histone demethylation as key mechanism of reactivation. In this study, we unveil the histone demethylase PHF8 as a direct initiator and regulator of cell-intrinsic immune response in acute myeloid leukemia (AML). Site-specific phosphorylation of PHF8 orchestrates epigenetic changes that upregulate cytosolic RNA sensors, particularly the TRIM25-RIG-I-IFIT5 axis, thereby triggering the cellular IFN-I response-differentiation-apoptosis network. This signaling cascade largely counteracts differentiation block and growth of human AML cells across various disease subtypes in vitro and in vivo. Through proteome analysis of over 200 primary AML bone marrow samples, we identify a distinct PHF8/IFN-I signature in half of the patient population, without significant associations with known clinically or genetically defined AML subgroups. This profile was absent in healthy CD34+ hematopoietic progenitor cells, suggesting therapeutic applicability in a large fraction of patients with AML. Pharmacological support of PHF8 phosphorylation significantly impairs the growth in samples from patients with primary AML. These findings provide novel opportunities for harnessing the cell-intrinsic immune response in the development of immunotherapeutic strategies against AML.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Epigenesis, Genetic
- Animals
- Histone Demethylases/genetics
- Histone Demethylases/metabolism
- Mice
- Interferon Type I/metabolism
- Cell Self Renewal
- Gene Expression Regulation, Leukemic
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Affiliation(s)
| | - Carolin Walter
- Institute of Medical Informatics, Gerhard-Domagk-Institute for Pathology, University Hospital Muenster, Muenster, Germany
| | - Joris Maximillian Frenz
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Center, University of Heidelberg, Heidelberg, Germany
| | - Franca Seifert
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
| | - Vijay Alla
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
| | - Thorben Hennig
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Center, University of Heidelberg, Heidelberg, Germany
| | - Linus Angenendt
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Basel, Switzerland
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk-Institute for Pathology, University Hospital Muenster, Muenster, Germany
| | - Sebastian Wolf
- Department of Hematology/Oncology, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Hubert Serve
- Department of Hematology/Oncology, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Thomas Oellerich
- Department of Hematology/Oncology, Johann Wolfgang Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Georg Lenz
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
| | | | | | - Otmar Huber
- Department of Biochemistry II, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ashok Kumar Jayavelu
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Center, University of Heidelberg, Heidelberg, Germany
| | - Jan-Henrik Mikesch
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
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3
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Doll S, Schweizer L, Bollwein C, Steiger K, Pfarr N, Walker M, Wörtler K, Knebel C, von Eisenhart-Rothe R, Hartmann W, Weichert W, Mann M, Kuhn PH, Specht K. Proteomic Characterization of Undifferentiated Small Round Cell Sarcomas with EWSR1- and CIC::DUX4-Translocations Reveals Diverging Tumor Biology and Distinct Diagnostic Markers. Mod Pathol 2024:100511. [PMID: 38705279 DOI: 10.1016/j.modpat.2024.100511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/07/2024]
Abstract
Undifferentiated small round cell sarcomas of bone and soft tissue (USRS) are a group of tumors with heterogenic genomic alterations sharing similar morphology. In the present study, we performed a comparative large-scale proteomic analysis of USRS (n=42) with diverse genomic translocations including classic Ewing sarcomas with EWSR1::FLI1 fusions (n=24) or EWSR1::ERG - fusions (n=4), sarcomas with an EWSR1 - rearrangement (n=2), CIC::DUX4 fusion (n=8), as well as tumors classified as USRS with no genetic data available (n=4). Proteins extracted from formalin-fixed, paraffin-embedded (FFPE) pretherapeutic biopsies were analyzed qualitatively and quantitatively using shot gun mass spectrometry (MS). More than 8000 protein groups could be quantified using data-independent acquisition. Unsupervised hierarchical cluster analysis based on proteomic data allowed stratification of the 42 cases into distinct groups reflecting the different molecular genotypes. Protein signatures that significantly correlated with the respective genomic translocations were identified and used to generate a heatmap of all 42 sarcomas with assignment of cases with unknown molecular genetic data to either the EWSR1- or CIC-rearranged groups. MS-based prediction of sarcoma subtypes was molecularly confirmed in two cases where next-generation sequencing was technically feasible. MS also detected proteins routinely used in the immunohistochemical approach for the differential diagnosis of USRS. BCL11B highly expressed in Ewing sarcomas and Bach2 as well as ETS-1 highly expressed in CIC::DUX4-associated sarcomas, were among proteins identified by the present proteomic study and were chosen for immunohistochemical confirmation of MS data in our study cohort. Differential expression of these 3 markers in the two genetic groups were further validated in an independent cohort of n= 34 USRS. Finally, our proteomic results point towards diverging signaling pathways in the different USRS subgroups.
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Affiliation(s)
- Sophia Doll
- Max-Planck-Institute for Biochemistry, Am Klopferspitz 18A, Martinsried, Germany
| | - Lisa Schweizer
- Max-Planck-Institute for Biochemistry, Am Klopferspitz 18A, Martinsried, Germany
| | - Christine Bollwein
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Nicole Pfarr
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Maria Walker
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Klaus Wörtler
- Musculoskeletal Radiology Section, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Carolin Knebel
- Department of Orthopaedic Surgery, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Ruediger von Eisenhart-Rothe
- Department of Orthopaedic Surgery, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | | | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany; German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Mann
- Max-Planck-Institute for Biochemistry, Am Klopferspitz 18A, Martinsried, Germany
| | - Peer-Hendrik Kuhn
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Katja Specht
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany.
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4
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Steigerwald S, Sinha A, Fort KL, Zeng WF, Niu L, Wichmann C, Kreutzmann A, Mourad D, Aizikov K, Grinfeld D, Makarov A, Mann M, Meier F. Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis. Mol Cell Proteomics 2024; 23:100713. [PMID: 38184013 PMCID: PMC10851225 DOI: 10.1016/j.mcpro.2024.100713] [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: 08/30/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024] Open
Abstract
Optimizing data-independent acquisition methods for proteomics applications often requires balancing spectral resolution and acquisition speed. Here, we describe a real-time full mass range implementation of the phase-constrained spectrum deconvolution method (ΦSDM) for Orbitrap mass spectrometry that increases mass resolving power without increasing scan time. Comparing its performance to the standard enhanced Fourier transformation signal processing revealed that the increased resolving power of ΦSDM is beneficial in areas of high peptide density and comes with a greater ability to resolve low-abundance signals. In a standard 2 h analysis of a 200 ng HeLa digest, this resulted in an increase of 16% in the number of quantified peptides. As the acquisition speed becomes even more important when using fast chromatographic gradients, we further applied ΦSDM methods to a range of shorter gradient lengths (21, 12, and 5 min). While ΦSDM improved identification rates and spectral quality in all tested gradients, it proved particularly advantageous for the 5 min gradient. Here, the number of identified protein groups and peptides increased by >15% in comparison to enhanced Fourier transformation processing. In conclusion, ΦSDM is an alternative signal processing algorithm for processing Orbitrap data that can improve spectral quality and benefit quantitative accuracy in typical proteomics experiments, especially when using short gradients.
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Affiliation(s)
- Sophia Steigerwald
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ankit Sinha
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kyle L Fort
- Thermo Fisher Scientific (GmbH), Bremen, Germany
| | - Wen-Feng Zeng
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lili Niu
- Department Clinical Proteomics, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Christoph Wichmann
- Department Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | | | | | | | - Matthias Mann
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Department Clinical Proteomics, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Florian Meier
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Functional Proteomics, Jena University Hospital, Jena, Germany.
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5
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Teunissen MBM, Pilgaard Møller LB, Løvendorf MB, Skov L, Bonefeld CM, Bekkenk MW, Clark RA, Mann M, Dyring-Andersen B. In-Depth Proteomic Map of Innate Lymphoid Cells from Healthy Human Skin and Blood. J Invest Dermatol 2024; 144:316-330.e3. [PMID: 37544588 DOI: 10.1016/j.jid.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/23/2023] [Accepted: 07/14/2023] [Indexed: 08/08/2023]
Abstract
Innate lymphoid cells (ILCs) are essential players in the skin-associated immune system, nevertheless little is known about their proteomes and proteomic diversity. In this study, we describe about 6,600 proteins constitutively expressed by ILC2s and ILC3s from healthy human skin and blood using state-of-the-art proteomics. Although the vast majority of proteins was expressed by both ILC subsets and in both compartments, the skin ILC2s and ILC3s were more distinct than their counterparts in blood. Only skin ILC3s expressed uniquely detected proteins. Our in-depth proteomic dataset allowed us to define the cluster of differentiation marker profiles of the ILC subsets, explore distribution and abundance of proteins known to have immunological functions, as well as identify subset-specific proteins that have not previously been implicated in ILC biology. Taken together, our analyses substantially expand understanding of the protein expression signatures of ILC subsets. Going forward, these proteomic datasets will serve as valuable resources for future studies of ILC biology.
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Affiliation(s)
- Marcel B M Teunissen
- Department of Dermatology and Amsterdam institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
| | - Line B Pilgaard Møller
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marianne B Løvendorf
- Department of Dermatology and Allergy, Copenhagen University Hospital - Herlev and Gentofte Hospital, Hellerup, Denmark; The Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lone Skov
- Department of Dermatology and Allergy, Copenhagen University Hospital - Herlev and Gentofte Hospital, Hellerup, Denmark
| | - Charlotte M Bonefeld
- The Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marcel W Bekkenk
- Department of Dermatology and Amsterdam institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Rachael A Clark
- Department of Dermatology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Matthias Mann
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Beatrice Dyring-Andersen
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Dermatology and Allergy, Copenhagen University Hospital - Herlev and Gentofte Hospital, Hellerup, Denmark; The Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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6
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Cervone DT, Moreno-Justicia R, Quesada JP, Deshmukh AS. Mass spectrometry-based proteomics approaches to interrogate skeletal muscle adaptations to exercise. Scand J Med Sci Sports 2024; 34:e14334. [PMID: 36973869 DOI: 10.1111/sms.14334] [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: 11/08/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 03/29/2023]
Abstract
Acute exercise and chronic exercise training elicit beneficial whole-body changes in physiology that ultimately depend on profound alterations to the dynamics of tissue-specific proteins. Since the work accomplished during exercise owes predominantly to skeletal muscle, it has received the majority of interest from exercise scientists that attempt to unravel adaptive mechanisms accounting for salutary metabolic effects and performance improvements that arise from training. Contemporary scientists are also beginning to use mass spectrometry-based proteomics, which is emerging as a powerful approach to interrogate the muscle protein signature in a more comprehensive manner. Collectively, these technologies facilitate the analysis of skeletal muscle protein dynamics from several viewpoints, including changes to intracellular proteins (expression proteomics), secreted proteins (secretomics), post-translational modifications as well as fiber-, cell-, and organelle-specific changes. This review aims to highlight recent literature that has leveraged new workflows and advances in mass spectrometry-based proteomics to further our understanding of training-related changes in skeletal muscle. We call attention to untapped areas in skeletal muscle proteomics research relating to exercise training and metabolism, as well as basic points of contention when applying mass spectrometry-based analyses, particularly in the study of human biology. We further encourage researchers to couple the hypothesis-generating and descriptive nature of omics data with functional analyses that propel our understanding of the complex adaptive responses in skeletal muscle that occur with acute and chronic exercise.
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Affiliation(s)
- Daniel T Cervone
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Roger Moreno-Justicia
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Júlia Prats Quesada
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Clinical Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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7
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Zurawska M, Basik M, Aguilar-Mahecha A, Dadlez M, Domanski D. A micro-flow, high-pH, reversed-phase peptide fractionation and collection system for targeted and in-depth proteomics of low-abundance proteins in limiting samples. MethodsX 2023; 11:102306. [PMID: 37577163 PMCID: PMC10413349 DOI: 10.1016/j.mex.2023.102306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/29/2023] [Indexed: 08/15/2023] Open
Abstract
We present a method and a simple system for high-pH RP-LC peptide fractionation of small sample amounts (30-60 µg), at micro-flow rates with micro-liter fraction collection using ammonium bicarbonate as an optimized buffer for system stability and robustness. The method is applicable to targeted mass spectrometry approaches and to in-depth proteomic studies where the amount of sample is limited. Using targeted proteomics with peptide standards, we present the method's analytical parameters, and potential in increasing the detection of low-abundance proteins that are difficult to quantify with direct targeted or global LC-MS analyses. This fractionation system increased peptide signals by up to 18-fold, while maintaining high quantitative precision, with high fractionation reproducibility across varied sample sets. In real applications, it increased the detection of targeted endogenous peptides by two-fold in a 25 cell-cycle-control protein panel, and in-depth MS analyses of nuclear extracts, it allowed the detection of up to 8,896 proteins with 138,417 peptides in 24-concatenated fractions compared to 3,344 proteins with 23,093 peptides without fractionation. In a relevant biological problem of CDK4/6-inhibitors and breast cancer, the method reproduced known information and revealed novel insights, highlighting that it can be successfully applied in studies involving low-abundance proteins and limited samples. •Tested nine high-pH buffer/solvent systems to obtain a robust, effective, and reproducible micro-flow fractionation method which was devoid of commonly encountered LC clogging/pressure issues after months of use.•Peptide enrichment method to improve detection and quantitation of low-abundance proteins in targeted and in-depth proteomic studies.•Can be applied to diverse protein samples where the available amount is limited.
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Affiliation(s)
- Marta Zurawska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Mark Basik
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | | | - Michal Dadlez
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dominik Domanski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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8
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Michaelis AC, Brunner AD, Zwiebel M, Meier F, Strauss MT, Bludau I, Mann M. The social and structural architecture of the yeast protein interactome. Nature 2023; 624:192-200. [PMID: 37968396 PMCID: PMC10700138 DOI: 10.1038/s41586-023-06739-5] [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: 11/18/2022] [Accepted: 10/11/2023] [Indexed: 11/17/2023]
Abstract
Cellular functions are mediated by protein-protein interactions, and mapping the interactome provides fundamental insights into biological systems. Affinity purification coupled to mass spectrometry is an ideal tool for such mapping, but it has been difficult to identify low copy number complexes, membrane complexes and complexes that are disrupted by protein tagging. As a result, our current knowledge of the interactome is far from complete, and assessing the reliability of reported interactions is challenging. Here we develop a sensitive high-throughput method using highly reproducible affinity enrichment coupled to mass spectrometry combined with a quantitative two-dimensional analysis strategy to comprehensively map the interactome of Saccharomyces cerevisiae. Thousand-fold reduced volumes in 96-well format enabled replicate analysis of the endogenous GFP-tagged library covering the entire expressed yeast proteome1. The 4,159 pull-downs generated a highly structured network of 3,927 proteins connected by 31,004 interactions, doubling the number of proteins and tripling the number of reliable interactions compared with existing interactome maps2. This includes very-low-abundance epigenetic complexes, organellar membrane complexes and non-taggable complexes inferred by abundance correlation. This nearly saturated interactome reveals that the vast majority of yeast proteins are highly connected, with an average of 16 interactors. Similar to social networks between humans, the average shortest distance between proteins is 4.2 interactions. AlphaFold-Multimer provided novel insights into the functional roles of previously uncharacterized proteins in complexes. Our web portal ( www.yeast-interactome.org ) enables extensive exploration of the interactome dataset.
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Affiliation(s)
| | - Andreas-David Brunner
- Max-Planck Institute of Biochemistry, Martinsried, Germany
- Drug Discovery Sciences, Boehringer Ingelheim Pharma, Biberach Riss, Germany
| | | | - Florian Meier
- Max-Planck Institute of Biochemistry, Martinsried, Germany
- Functional Proteomics, Jena University Hospital, Jena, Germany
| | | | - Isabell Bludau
- Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Max-Planck Institute of Biochemistry, Martinsried, Germany.
- NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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9
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Chen Y, Du Z, Zhao H, Fang W, Liu T, Zhang Y, Zhang W, Qin W. SPPUSM: An MS/MS spectra merging strategy for improved low-input and single-cell proteome identification. Anal Chim Acta 2023; 1279:341793. [PMID: 37827637 DOI: 10.1016/j.aca.2023.341793] [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: 06/11/2023] [Revised: 08/26/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023]
Abstract
Single and rare cell analysis provides unique insights into the investigation of biological processes and disease progress by resolving the cellular heterogeneity that is masked by bulk measurements. Although many efforts have been made, the techniques used to measure the proteome in trace amounts of samples or in single cells still lag behind those for DNA and RNA due to the inherent non-amplifiable nature of proteins and the sensitivity limitation of current mass spectrometry. Here, we report an MS/MS spectra merging strategy termed SPPUSM (same precursor-produced unidentified spectra merging) for improved low-input and single-cell proteome data analysis. In this method, all the unidentified MS/MS spectra from multiple test files are first extracted. Then, the corresponding MS/MS spectra produced by the same precursor ion from different files are matched according to their precursor mass and retention time (RT) and are merged into one new spectrum. The newly merged spectra with more fragment ions are next searched against the database to increase the MS/MS spectra identification and proteome coverage. Further improvement can be achieved by increasing the number of test files and spectra to be merged. Up to 18.2% improvement in protein identification was achieved for 1 ng HeLa peptides by SPPUSM. Reliability evaluation by the "entrapment database" strategy using merged spectra from human and E. coli revealed a marginal error rate for the proposed method. For application in single cell proteome (SCP) study, identification enhancement of 28%-61% was achieved for proteins for different SCP data. Furthermore, a lower abundance was found for the SPPUSM-identified peptides, indicating its potential for more sensitive low sample input and SCP studies.
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Affiliation(s)
- Yongle Chen
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Zhuokun Du
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Hongxian Zhao
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Wei Fang
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Tong Liu
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Wanjun Zhang
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China; College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China
| | - Weijie Qin
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China; College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China.
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10
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Schweizer L, Schaller T, Zwiebel M, Karayel Ö, Müller‐Reif JB, Zeng W, Dintner S, Nordmann TM, Hirschbühl K, Märkl B, Claus R, Mann M. Quantitative multiorgan proteomics of fatal COVID-19 uncovers tissue-specific effects beyond inflammation. EMBO Mol Med 2023; 15:e17459. [PMID: 37519267 PMCID: PMC10493576 DOI: 10.15252/emmm.202317459] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
SARS-CoV-2 may directly and indirectly damage lung tissue and other host organs, but there are few system-wide, untargeted studies of these effects on the human body. Here, we developed a parallelized mass spectrometry (MS) proteomics workflow enabling the rapid, quantitative analysis of hundreds of virus-infected FFPE tissues. The first layer of response to SARS-CoV-2 in all tissues was dominated by circulating inflammatory molecules. Beyond systemic inflammation, we differentiated between systemic and true tissue-specific effects to reflect distinct COVID-19-associated damage patterns. Proteomic changes in the lungs resembled those of diffuse alveolar damage (DAD) in non-COVID-19 patients. Extensive organ-specific changes were also evident in the kidneys, liver, and lymphatic and vascular systems. Secondary inflammatory effects in the brain were related to rearrangements in neurotransmitter receptors and myelin degradation. These MS-proteomics-derived results contribute substantially to our understanding of COVID-19 pathomechanisms and suggest strategies for organ-specific therapeutic interventions.
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Affiliation(s)
- Lisa Schweizer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Tina Schaller
- Pathology, Medical FacultyUniversity of AugsburgAugsburgGermany
| | - Maximilian Zwiebel
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Özge Karayel
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
Department of Physiological ChemistryGenentechSouth San FranciscoUSA
| | | | - Wen‐Feng Zeng
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | | | - Thierry M Nordmann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Klaus Hirschbühl
- Hematology and Oncology, Medical FacultyUniversity of AugsburgAugsburgGermany
| | - Bruno Märkl
- Pathology, Medical FacultyUniversity of AugsburgAugsburgGermany
| | - Rainer Claus
- Pathology, Medical FacultyUniversity of AugsburgAugsburgGermany
- Hematology and Oncology, Medical FacultyUniversity of AugsburgAugsburgGermany
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
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11
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Bahrami E, Schmid JP, Jurinovic V, Becker M, Wirth AK, Ludwig R, Kreissig S, Duque Angel TV, Amend D, Hunt K, Öllinger R, Rad R, Frenz JM, Solovey M, Ziemann F, Mann M, Vick B, Wichmann C, Herold T, Jayavelu AK, Jeremias I. Combined proteomics and CRISPR‒Cas9 screens in PDX identify ADAM10 as essential for leukemia in vivo. Mol Cancer 2023; 22:107. [PMID: 37422628 PMCID: PMC10329331 DOI: 10.1186/s12943-023-01803-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 06/08/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Acute leukemias represent deadly malignancies that require better treatment. As a challenge, treatment is counteracted by a microenvironment protecting dormant leukemia stem cells. METHODS To identify responsible surface proteins, we performed deep proteome profiling on minute numbers of dormant patient-derived xenograft (PDX) leukemia stem cells isolated from mice. Candidates were functionally screened by establishing a comprehensive CRISPR‒Cas9 pipeline in PDX models in vivo. RESULTS A disintegrin and metalloproteinase domain-containing protein 10 (ADAM10) was identified as an essential vulnerability required for the survival and growth of different types of acute leukemias in vivo, and reconstitution assays in PDX models confirmed the relevance of its sheddase activity. Of translational importance, molecular or pharmacological targeting of ADAM10 reduced PDX leukemia burden, cell homing to the murine bone marrow and stem cell frequency, and increased leukemia response to conventional chemotherapy in vivo. CONCLUSIONS These findings identify ADAM10 as an attractive therapeutic target for the future treatment of acute leukemias.
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Affiliation(s)
- Ehsan Bahrami
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
| | - Jan Philipp Schmid
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
| | - Vindi Jurinovic
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Department of Medicine III, LMU University Hospital, LMU Munich, Munich, Germany
| | - Martin Becker
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
| | - Anna-Katharina Wirth
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
| | - Romina Ludwig
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
| | - Sophie Kreissig
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Tania Vanessa Duque Angel
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
| | - Diana Amend
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
| | - Katharina Hunt
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
| | - Rupert Öllinger
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, and Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, Technische Universität München, Munich, Germany
| | - Roland Rad
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, and Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, Technische Universität München, Munich, Germany
| | - Joris Maximilian Frenz
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
| | - Maria Solovey
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Chair of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Munich, Germany
| | - Frank Ziemann
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Department of Medicine III, LMU University Hospital, LMU Munich, Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
| | - Christian Wichmann
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Tobias Herold
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Department of Medicine III, LMU University Hospital, LMU Munich, Munich, Germany
| | - Ashok Kumar Jayavelu
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Feodor-Lynen-Str. 21, Munich, 81377 Germany
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
- Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital, LMU Munich, Munich, Germany
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12
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Swietlik JJ, Bärthel S, Falcomatà C, Fink D, Sinha A, Cheng J, Ebner S, Landgraf P, Dieterich DC, Daub H, Saur D, Meissner F. Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation. Nat Commun 2023; 14:2642. [PMID: 37156840 PMCID: PMC10167354 DOI: 10.1038/s41467-023-38171-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Cell-selective proteomics is a powerful emerging concept to study heterocellular processes in tissues. However, its high potential to identify non-cell-autonomous disease mechanisms and biomarkers has been hindered by low proteome coverage. Here, we address this limitation and devise a comprehensive azidonorleucine labeling, click chemistry enrichment, and mass spectrometry-based proteomics and secretomics strategy to dissect aberrant signals in pancreatic ductal adenocarcinoma (PDAC). Our in-depth co-culture and in vivo analyses cover more than 10,000 cancer cell-derived proteins and reveal systematic differences between molecular PDAC subtypes. Secreted proteins, such as chemokines and EMT-promoting matrisome proteins, associated with distinct macrophage polarization and tumor stromal composition, differentiate classical and mesenchymal PDAC. Intriguingly, more than 1,600 cancer cell-derived proteins including cytokines and pre-metastatic niche formation-associated factors in mouse serum reflect tumor activity in circulation. Our findings highlight how cell-selective proteomics can accelerate the discovery of diagnostic markers and therapeutic targets in cancer.
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Affiliation(s)
- Jonathan J Swietlik
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefanie Bärthel
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Chiara Falcomatà
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Diana Fink
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Ankit Sinha
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jingyuan Cheng
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefan Ebner
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Peter Landgraf
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Daniela C Dieterich
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Henrik Daub
- NEOsphere Biotechnologies GmbH, Martinsried, Germany
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.
| | - Felix Meissner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany.
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13
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Phlairaharn T, Ye Z, Krismer E, Pedersen AK, Pietzner M, Olsen JV, Schoof EM, Searle BC. Optimizing linear ion trap data independent acquisition towards single cell proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529444. [PMID: 36865114 PMCID: PMC9980145 DOI: 10.1101/2023.02.21.529444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
A linear ion trap (LIT) is an affordable, robust mass spectrometer that proves fast scanning speed and high sensitivity, where its primary disadvantage is inferior mass accuracy compared to more commonly used time-of-flight (TOF) or orbitrap (OT) mass analyzers. Previous efforts to utilize the LIT for low-input proteomics analysis still rely on either built-in OTs for collecting precursor data or OT-based library generation. Here, we demonstrate the potential versatility of the LIT for low-input proteomics as a stand-alone mass analyzer for all mass spectrometry measurements, including library generation. To test this approach, we first optimized LIT data acquisition methods and performed library-free searches with and without entrapment peptides to evaluate both the detection and quantification accuracy. We then generated matrix-matched calibration curves to estimate the lower limit of quantification using only 10 ng of starting material. While LIT-MS1 measurements provided poor quantitative accuracy, LIT-MS2 measurements were quantitatively accurate down to 0.5 ng on column. Finally, we optimized a suitable strategy for spectral library generation from low-input material, which we used to analyze single-cell samples by LIT-DIA using LIT-based libraries generated from as few as 40 cells.
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14
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Calnexin, More Than Just a Molecular Chaperone. Cells 2023; 12:cells12030403. [PMID: 36766745 PMCID: PMC9913998 DOI: 10.3390/cells12030403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Calnexin is a type I integral endoplasmic reticulum (ER) membrane protein with an N-terminal domain that resides in the lumen of the ER and a C-terminal domain that extends into the cytosol. Calnexin is commonly referred to as a molecular chaperone involved in the folding and quality control of membrane-associated and secreted proteins, a function that is attributed to its ER- localized domain with a structure that bears a strong resemblance to another luminal ER chaperone and Ca2+-binding protein known as calreticulin. Studies have discovered that the cytosolic C-terminal domain of calnexin undergoes distinct post-translational modifications and interacts with a variety of proteins. Here, we discuss recent findings and hypothesize that the post-translational modifications of the calnexin C-terminal domain and its interaction with specific cytosolic proteins play a role in coordinating ER functions with events taking place in the cytosol and other cellular compartments.
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15
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Zhou Y, Sun R, Li S, Liang X, Qian L, Yue L, Guo T. High-Throughput and In-Depth Proteomic Profiling of 5 μL Plasma and Serum Using TMTpro 16-Plex. Methods Mol Biol 2023; 2628:81-92. [PMID: 36781780 DOI: 10.1007/978-1-0716-2978-9_6] [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: 04/25/2023]
Abstract
High-throughput and in-depth proteomic analysis of plasma and serum samples remains challenging due to the presence of multiple high-abundance proteins. Here, we provide a detailed protocol for proteomic analysis of serum and plasma specimens using a high-abundance protein depletion kit and TMTpro 16-plex reagents. This method requires only 5 μL serum or plasma, identifying and quantifying about 1000 proteins. A batch of 16 samples can be processed in 36 h. On average, each sample consumes about 1.5 h of mass spectrometer instrument time. Overall, our method can identify proteins across six orders of magnitude with high reproducibility (CV < 20%) using a shorter instrument time and less sample volume compared to existing methods. Thus, the method is suitable to be applied to large-scale proteomic studies.
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Affiliation(s)
- Yan Zhou
- iMarker lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Rui Sun
- iMarker lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Sainan Li
- iMarker lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Xiao Liang
- iMarker lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Liujia Qian
- iMarker lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Liang Yue
- iMarker lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Tiannan Guo
- iMarker lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China.
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16
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Bhatia HS, Brunner AD, Öztürk F, Kapoor S, Rong Z, Mai H, Thielert M, Ali M, Al-Maskari R, Paetzold JC, Kofler F, Todorov MI, Molbay M, Kolabas ZI, Negwer M, Hoeher L, Steinke H, Dima A, Gupta B, Kaltenecker D, Caliskan ÖS, Brandt D, Krahmer N, Müller S, Lichtenthaler SF, Hellal F, Bechmann I, Menze B, Theis F, Mann M, Ertürk A. Spatial proteomics in three-dimensional intact specimens. Cell 2022; 185:5040-5058.e19. [PMID: 36563667 DOI: 10.1016/j.cell.2022.11.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/13/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]
Abstract
Spatial molecular profiling of complex tissues is essential to investigate cellular function in physiological and pathological states. However, methods for molecular analysis of large biological specimens imaged in 3D are lacking. Here, we present DISCO-MS, a technology that combines whole-organ/whole-organism clearing and imaging, deep-learning-based image analysis, robotic tissue extraction, and ultra-high-sensitivity mass spectrometry. DISCO-MS yielded proteome data indistinguishable from uncleared samples in both rodent and human tissues. We used DISCO-MS to investigate microglia activation along axonal tracts after brain injury and characterized early- and late-stage individual amyloid-beta plaques in a mouse model of Alzheimer's disease. DISCO-bot robotic sample extraction enabled us to study the regional heterogeneity of immune cells in intact mouse bodies and aortic plaques in a complete human heart. DISCO-MS enables unbiased proteome analysis of preclinical and clinical tissues after unbiased imaging of entire specimens in 3D, identifying diagnostic and therapeutic opportunities for complex diseases. VIDEO ABSTRACT.
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Affiliation(s)
- Harsharan Singh Bhatia
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Andreas-David Brunner
- Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Str. 65, D-88400 Biberach Riss, Germany
| | - Furkan Öztürk
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Saketh Kapoor
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Zhouyi Rong
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Hongcheng Mai
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Marvin Thielert
- Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Mayar Ali
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Graduate School of Neuroscience (GSN), 82152 Munich, Germany
| | - Rami Al-Maskari
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany
| | - Johannes Christian Paetzold
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany; Biomedical Image Analysis Group, Department of Computing, Imperial College London, London SW7 2AZ, UK
| | - Florian Kofler
- Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany; Helmholtz AI, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Neuroradiology, Klinikum rechts der Isar, 81675 Munich, Germany
| | - Mihail Ivilinov Todorov
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Muge Molbay
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Zeynep Ilgin Kolabas
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Graduate School of Neuroscience (GSN), 82152 Munich, Germany
| | - Moritz Negwer
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Luciano Hoeher
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Hanno Steinke
- Institute of Anatomy, University of Leipzig, 04109 Leipzig, Germany
| | - Alina Dima
- Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany
| | - Basavdatta Gupta
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Doris Kaltenecker
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Institute for Diabetes and Cancer, Helmholz Zentrum München, 85764 Neuherberg, Germany
| | - Özüm Sehnaz Caliskan
- Institute for Diabetes and Obesity, Helmholz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research, Helmholz Zentrum München, 85764 Neuherberg, Germany
| | - Daniel Brandt
- Institute for Diabetes and Obesity, Helmholz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research, Helmholz Zentrum München, 85764 Neuherberg, Germany
| | - Natalie Krahmer
- Institute for Diabetes and Obesity, Helmholz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research, Helmholz Zentrum München, 85764 Neuherberg, Germany
| | - Stephan Müller
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Stefan Frieder Lichtenthaler
- Graduate School of Neuroscience (GSN), 82152 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Farida Hellal
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Ingo Bechmann
- Institute of Anatomy, University of Leipzig, 04109 Leipzig, Germany
| | - Bjoern Menze
- Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany; Department for Quantitative Biomedicine, University of Zurich, 8006 Zurich, Switzerland
| | - Fabian Theis
- Institute of Computational Biology, Helmholz Zentrum München, 85764 Neuherberg, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany; Department of Mathematics, Technical University of Munich, 85748 Garching, Germany
| | - Matthias Mann
- Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Ali Ertürk
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Graduate School of Neuroscience (GSN), 82152 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany.
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17
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Reduced mitochondria provide an essential function for the cytosolic methionine cycle. Curr Biol 2022; 32:5057-5068.e5. [PMID: 36347252 PMCID: PMC9746703 DOI: 10.1016/j.cub.2022.10.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/15/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
The loss of mitochondria in oxymonad protists has been associated with the redirection of the essential Fe-S cluster assembly to the cytosol. Yet as our knowledge of diverse free-living protists broadens, the list of functions of their mitochondrial-related organelles (MROs) expands. We revealed another such function in the closest oxymonad relative, Paratrimastix pyriformis, after we solved the proteome of its MRO with high accuracy, using localization of organelle proteins by isotope tagging (LOPIT). The newly assigned enzymes connect to the glycine cleavage system (GCS) and produce folate derivatives with one-carbon units and formate. These are likely to be used by the cytosolic methionine cycle involved in S-adenosyl methionine recycling. The data provide consistency with the presence of the GCS in MROs of free-living species and its absence in most endobionts, which typically lose the methionine cycle and, in the case of oxymonads, the mitochondria.
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18
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Pacakova L, Harant K, Volf P, Lestinova T. Three types of Leishmania mexicana amastigotes: Proteome comparison by quantitative proteomic analysis. Front Cell Infect Microbiol 2022; 12:1022448. [DOI: 10.3389/fcimb.2022.1022448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
Leishmania is the unicellular parasite transmitted by phlebotomine sand fly bite. It exists in two different forms; extracellular promastigotes, occurring in the gut of sand flies, and intracellular, round-shaped amastigotes residing mainly in vertebrate macrophages. As amastigotes originating from infected animals are often present in insufficient quality and quantity, two alternative types of amastigotes were introduced for laboratory experiments: axenic amastigotes and amastigotes from macrophages infected in vitro. Nevertheless, there is very little information about the degree of similarity/difference among these three types of amastigotes on proteomic level, whose comparison is crucial for assessing the suitability of using alternative types of amastigotes in experiments. In this study, L. mexicana amastigotes obtained from lesion of infected BALB/c mice were proteomically compared with alternatively cultivated amastigotes (axenic and macrophage-derived ones). Amastigotes of all three types were isolated, individually treated and analysed by LC-MS/MS proteomic analysis with quantification using TMT10-plex isobaric labeling. Significant differences were observed in the abundance of metabolic enzymes, virulence factors and proteins involved in translation and condensation of DNA. The most pronounced differences were observed between axenic amastigotes and lesion-derived amastigotes, macrophage-derived amastigotes were mostly intermediate between axenic and lesion-derived ones.
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19
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King CD, Kapp KL, Arul AB, Choi MJ, Robinson RAS. Advancements in automation for plasma proteomics sample preparation. Mol Omics 2022; 18:828-839. [PMID: 36048090 PMCID: PMC9879274 DOI: 10.1039/d2mo00122e] [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: 01/28/2023]
Abstract
Automation is necessary to increase sample processing throughput for large-scale clinical analyses. Replacement of manual pipettes with robotic liquid handler systems is especially helpful in processing blood-based samples, such as plasma and serum. These samples are very heterogenous, and protein expression can vary greatly from sample-to-sample, even for healthy controls. Detection of true biological changes requires that variation from sample preparation steps and downstream analytical detection methods, such as mass spectrometry, remains low. In this mini-review, we discuss plasma proteomics protocols and the benefits of automation towards enabling detection of low abundant proteins and providing low sample error and increased sample throughput. This discussion includes considerations for automation of major sample depletion and/or enrichment strategies for plasma toward mass spectrometry detection.
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Affiliation(s)
- Christina D King
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Kathryn L Kapp
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee 37232, USA
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20
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Phlairaharn T, Grégoire S, Woltereck LR, Petrosius V, Furtwängler B, Searle BC, Schoof EM. High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps. J Proteome Res 2022; 21:2815-2826. [DOI: 10.1021/acs.jproteome.2c00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Teeradon Phlairaharn
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
- Department of Chemistry, Technical University of Munich, Munich 80333, Germany
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, United States
| | - Samuel Grégoire
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
- Computational Biology Unit, de Duve Institute, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Lukas R. Woltereck
- Department of Chemistry, Technical University of Munich, Munich 80333, Germany
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
| | - Valdemaras Petrosius
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
| | - Benjamin Furtwängler
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen 2200, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Brian C. Searle
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, United States
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Erwin M. Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
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21
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Diamanti K, Cavalli M, Pereira MJ, Pan G, Castillejo-López C, Kumar C, Mundt F, Komorowski J, Deshmukh AS, Mann M, Korsgren O, Eriksson JW, Wadelius C. Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes, and normal tissues. CELL REPORTS MEDICINE 2022; 3:100763. [PMID: 36198307 PMCID: PMC9589007 DOI: 10.1016/j.xcrm.2022.100763] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/02/2022] [Accepted: 09/13/2022] [Indexed: 11/28/2022]
Abstract
Environmental and genetic factors cause defects in pancreatic islets driving type 2 diabetes (T2D) together with the progression of multi-tissue insulin resistance. Mass spectrometry proteomics on samples from five key metabolic tissues of a cross-sectional cohort of 43 multi-organ donors provides deep coverage of their proteomes. Enrichment analysis of Gene Ontology terms provides a tissue-specific map of altered biological processes across healthy, prediabetes (PD), and T2D subjects. We find widespread alterations in several relevant biological pathways, including increase in hemostasis in pancreatic islets of PD, increase in the complement cascade in liver and pancreatic islets of PD, and elevation in cholesterol biosynthesis in liver of T2D. Our findings point to inflammatory, immune, and vascular alterations in pancreatic islets in PD that are hypotheses to be tested for potential contributions to hormonal perturbations such as impaired insulin and increased glucagon production. This multi-tissue proteomic map suggests tissue-specific metabolic dysregulations in T2D.
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Affiliation(s)
- Klev Diamanti
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marco Cavalli
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maria J. Pereira
- Department of Medical Sciences, Clinical Diabetes and Metabolism, Uppsala University, Uppsala, Sweden
| | - Gang Pan
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Casimiro Castillejo-López
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Chanchal Kumar
- Translational Science & Experimental Medicine, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden,Karolinska Institutet/AstraZeneca Integrated CardioMetabolic Center (KI/AZ ICMC), Department of Medicine, Novum, Huddinge, Sweden
| | - Filip Mundt
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark,Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Jan Komorowski
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden,Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland,Washington National Primate Research Center, Seattle, WA, USA,Swedish Collegium for Advanced Study, Uppsala, Sweden
| | - Atul S. Deshmukh
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Olle Korsgren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden,Department of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jan W. Eriksson
- Department of Medical Sciences, Clinical Diabetes and Metabolism, Uppsala University, Uppsala, Sweden
| | - Claes Wadelius
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden,Corresponding author
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22
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The TRESLIN-MTBP complex couples completion of DNA replication with S/G2 transition. Mol Cell 2022; 82:3350-3365.e7. [PMID: 36049481 PMCID: PMC9506001 DOI: 10.1016/j.molcel.2022.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/16/2022] [Accepted: 08/04/2022] [Indexed: 12/14/2022]
Abstract
It has been proposed that ATR kinase senses the completion of DNA replication to initiate the S/G2 transition. In contrast to this model, we show here that the TRESLIN-MTBP complex prevents a premature entry into G2 from early S-phase independently of ATR/CHK1 kinases. TRESLIN-MTBP acts transiently at pre-replication complexes (preRCs) to initiate origin firing and is released after the subsequent recruitment of CDC45. This dynamic behavior of TRESLIN-MTBP implements a monitoring system that checks the activation of replication forks and senses the rate of origin firing to prevent the entry into G2. This system detects the decline in the number of origins of replication that naturally occurs in very late S, which is the signature that cells use to determine the completion of DNA replication and permit the S/G2 transition. Our work introduces TRESLIN-MTBP as a key player in cell-cycle control independent of canonical checkpoints.
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23
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Skowronek P, Thielert M, Voytik E, Tanzer MC, Hansen FM, Willems S, Karayel Ö, Brunner AD, Meier F, Mann M. Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF. Mol Cell Proteomics 2022; 21:100279. [PMID: 35944843 PMCID: PMC9465115 DOI: 10.1016/j.mcpro.2022.100279] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 11/05/2022] Open
Abstract
Data-independent acquisition (DIA) methods have become increasingly attractive in mass spectrometry–based proteomics because they enable high data completeness and a wide dynamic range. Recently, we combined DIA with parallel accumulation–serial fragmentation (dia-PASEF) on a Bruker trapped ion mobility (IM) separated quadrupole time-of-flight mass spectrometer. This requires alignment of the IM separation with the downstream mass selective quadrupole, leading to a more complex scheme for dia-PASEF window placement compared with DIA. To achieve high data completeness and deep proteome coverage, here we employ variable isolation windows that are placed optimally depending on precursor density in the m/z and IM plane. This is implemented in the freely available py_diAID (Python package for DIA with an automated isolation design) package. In combination with in-depth project-specific proteomics libraries and the Evosep liquid chromatography system, we reproducibly identified over 7700 proteins in a human cancer cell line in 44 min with quadruplicate single-shot injections at high sensitivity. Even at a throughput of 100 samples per day (11 min liquid chromatography gradients), we consistently quantified more than 6000 proteins in mammalian cell lysates by injecting four replicates. We found that optimal dia-PASEF window placement facilitates in-depth phosphoproteomics with very high sensitivity, quantifying more than 35,000 phosphosites in a human cancer cell line stimulated with an epidermal growth factor in triplicate 21 min runs. This covers a substantial part of the regulated phosphoproteome with high sensitivity, opening up for extensive systems-biological studies. Optimal dia-PASEF window design with py_diAID combined with deep libraries. Quantification of the HeLa cell proteome to a depth of >7700 in only 44 min. Ion mobility–resolved phosphoproteomics determines >35,000 class I phosphosites. py_diAID is freely available as GUI, CLI, and Python modules.
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24
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Zhang Z, Dovichi NJ. Seamlessly Integrated Miniaturized Filter-Aided Sample Preparation Method to Fractionation Techniques for Fast, Loss-Less, and In-Depth Proteomics Analysis of 1 μg of Cell Lysates at Low Cost. Anal Chem 2022; 94:10135-10141. [PMID: 35796025 PMCID: PMC9897233 DOI: 10.1021/acs.analchem.2c01396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We report an integrated platform that enabled a seamlessly coupling miniaturized filter-aided sample preparation (MICROFASP) method to high-pH reversed phase (RP) or strong cation exchange (SCX) microreactors for low-loss sample preparation and fractionation of 1 μg of cell lysates prior to LC-ESI-MS/MS analysis. Due to the reduced size of the microreactor, only 5 μL of buffer volume is required to generate each fraction, which speeds both elution and lyophilization. The fraction was directly eluted into an autosampler insert vial for LC-MS analysis to reduce sample transfer steps and minimize sample loss as well as contamination. The flow-through sample generated during the loading step was also collected and analyzed. The integrated platform generated 48,890 unique peptides and 4723 protein groups from 1 μg of a K562 cell lysate using MICROFASP and C18 microreactor-based high-pH RP fractionation methods, which are comparable with the state-of-the-art result using in-StageTip sample preparation and nanoflow RPLC-based fractionation methods but with a significant reduction in cost and time. Both pH gradient elution and salt gradient elution approaches provide high reproducibility for the SCX microreactor-based fractionation method. This integrated platform has significant potential in deep proteomics analysis of mass-limited samples with reduced time and equipment requirements.
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Affiliation(s)
- Zhenbin Zhang
- Institute of Drug Discovery Technology, Ningbo University, Zhejiang 315211, China
| | - Norman J. Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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25
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Ion-pair Reversed-phase×Low-pH Reversed-phase Two-dimensional Liquid Chromatography for In-depth Proteomic Profiling. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-022-2166-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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26
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Methacrylic Acid-Based Regenerative Biomaterials: Explorations into the MAAgic. REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE 2022. [DOI: 10.1007/s40883-022-00263-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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27
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Ferreira JV, da Rosa Soares A, Pereira P. Cell Non-autonomous Proteostasis Regulation in Aging and Disease. Front Neurosci 2022; 16:878296. [PMID: 35757551 PMCID: PMC9220288 DOI: 10.3389/fnins.2022.878296] [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: 02/17/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Aging is a risk factor for a number of diseases, being the more notorious ones perhaps neurodegenerative diseases such as Alzheimer's and Parkinson's. These and other age-related pathologies are often associated with accumulation of proteotoxic material inside cells, as well as with the accumulation of protein deposits extracellularly. It is widely accepted that this accumulation of toxic proteins trails a progressive decline in the mechanisms that regulate protein homeostasis, or proteostasis, during aging. However, despite significant efforts, the progress in terms of novel or improved therapies targeting accumulation of proteotoxic material has been rather limited. For example, clinical trials for new drugs aimed at treating Alzheimer's disease, by preventing accumulation of toxic proteins, have notoriously failed. On the other hand, it is becoming increasingly apparent that regulation of proteostasis is not a cell autonomous process. In fact, cells rely on complex transcellular networks to maintain tissue and organ homeostasis involving endocrine and paracrine signaling pathways. In this review we will discuss the impact of cell non-autonomous proteostasis mechanisms and their impact in aging and disease. We will focus on how transcellular proteostasis networks can shed new light into stablished paradigms about the aging of organisms.
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Affiliation(s)
- Joao Vasco Ferreira
- Proteostasis and Intercellular Communication Lab, Chronic Diseases Research Centre (CEDOC), NOVA Medical School, Faculdade de Ciencias Medicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Ana da Rosa Soares
- Proteostasis and Intercellular Communication Lab, Chronic Diseases Research Centre (CEDOC), NOVA Medical School, Faculdade de Ciencias Medicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Paulo Pereira
- Proteostasis and Intercellular Communication Lab, Chronic Diseases Research Centre (CEDOC), NOVA Medical School, Faculdade de Ciencias Medicas, Universidade NOVA de Lisboa, Lisbon, Portugal
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28
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Karayel O, Virreira Winter S, Padmanabhan S, Kuras YI, Vu DT, Tuncali I, Merchant K, Wills AM, Scherzer CR, Mann M. Proteome profiling of cerebrospinal fluid reveals biomarker candidates for Parkinson's disease. Cell Rep Med 2022; 3:100661. [PMID: 35732154 PMCID: PMC9245058 DOI: 10.1016/j.xcrm.2022.100661] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/29/2021] [Accepted: 05/23/2022] [Indexed: 11/16/2022]
Abstract
Parkinson's disease (PD) is a growing burden worldwide, and there is no reliable biomarker used in clinical routines to date. Cerebrospinal fluid (CSF) is routinely collected in patients with neurological symptoms and should closely reflect alterations in PD patients' brains. Here, we describe a scalable and sensitive mass spectrometry (MS)-based proteomics workflow for CSF proteome profiling. From two independent cohorts with over 200 individuals, our workflow reproducibly quantifies over 1,700 proteins from minimal CSF amounts. Machine learning determines OMD, CD44, VGF, PRL, and MAN2B1 to be altered in PD patients or to significantly correlate with clinical scores. We also uncover signatures of enhanced neuroinflammation in LRRK2 G2019S carriers, as indicated by increased levels of CTSS, PLD4, and HLA proteins. A comparison with our previously acquired urinary proteomes reveals a large overlap in PD-associated changes, including lysosomal proteins, opening up new avenues to improve our understanding of PD pathogenesis.
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Affiliation(s)
- Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sebastian Virreira Winter
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | | | - Yuliya I Kuras
- APDA Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA; Precision Neurology Program, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Duc Tung Vu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Idil Tuncali
- APDA Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA; Precision Neurology Program, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Kalpana Merchant
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Anne-Marie Wills
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Clemens R Scherzer
- APDA Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA; Precision Neurology Program, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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29
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Murgia M, Ciciliot S, Nagaraj N, Reggiani C, Schiaffino S, Franchi MV, Pišot R, Šimunič B, Toniolo L, Blaauw B, Sandri M, Biolo G, Flück M, Narici MV, Mann M. Signatures of muscle disuse in spaceflight and bed rest revealed by single muscle fiber proteomics. PNAS NEXUS 2022; 1:pgac086. [PMID: 36741463 PMCID: PMC9896895 DOI: 10.1093/pnasnexus/pgac086] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/07/2022] [Indexed: 02/07/2023]
Abstract
Astronauts experience dramatic loss of muscle mass, decreased strength, and insulin resistance, despite performing daily intense physical exercise that would lead to muscle growth on Earth. Partially mimicking spaceflight, prolonged bed rest causes muscle atrophy, loss of force, and glucose intolerance. To unravel the underlying mechanisms, we employed highly sensitive single fiber proteomics to detail the molecular remodeling caused by unloading and inactivity during bed rest and changes of the muscle proteome of astronauts before and after a mission on the International Space Station. Muscle focal adhesions, involved in fiber-matrix interaction and insulin receptor stabilization, are prominently downregulated in both bed rest and spaceflight and restored upon reloading. Pathways of antioxidant response increased strongly in slow but not in fast muscle fibers. Unloading alone upregulated markers of neuromuscular damage and the pathway controlling EIF5A hypusination. These proteomic signatures of mechanical unloading in muscle fiber subtypes contribute to disentangle the effect of microgravity from the pleiotropic challenges of spaceflight.
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Affiliation(s)
| | - Stefano Ciciliot
- Veneto Institute of Molecular Medicine, Via Orus 2, 35129 Padua, Italy,Department of Molecular Medicine, University of Pavia, Via Forlanini 6, 27100 Pavia, Italy
| | | | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, 35131 Padua, Italy,Science and Research Center Koper, Institute for Kinesiology Research, Garibaldijeva Street 1, 6000 Koper, Slovenia
| | | | - Martino V Franchi
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, 35131 Padua, Italy
| | - Rado Pišot
- Science and Research Center Koper, Institute for Kinesiology Research, Garibaldijeva Street 1, 6000 Koper, Slovenia
| | - Boštjan Šimunič
- Science and Research Center Koper, Institute for Kinesiology Research, Garibaldijeva Street 1, 6000 Koper, Slovenia
| | - Luana Toniolo
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, 35131 Padua, Italy
| | - Bert Blaauw
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, 35131 Padua, Italy,Veneto Institute of Molecular Medicine, Via Orus 2, 35129 Padua, Italy
| | - Marco Sandri
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, 35131 Padua, Italy,Veneto Institute of Molecular Medicine, Via Orus 2, 35129 Padua, Italy
| | - Gianni Biolo
- Clinical Department of Medical, Surgical and Health Sciences, Strada di Fiume 447, 34149 Trieste, Italy
| | - Martin Flück
- Department of Medicine, University of Fribourg, Chemin du Musee 5, 1700 Fribourg, Switzerland
| | - Marco V Narici
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, 35131 Padua, Italy,Science and Research Center Koper, Institute for Kinesiology Research, Garibaldijeva Street 1, 6000 Koper, Slovenia,CIR-MYO Myology Center, Viale G Colombo 3, 35121 Padua, Italy
| | - Matthias Mann
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany,NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, Building 6.1, 2200 Copenhagen, Denmark
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30
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Alves G, Ogurtsov A, Karlsson R, Jaén-Luchoro D, Piñeiro-Iglesias B, Salvà-Serra F, Andersson B, Moore ERB, Yu YK. Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:917-931. [PMID: 35500907 PMCID: PMC9164240 DOI: 10.1021/jasms.1c00347] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 06/01/2023]
Abstract
Fast and accurate identifications of pathogenic bacteria along with their associated antibiotic resistance proteins are of paramount importance for patient treatments and public health. To meet this goal from the mass spectrometry aspect, we have augmented the previously published Microorganism Classification and Identification (MiCId) workflow for this capability. To evaluate the performance of this augmented workflow, we have used MS/MS datafiles from samples of 10 antibiotic resistance bacterial strains belonging to three different species: Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The evaluation shows that MiCId's workflow has a sensitivity value around 85% (with a lower bound at about 72%) and a precision greater than 95% in identifying antibiotic resistance proteins. In addition to having high sensitivity and precision, MiCId's workflow is fast and portable, making it a valuable tool for rapid identifications of bacteria as well as detection of their antibiotic resistance proteins. It performs microorganismal identifications, protein identifications, sample biomass estimates, and antibiotic resistance protein identifications in 6-17 min per MS/MS sample using computing resources that are available in most desktop and laptop computers. We have also demonstrated other use of MiCId's workflow. Using MS/MS data sets from samples of two bacterial clonal isolates, one being antibiotic-sensitive while the other being multidrug-resistant, we applied MiCId's workflow to investigate possible mechanisms of antibiotic resistance in these pathogenic bacteria; the results showed that MiCId's conclusions agree with the published study. The new version of MiCId (v.07.01.2021) is freely available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.
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Affiliation(s)
- Gelio Alves
- National
Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Aleksey Ogurtsov
- National
Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Roger Karlsson
- Department
of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
- Department
of Clinical Microbiology, Sahlgrenska University
Hospital, 40234 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research (CARe), University of Gothenburg, 40016 Gothenburg, Sweden
- Nanoxis
Consulting AB, 40234 Gothenburg, Sweden
| | - Daniel Jaén-Luchoro
- Department
of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research (CARe), University of Gothenburg, 40016 Gothenburg, Sweden
- Culture Collection
University of Gothenburg (CCUG), Sahlgrenska
Academy of the University of Gothenburg, 40234 Gothenburg, Sweden
| | - Beatriz Piñeiro-Iglesias
- Department
of Clinical Microbiology, Sahlgrenska University
Hospital, 40234 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research (CARe), University of Gothenburg, 40016 Gothenburg, Sweden
| | - Francisco Salvà-Serra
- Department
of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
- Department
of Clinical Microbiology, Sahlgrenska University
Hospital, 40234 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research (CARe), University of Gothenburg, 40016 Gothenburg, Sweden
- Culture Collection
University of Gothenburg (CCUG), Sahlgrenska
Academy of the University of Gothenburg, 40234 Gothenburg, Sweden
- Microbiology,
Department of Biology, University of the
Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Björn Andersson
- Bioinformatics
Core Facility at Sahlgrenska Academy, University
of Gothenburg, Box 413, 40530 Gothenburg, Sweden
| | - Edward R. B. Moore
- Department
of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
- Department
of Clinical Microbiology, Sahlgrenska University
Hospital, 40234 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research (CARe), University of Gothenburg, 40016 Gothenburg, Sweden
- Culture Collection
University of Gothenburg (CCUG), Sahlgrenska
Academy of the University of Gothenburg, 40234 Gothenburg, Sweden
| | - Yi-Kuo Yu
- National
Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
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31
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Hostrup M, Lemminger AK, Stocks B, Gonzalez-Franquesa A, Larsen JK, Quesada JP, Thomassen M, Weinert BT, Bangsbo J, Deshmukh AS. High-intensity interval training remodels the proteome and acetylome of human skeletal muscle. eLife 2022; 11:69802. [PMID: 35638262 PMCID: PMC9154743 DOI: 10.7554/elife.69802] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 05/11/2022] [Indexed: 12/27/2022] Open
Abstract
Exercise is an effective strategy in the prevention and treatment of metabolic diseases. Alterations in the skeletal muscle proteome, including post-translational modifications, regulate its metabolic adaptations to exercise. Here, we examined the effect of high-intensity interval training (HIIT) on the proteome and acetylome of human skeletal muscle, revealing the response of 3168 proteins and 1263 lysine acetyl-sites on 464 acetylated proteins. We identified global protein adaptations to exercise training involved in metabolism, excitation-contraction coupling, and myofibrillar calcium sensitivity. Furthermore, HIIT increased the acetylation of mitochondrial proteins, particularly those of complex V. We also highlight the regulation of exercise-responsive histone acetyl-sites. These data demonstrate the plasticity of the skeletal muscle proteome and acetylome, providing insight into the regulation of contractile, metabolic and transcriptional processes within skeletal muscle. Herein, we provide a substantial hypothesis-generating resource to stimulate further mechanistic research investigating how exercise improves metabolic health.
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Affiliation(s)
- Morten Hostrup
- Section of Integrative Physiology, Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Anders Krogh Lemminger
- Section of Integrative Physiology, Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Ben Stocks
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alba Gonzalez-Franquesa
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Kjærgaard Larsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julia Prats Quesada
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Thomassen
- Section of Integrative Physiology, Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Brian Tate Weinert
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
| | - Jens Bangsbo
- Section of Integrative Physiology, Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Atul Shahaji Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,The Novo Nordisk Foundation Center for Protein Research, Clinical Proteomics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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32
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Skowronek P, Meier F. High-Throughput Mass Spectrometry-Based Proteomics with dia-PASEF. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2456:15-27. [PMID: 35612732 DOI: 10.1007/978-1-0716-2124-0_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ion mobility separation is becoming an integral part in mass spectrometry-based proteomics. Here we describe the use of a trapped ion mobility-quadrupole time-of-flight (TIMS-QTOF) mass spectrometer for high-throughput label-free quantification with data-independent acquisition. The parallel accumulation-serial fragmentation (PASEF) operation mode positions the mass-selecting quadrupole as a function of the TIMS separation, which allows highly efficient data-independent acquisition schemes (dia-PASEF), but also increases complexity in the method design. We provide a step-by-step protocol for instrument setup, method design, data acquisition and ion mobility-aware, library-based data analysis with Spectronaut. We highlight key acquisition parameters and illustrate their optimization for short gradients. Using the EvosepOne liquid chromatography system, we demonstrate expected results for the analysis of a human cancer cell line at a throughput of 60 samples per day, leading to the quantification of about 6000 protein groups with very high reproducibility. Importantly, the protocol can be readily adapted to other gradients and sample types such as modified peptides.
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Affiliation(s)
- Patricia Skowronek
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Meier
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany. .,Functional Proteomics, Jena University Hospital, Jena, Germany.
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33
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Mund A, Coscia F, Kriston A, Hollandi R, Kovács F, Brunner AD, Migh E, Schweizer L, Santos A, Bzorek M, Naimy S, Rahbek-Gjerdrum LM, Dyring-Andersen B, Bulkescher J, Lukas C, Eckert MA, Lengyel E, Gnann C, Lundberg E, Horvath P, Mann M. Deep Visual Proteomics defines single-cell identity and heterogeneity. Nat Biotechnol 2022; 40:1231-1240. [PMID: 35590073 PMCID: PMC9371970 DOI: 10.1038/s41587-022-01302-5] [Citation(s) in RCA: 131] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/30/2022] [Indexed: 02/07/2023]
Abstract
Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here, we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven image analysis of cellular phenotypes with automated single-cell or single-nucleus laser microdissection and ultra-high-sensitivity mass spectrometry. DVP links protein abundance to complex cellular or subcellular phenotypes while preserving spatial context. By individually excising nuclei from cell culture, we classified distinct cell states with proteomic profiles defined by known and uncharacterized proteins. In an archived primary melanoma tissue, DVP identified spatially resolved proteome changes as normal melanocytes transition to fully invasive melanoma, revealing pathways that change in a spatial manner as cancer progresses, such as mRNA splicing dysregulation in metastatic vertical growth that coincides with reduced interferon signaling and antigen presentation. The ability of DVP to retain precise spatial proteomic information in the tissue context has implications for the molecular profiling of clinical samples. Deep Visual Proteomics combines machine learning, automated image analysis and single-cell proteomics.
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Affiliation(s)
- Andreas Mund
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Fabian Coscia
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Spatial Proteomics Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - András Kriston
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.,Single-Cell Technologies Ltd., Szeged, Hungary
| | - Réka Hollandi
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Ferenc Kovács
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.,Single-Cell Technologies Ltd., Szeged, Hungary
| | - Andreas-David Brunner
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ede Migh
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Lisa Schweizer
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Alberto Santos
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark.,Big Data Institute, Li-Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Michael Bzorek
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Soraya Naimy
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Lise Mette Rahbek-Gjerdrum
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark.,Institute for Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Beatrice Dyring-Andersen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark.,Leo Foundation Skin Immunology Research Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jutta Bulkescher
- Protein Imaging Platform, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Lukas
- Protein Imaging Platform, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mark Adam Eckert
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Christian Gnann
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.,Department of Bioengineering, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary. .,Single-Cell Technologies Ltd., Szeged, Hungary. .,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
| | - Matthias Mann
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
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34
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Niu L, Geyer PE, Gupta R, Santos A, Meier F, Doll S, Wewer Albrechtsen NJ, Klein S, Ortiz C, Uschner FE, Schierwagen R, Trebicka J, Mann M. Dynamic human liver proteome atlas reveals functional insights into disease pathways. Mol Syst Biol 2022; 18:e10947. [PMID: 35579278 PMCID: PMC9112488 DOI: 10.15252/msb.202210947] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/12/2022] Open
Abstract
Deeper understanding of liver pathophysiology would benefit from a comprehensive quantitative proteome resource at cell type resolution to predict outcome and design therapy. Here, we quantify more than 150,000 sequence‐unique peptides aggregated into 10,000 proteins across total liver, the major liver cell types, time course of primary cell cultures, and liver disease states. Bioinformatic analysis reveals that half of hepatocyte protein mass is comprised of enzymes and 23% of mitochondrial proteins, twice the proportion of other liver cell types. Using primary cell cultures, we capture dynamic proteome remodeling from tissue states to cell line states, providing useful information for biological or pharmaceutical research. Our extensive data serve as spectral library to characterize a human cohort of non‐alcoholic steatohepatitis and cirrhosis. Dramatic proteome changes in liver tissue include signatures of hepatic stellate cell activation resembling liver cirrhosis and providing functional insights. We built a web‐based dashboard application for the interactive exploration of our resource (www.liverproteome.org).
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Affiliation(s)
- Lili Niu
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Rajat Gupta
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alberto Santos
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Center for Health Data Science, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Florian Meier
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sophia Doll
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Nicolai J Wewer Albrechtsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sabine Klein
- Department of Internal Medicine I, Goethe University Clinic Frankfurt, Frankfurt, Germany.,Department of Internal Medicine B, WW University Münster, Münster, Germany
| | - Cristina Ortiz
- Department of Internal Medicine I, Goethe University Clinic Frankfurt, Frankfurt, Germany
| | - Frank E Uschner
- Department of Internal Medicine I, Goethe University Clinic Frankfurt, Frankfurt, Germany.,Department of Internal Medicine B, WW University Münster, Münster, Germany
| | - Robert Schierwagen
- Department of Internal Medicine I, Goethe University Clinic Frankfurt, Frankfurt, Germany.,Department of Internal Medicine B, WW University Münster, Münster, Germany
| | - Jonel Trebicka
- Department of Internal Medicine I, Goethe University Clinic Frankfurt, Frankfurt, Germany.,Department of Internal Medicine B, WW University Münster, Münster, Germany.,European Foundation for the Study of Chronic Failure, EFCLIF, Barcelona, Spain
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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35
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Archakov A, Vavilov N, Ilgisonis E, Lisitsa A, Ponomarenko E, Farafonova T, Tikhonova O, Zgoda V. Number of Detected Proteins as the Function of the Sensitivity of Proteomic
Technology in Human Liver Cells. Curr Protein Pept Sci 2022; 23:290-298. [DOI: 10.2174/1389203723666220526092941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/14/2022] [Accepted: 03/25/2022] [Indexed: 11/22/2022]
Abstract
Aims:
The main goal of the Russian part of C-HPP is to detect and functionally annotate
missing proteins (PE2-PE4) encoded by human chromosome 18. To achieve this goal, it is necessary to
use the most sensitive methods of analysis.
Background:
However, identifying such proteins in a complex biological mixture using mass spectrometry
(MS)-based methods is difficult due to the insufficient sensitivity of proteomic analysis methods.
A possible solution to the problem is the pre-fractionation of a complex biological sample at the
sample preparation stage.
Objective:
This study aims to measure the detection limit of SRM SIS analysis using a standard set of
UPS1 proteins and find a way to enhance the sensitivity of the analysis and to, detect proteins encoded
by the human chromosome 18 in liver tissue samples, and compare the data with transcriptomic analysis
of the same samples.
Methods:
Mass spectrometry, data-dependent acquisition, selected reaction monitoring, highperformance
liquid chromatography, data-dependent acquisition in combination with pre-fractionation
by alkaline reversed-phase chromatography, selected reaction monitoring in combination with prefractionation
by alkaline reversed-phase chromatography methods were used in this study.
Results:
The results revealed that 100% of UPS1 proteins in a mixture could only be identified at a
concentration of at least 10-9 М. The decrease in concentration leads to protein losses associated with
technology sensitivity, and no UPS1 protein is detected at a concentration of 10-13 М. Therefore, the
two-dimensional fractionation of samples was applied to improve sensitivity. The human liver tissue
was examined by selected reaction monitoring and shotgun methods of MS analysis using onedimensional
and two-dimensional fractionation to identify the proteins encoded by human chromosome
18. A total of 134 proteins were identified. The overlap between proteomic and transcriptomic data in
human liver tissue was ~50%.
Conclusion:
The sample concentration technique is well suited for a standard UPS1 system that is not
contaminated with a complex biological sample. However, it is not suitable for use with a complex biological
protein mixture. Thus, it is necessary to develop more sophisticated fractionation systems for the
detection of all low-copy proteins. This weak convergence is due to the low sensitivity of proteomic
technology compared to transcriptomic approaches. Also, total mRNA was used to perform RNA-seq
analysis, but not all detected mRNA molecules could be translated into proteins. This introduces additional
uncertainty in the data; in the future, we plan to study only translated mRNA molecules-the translatome.
Data is available via ProteomeXchange with identifier PXD026997.
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Affiliation(s)
- Alexander Archakov
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
| | - Nikita Vavilov
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
| | - Ekaterina Ilgisonis
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
| | - Andrey Lisitsa
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
- East China University of Technology, Nanchang City, Jiangxi, China
- East-Siberian Research and Education Center, Tyumen, Russia
| | - Elena Ponomarenko
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
| | - Tatiana Farafonova
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
| | - Olga Tikhonova
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
| | - Victor Zgoda
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
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36
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Ramos Y, Almeida A, Carpio J, Rodríguez‐Ulloa A, Perera Y, González LJ, Wiśniewski JR, Besada V. Gel electrophoresis/electroelution sorting fractionator combined with filter aided sample preparation for deep proteomic analysis. J Sep Sci 2022; 45:1784-1796. [DOI: 10.1002/jssc.202100992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Yassel Ramos
- Proteomics Group System Biology Department Center for Genetic Engineering and Biotechnology Havana Cuba
| | - Alexis Almeida
- Proteomics Group System Biology Department Center for Genetic Engineering and Biotechnology Havana Cuba
| | - Jenis Carpio
- Proteomics Group System Biology Department Center for Genetic Engineering and Biotechnology Havana Cuba
| | - Arielis Rodríguez‐Ulloa
- Proteomics Group System Biology Department Center for Genetic Engineering and Biotechnology Havana Cuba
| | - Yasser Perera
- China‐Cuba Biotechnology Joint Innovation Center (CCBJIC) Yongzhou Zhong Gu Biotechnology Co., Ltd Hunan Province China
- Molecular Oncology Group Pharmacology Department, Center for Genetic Engineering and Biotechnology Havana Cuba
| | - Luis J. González
- Proteomics Group System Biology Department Center for Genetic Engineering and Biotechnology Havana Cuba
| | - Jacek R. Wiśniewski
- Biochemical Proteomics Group Department of Proteomics and Signal Transduction Max‐Planck‐Institute of Biochemistry Martinsried Germany
| | - Vladimir Besada
- Proteomics Group System Biology Department Center for Genetic Engineering and Biotechnology Havana Cuba
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37
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Gindlhuber J, Schinagl M, Liesinger L, Darnhofer B, Tomin T, Schittmayer M, Birner-Gruenberger R. Hepatocyte Proteome Alterations Induced by Individual and Combinations of Common Free Fatty Acids. Int J Mol Sci 2022; 23:3356. [PMID: 35328776 PMCID: PMC8951603 DOI: 10.3390/ijms23063356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 12/12/2022] Open
Abstract
Non-alcoholic fatty liver disease is a pathology with a hard-to-detect onset and is estimated to be present in a quarter of the adult human population. To improve our understanding of the development of non-alcoholic fatty liver disease, we treated a human hepatoma cell line model, HepG2, with increasing concentrations of common fatty acids, namely myristic, palmitic and oleic acid. To reproduce more physiologically representative conditions, we also included combinations of these fatty acids and monitored the cellular response with an in-depth proteomics approach and imaging techniques. The two saturated fatty acids initially presented a similar phenotype of a dose-dependent decrease in growth rates and impaired lipid droplet formation. Detailed analysis revealed that the drop in the growth rates was due to delayed cell-cycle progression following myristic acid treatment, whereas palmitic acid led to cellular apoptosis. In contrast, oleic acid, as well as saturated fatty acid mixtures with oleic acid, led to a dose-dependent increase in lipid droplet volume without adverse impacts on cell growth. Comparing the effects of harmful single-fatty-acid treatments and the well-tolerated fatty acid mixes on the cellular proteome, we were able to differentiate between fatty-acid-specific cellular responses and likely common lipotoxic denominators.
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Affiliation(s)
- Juergen Gindlhuber
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (J.G.); (M.S.); (L.L.); (B.D.)
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, 1060 Vienna, Austria; (T.T.); (M.S.)
| | - Maximilian Schinagl
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (J.G.); (M.S.); (L.L.); (B.D.)
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, 1060 Vienna, Austria; (T.T.); (M.S.)
| | - Laura Liesinger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (J.G.); (M.S.); (L.L.); (B.D.)
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, 1060 Vienna, Austria; (T.T.); (M.S.)
| | - Barbara Darnhofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (J.G.); (M.S.); (L.L.); (B.D.)
| | - Tamara Tomin
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, 1060 Vienna, Austria; (T.T.); (M.S.)
| | - Matthias Schittmayer
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, 1060 Vienna, Austria; (T.T.); (M.S.)
| | - Ruth Birner-Gruenberger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (J.G.); (M.S.); (L.L.); (B.D.)
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, 1060 Vienna, Austria; (T.T.); (M.S.)
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38
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Engineered nanoparticles enable deep proteomics studies at scale by leveraging tunable nano-bio interactions. Proc Natl Acad Sci U S A 2022; 119:e2106053119. [PMID: 35275789 PMCID: PMC8931255 DOI: 10.1073/pnas.2106053119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceDeep profiling of the plasma proteome at scale has been a challenge for traditional approaches. We achieve superior performance across the dimensions of precision, depth, and throughput using a panel of surface-functionalized superparamagnetic nanoparticles in comparison to conventional workflows for deep proteomics interrogation. Our automated workflow leverages competitive nanoparticle-protein binding equilibria that quantitatively compress the large dynamic range of proteomes to an accessible scale. Using machine learning, we dissect the contribution of individual physicochemical properties of nanoparticles to the composition of protein coronas. Our results suggest that nanoparticle functionalization can be tailored to protein sets. This work demonstrates the feasibility of deep, precise, unbiased plasma proteomics at a scale compatible with large-scale genomics enabling multiomic studies.
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Brunner A, Thielert M, Vasilopoulou C, Ammar C, Coscia F, Mund A, Hoerning OB, Bache N, Apalategui A, Lubeck M, Richter S, Fischer DS, Raether O, Park MA, Meier F, Theis FJ, Mann M. Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation. Mol Syst Biol 2022; 18:e10798. [PMID: 35226415 PMCID: PMC8884154 DOI: 10.15252/msb.202110798] [Citation(s) in RCA: 198] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
Single‐cell technologies are revolutionizing biology but are today mainly limited to imaging and deep sequencing. However, proteins are the main drivers of cellular function and in‐depth characterization of individual cells by mass spectrometry (MS)‐based proteomics would thus be highly valuable and complementary. Here, we develop a robust workflow combining miniaturized sample preparation, very low flow‐rate chromatography, and a novel trapped ion mobility mass spectrometer, resulting in a more than 10‐fold improved sensitivity. We precisely and robustly quantify proteomes and their changes in single, FACS‐isolated cells. Arresting cells at defined stages of the cell cycle by drug treatment retrieves expected key regulators. Furthermore, it highlights potential novel ones and allows cell phase prediction. Comparing the variability in more than 430 single‐cell proteomes to transcriptome data revealed a stable‐core proteome despite perturbation, while the transcriptome appears stochastic. Our technology can readily be applied to ultra‐high sensitivity analyses of tissue material, posttranslational modifications, and small molecule studies from small cell counts to gain unprecedented insights into cellular heterogeneity in health and disease.
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Affiliation(s)
- Andreas‐David Brunner
- Proteomics and Signal Transduction Max‐Planck Institute of Biochemistry Martinsried Germany
| | - Marvin Thielert
- Proteomics and Signal Transduction Max‐Planck Institute of Biochemistry Martinsried Germany
| | - Catherine Vasilopoulou
- Proteomics and Signal Transduction Max‐Planck Institute of Biochemistry Martinsried Germany
| | - Constantin Ammar
- Proteomics and Signal Transduction Max‐Planck Institute of Biochemistry Martinsried Germany
| | - Fabian Coscia
- NNF Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Andreas Mund
- NNF Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | | | | | | | | | - Sabrina Richter
- Helmholtz Zentrum München – German Research Center for Environmental Health Institute of Computational Biology Neuherberg Germany
- TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany
| | - David S Fischer
- Helmholtz Zentrum München – German Research Center for Environmental Health Institute of Computational Biology Neuherberg Germany
- TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany
| | | | | | - Florian Meier
- Proteomics and Signal Transduction Max‐Planck Institute of Biochemistry Martinsried Germany
- Functional Proteomics Jena University Hospital Jena Germany
| | - Fabian J Theis
- Helmholtz Zentrum München – German Research Center for Environmental Health Institute of Computational Biology Neuherberg Germany
- TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany
| | - Matthias Mann
- Proteomics and Signal Transduction Max‐Planck Institute of Biochemistry Martinsried Germany
- NNF Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
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40
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A Bioinformatics Approach to Mine the Microbial Proteomic Profile of COVID-19 Mass Spectrometry Data. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2010010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mass spectrometry (MS) is one of the key technologies used in proteomics. The majority of studies carried out using proteomics have focused on identifying proteins in biological samples such as human plasma to pin down prognostic or diagnostic biomarkers associated with particular conditions or diseases. This study aims to quantify microbial (viral and bacterial) proteins in healthy human plasma. MS data of healthy human plasma were searched against the complete proteomes of all available viruses and bacteria. With this baseline established, the same strategy was applied to characterize the metaproteomic profile of different SARS-CoV-2 disease stages in the plasma of patients. Two SARS-CoV-2 proteins were detected with a high confidence and could serve as the early markers of SARS-CoV-2 infection. The complete bacterial and viral protein content in SARS-CoV-2 samples was compared for the different disease stages. The number of viral proteins was found to increase significantly with the progression of the infection, at the expense of bacterial proteins. This strategy can be extended to aid in the development of early diagnostic tests for other infectious diseases based on the presence of microbial biomarkers in human plasma samples.
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41
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Heat shock induces premature transcript termination and reconfigures the human transcriptome. Mol Cell 2022; 82:1573-1588.e10. [PMID: 35114099 PMCID: PMC9098121 DOI: 10.1016/j.molcel.2022.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/30/2021] [Accepted: 01/07/2022] [Indexed: 12/14/2022]
Abstract
The heat shock (HS) response involves rapid induction of HS genes, whereas transcriptional repression is established more slowly at most other genes. Previous data suggested that such repression results from inhibition of RNA polymerase II (RNAPII) pause release, but here, we show that HS strongly affects other phases of the transcription cycle. Intriguingly, while elongation rates increase upon HS, processivity markedly decreases, so that RNAPII frequently fails to reach the end of genes. Indeed, HS results in widespread premature transcript termination at cryptic, intronic polyadenylation (IPA) sites near gene 5'-ends, likely via inhibition of U1 telescripting. This results in dramatic reconfiguration of the human transcriptome with production of new, previously unannotated, short mRNAs that accumulate in the nucleus. Together, these results shed new light on the basic transcription mechanisms induced by growth at elevated temperature and show that a genome-wide shift toward usage of IPA sites can occur under physiological conditions.
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42
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Ahrens CH, Wade JT, Champion MM, Langer JD. A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry. J Bacteriol 2022; 204:e0035321. [PMID: 34748388 PMCID: PMC8765459 DOI: 10.1128/jb.00353-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using standard experimental approaches. Consequently, we still know few small proteins even in well-studied prokaryotic model organisms. Mass spectrometry (MS) has great potential for the discovery, validation, and functional characterization of small proteins. However, standard MS approaches are poorly suited to the identification of both known and novel small proteins due to limitations at each step of a typical proteomics workflow, i.e., sample preparation, protease digestion, liquid chromatography, MS data acquisition, and data analysis. Here, we outline the major MS-based workflows and bioinformatic pipelines used for small protein discovery and validation. Special emphasis is placed on highlighting the adjustments required to improve detection and data quality for small proteins. We discuss both the unbiased detection of small proteins and the targeted analysis of small proteins of interest. Finally, we provide guidelines to prioritize novel small proteins, and an outlook on methods with particular potential to further improve comprehensive discovery and characterization of small proteins.
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Affiliation(s)
- Christian H. Ahrens
- Agroscope, Method Development and Analytics & SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Julian D. Langer
- Mass Spectrometry and Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany
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43
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Technique development of high-throughput and high-sensitivity sample preparation and separation for proteomics. Bioanalysis 2021; 14:101-111. [PMID: 34854341 DOI: 10.4155/bio-2021-0202] [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: 11/17/2022] Open
Abstract
Sample preparation and separation methods determine the sensitivity and the quantification accuracy of the proteomics analysis. This article covers a comprehensive review of the recent technique development of high-throughput and high-sensitivity sample preparation and separation methods in proteomics research.
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44
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Sarkar A, Nazir A. Carrying Excess Baggage Can Slowdown Life: Protein Clearance Machineries That Go Awry During Aging and the Relevance of Maintaining Them. Mol Neurobiol 2021; 59:821-840. [PMID: 34792731 DOI: 10.1007/s12035-021-02640-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/05/2021] [Indexed: 01/07/2023]
Abstract
Cellular homeostasis is maintained by rapid and systematic cleansing of aberrant and aggregated proteins within cells. Neurodegenerative diseases (NDs) especially Parkinson's and Alzheimer's disease are known to be associated with multiple factors, most important being impaired clearance of aggregates, resulting in the accumulation of specific aggregated protein in the brain. Protein quality control (PQC) of proteostasis network comprises proteolytic machineries and chaperones along with their regulators to ensure precise operation and maintenance of proteostasis. Such regulatory factors coordinate among each other multiple functional aspects related to proteins, including their synthesis, folding, transport, and degradation. During aging due to inevitable endogenous and external stresses, sustaining a proteome balance is a challenging task. Such stresses decline the capacity of the proteostasis network compromising the proteome integrity, affecting the fundamental physiological processes including reproductive fitness of the organism. This review focuses on highlighting proteome-wide changes during aging and the strategies for proteostasis improvements. The possibility of augmenting the proteostasis network either via genetic or pharmacological interventions may be a promising strategy towards delaying age-associated pathological consequences due to proteome disbalance, thus promoting healthy aging and prolonged longevity.
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Affiliation(s)
- Arunabh Sarkar
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, UP, 226031, India
| | - Aamir Nazir
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, UP, 226031, India.
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45
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Eckert S, Chang YC, Bayer FP, The M, Kuhn PH, Weichert W, Kuster B. Evaluation of Disposable Trap Column nanoLC-FAIMS-MS/MS for the Proteomic Analysis of FFPE Tissue. J Proteome Res 2021; 20:5402-5411. [PMID: 34735149 DOI: 10.1021/acs.jproteome.1c00695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteomic biomarker discovery using formalin-fixed paraffin-embedded (FFPE) tissue requires robust workflows to support the analysis of large cohorts of patient samples. It also requires finding a reasonable balance between achieving a high proteomic depth and limiting the overall analysis time. To this end, we evaluated the merits of online coupling of single-use disposable trap column nanoflow liquid chromatography, high-field asymmetric-waveform ion-mobility spectrometry (FAIMS), and tandem mass spectrometry (nLC-FAIMS-MS/MS). The data show that ≤600 ng of peptide digest should be loaded onto the chromatographic part of the system. Careful characterization of the FAIMS settings enabled the choice of optimal combinations of compensation voltages (CVs) as a function of the employed LC gradient time. We found nLC-FAIMS-MS/MS to be on par with StageTip-based off-line basic pH reversed-phase fractionation in terms of proteomic depth and reproducibility of protein quantification (coefficient of variation ≤15% for 90% of all proteins) but requiring 50% less sample and substantially reducing sample handling. Using FFPE materials from the lymph node, lung, and prostate tissue as examples, we show that nLC-FAIMS-MS/MS can identify 5000-6000 proteins from the respective tissue within a total of 3 h of analysis time.
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Affiliation(s)
- Stephan Eckert
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany.,Institute of Pathology, Technical University of Munich (TUM), Munich 81675, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Yun-Chien Chang
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany
| | - Peer-Hendrik Kuhn
- Institute of Pathology, Technical University of Munich (TUM), Munich 81675, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University of Munich (TUM), Munich 81675, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising 85354, Germany
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46
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Aballo TJ, Roberts DS, Melby JA, Buck KM, Brown KA, Ge Y. Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro. J Proteome Res 2021; 20:4203-4211. [PMID: 34236868 PMCID: PMC8349881 DOI: 10.1021/acs.jproteome.1c00446] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Global bottom-up mass spectrometry (MS)-based proteomics is widely used for protein identification and quantification to achieve a comprehensive understanding of the composition, structure, and function of the proteome. However, traditional sample preparation methods are time-consuming, typically including overnight tryptic digestion, extensive sample cleanup to remove MS-incompatible surfactants, and offline sample fractionation to reduce proteome complexity prior to online liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Thus, there is a need for a fast, robust, and reproducible method for protein identification and quantification from complex proteomes. Herein, we developed an ultrafast bottom-up proteomics method enabled by Azo, a photocleavable, MS-compatible surfactant that effectively solubilizes proteins and promotes rapid tryptic digestion, combined with the Bruker timsTOF Pro, which enables deeper proteome coverage through trapped ion mobility spectrometry (TIMS) and parallel accumulation-serial fragmentation (PASEF) of peptides. We applied this method to analyze the complex human cardiac proteome and identified nearly 4000 protein groups from as little as 1 mg of human heart tissue in a single one-dimensional LC-TIMS-MS/MS run with high reproducibility. Overall, we anticipate this ultrafast, robust, and reproducible bottom-up method empowered by both Azo and the timsTOF Pro will be generally applicable and greatly accelerate the throughput of large-scale quantitative proteomic studies. Raw data are available via the MassIVE repository with identifier MSV000087476.
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Affiliation(s)
- Timothy J Aballo
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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47
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Frauenstein A, Ebner S, Hansen FM, Sinha A, Phulphagar K, Swatek K, Hornburg D, Mann M, Meissner F. Identification of covalent modifications regulating immune signaling complex composition and phenotype. Mol Syst Biol 2021; 17:e10125. [PMID: 34318608 PMCID: PMC8447602 DOI: 10.15252/msb.202010125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 11/23/2022] Open
Abstract
Cells signal through rearrangements of protein communities governed by covalent modifications and reversible interactions of distinct sets of proteins. A method that identifies those post‐transcriptional modifications regulating signaling complex composition and functional phenotypes in one experimental setup would facilitate an efficient identification of novel molecular signaling checkpoints. Here, we devised modifications, interactions and phenotypes by affinity purification mass spectrometry (MIP‐APMS), comprising the streamlined cloning and transduction of tagged proteins into functionalized reporter cells as well as affinity chromatography, followed by MS‐based quantification. We report the time‐resolved interplay of more than 50 previously undescribed modification and hundreds of protein–protein interactions of 19 immune protein complexes in monocytes. Validation of interdependencies between covalent, reversible, and functional protein complex regulations by knockout or site‐specific mutation revealed ISGylation and phosphorylation of TRAF2 as well as ARHGEF18 interaction in Toll‐like receptor 2 signaling. Moreover, we identify distinct mechanisms of action for small molecule inhibitors of p38 (MAPK14). Our method provides a fast and cost‐effective pipeline for the molecular interrogation of protein communities in diverse biological systems and primary cells.
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Affiliation(s)
- Annika Frauenstein
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefan Ebner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Fynn M Hansen
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ankit Sinha
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kshiti Phulphagar
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kirby Swatek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel Hornburg
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Felix Meissner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.,Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany
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48
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Zheng R, Govorukhina N, Arrey TN, Pynn C, van der Zee A, Marko-Varga G, Bischoff R, Boychenko A. Online-2D NanoLC-MS for Crude Serum Proteome Profiling: Assessing Sample Preparation Impact on Proteome Composition. Anal Chem 2021; 93:9663-9668. [PMID: 34236853 DOI: 10.1021/acs.analchem.1c01291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although current LC-MS technology permits scientists to efficiently screen clinical samples in translational research, e.g., steroids, biogenic amines, and even plasma or serum proteomes, in a daily routine, maintaining the balance between throughput and analytical depth is still a limiting factor. A typical approach to enhance the proteome depth is employing offline two-dimensional (2D) fractionation techniques before reversed-phase nanoLC-MS/MS analysis (1D-nanoLC-MS). These additional sample preparation steps usually require extensive sample manipulation, which could result in sample alteration and sample loss. Here, we present and compare 1D-nanoLC-MS with an automated online-2D high-pH RP × low pH RP separation method for deep proteome profiling using a nanoLC system coupled to a high-resolution accurate-mass mass spectrometer. The proof-of-principle study permitted the identification of ca. 500 proteins with ∼10,000 peptides in 15 enzymatically digested crude serum samples collected from healthy donors in 3 laboratories across Europe. The developed method identified 60% more peptides in comparison with conventional 1D nanoLC-MS/MS analysis with ca. 4 times lower throughput while retaining the quantitative information. Serum sample preparation related changes were revealed by applying unsupervised classification techniques and, therefore, must be taken into account while planning multicentric biomarker discovery and validation studies. Overall, this novel method reduces sample complexity and boosts the number of peptide and protein identifications without the need for extra sample handling procedures for samples equivalent to less than 1 μL of blood, which expands the space for potential biomarker discovery by looking deeper into the composition of biofluids.
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Affiliation(s)
- Runsheng Zheng
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Tabiwang N Arrey
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany
| | - Christopher Pynn
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Ate van der Zee
- University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - György Marko-Varga
- Clinical Protein Science and Imaging, Lund University, Box 117, S-22100 Lund, Sweden
| | - Rainer Bischoff
- Department of Analytical Biochemistry, University of Groningen, 9713 AV Groningen, The Netherlands
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49
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Mao Y, Wang X, Huang P, Tian R. Spatial proteomics for understanding the tissue microenvironment. Analyst 2021; 146:3777-3798. [PMID: 34042124 DOI: 10.1039/d1an00472g] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The human body comprises rich populations of cells, which are arranged into tissues and organs with diverse functionalities. These cells exhibit a broad spectrum of phenotypes and are often organized as a heterogeneous but sophisticatedly regulated ecosystem - tissue microenvironment, inside which every cell interacts with and is reciprocally influenced by its surroundings through its life span. Therefore, it is critical to comprehensively explore the cellular machinery and biological processes in the tissue microenvironment, which is best exemplified by the tumor microenvironment (TME). The past decade has seen increasing advances in the field of spatial proteomics, the main purpose of which is to characterize the abundance and spatial distribution of proteins and their post-translational modifications in the microenvironment of diseased tissues. Herein, we outline the achievements and remaining challenges of mass spectrometry-based tissue spatial proteomics. Exciting technology developments along with important biomedical applications of spatial proteomics are highlighted. In detail, we focus on high-quality resources built by scalpel macrodissection-based region-resolved proteomics, method development of sensitive sample preparation for laser microdissection-based spatial proteomics, and antibody recognition-based multiplexed tissue imaging. In the end, critical issues and potential future directions for spatial proteomics are also discussed.
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Affiliation(s)
- Yiheng Mao
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China. and Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xi Wang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China and Shenzhen People's Hospital, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518020, China
| | - Peiwu Huang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
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50
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Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Nature 2021; 594:246-252. [PMID: 33845483 DOI: 10.1038/s41586-021-03493-4] [Citation(s) in RCA: 364] [Impact Index Per Article: 121.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
The emergence and global spread of SARS-CoV-2 has resulted in the urgent need for an in-depth understanding of molecular functions of viral proteins and their interactions with the host proteome. Several individual omics studies have extended our knowledge of COVID-19 pathophysiology1-10. Integration of such datasets to obtain a holistic view of virus-host interactions and to define the pathogenic properties of SARS-CoV-2 is limited by the heterogeneity of the experimental systems. Here we report a concurrent multi-omics study of SARS-CoV-2 and SARS-CoV. Using state-of-the-art proteomics, we profiled the interactomes of both viruses, as well as their influence on the transcriptome, proteome, ubiquitinome and phosphoproteome of a lung-derived human cell line. Projecting these data onto the global network of cellular interactions revealed crosstalk between the perturbations taking place upon infection with SARS-CoV-2 and SARS-CoV at different levels and enabled identification of distinct and common molecular mechanisms of these closely related coronaviruses. The TGF-β pathway, known for its involvement in tissue fibrosis, was specifically dysregulated by SARS-CoV-2 ORF8 and autophagy was specifically dysregulated by SARS-CoV-2 ORF3. The extensive dataset (available at https://covinet.innatelab.org ) highlights many hotspots that could be targeted by existing drugs and may be used to guide rational design of virus- and host-directed therapies, which we exemplify by identifying inhibitors of kinases and matrix metalloproteases with potent antiviral effects against SARS-CoV-2.
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