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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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2
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Serrano LR, Peters-Clarke TM, Arrey TN, Damoc E, Robinson ML, Lancaster NM, Shishkova E, Moss C, Pashkova A, Sinitcyn P, Brademan DR, Quarmby ST, Peterson AC, Zeller M, Hermanson D, Stewart H, Hock C, Makarov A, Zabrouskov V, Coon JJ. The One Hour Human Proteome. Mol Cell Proteomics 2024; 23:100760. [PMID: 38579929 DOI: 10.1016/j.mcpro.2024.100760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/23/2024] [Accepted: 03/29/2024] [Indexed: 04/07/2024] Open
Abstract
We describe deep analysis of the human proteome in less than 1 h. We achieve this expedited proteome characterization by leveraging state-of-the-art sample preparation, chromatographic separations, and data analysis tools, and by using the new Orbitrap Astral mass spectrometer equipped with a quadrupole mass filter, a high-field Orbitrap mass analyzer, and an asymmetric track lossless (Astral) mass analyzer. The system offers high tandem mass spectrometry acquisition speed of 200 Hz and detects hundreds of peptide sequences per second within data-independent acquisition or data-dependent acquisition modes of operation. The fast-switching capabilities of the new quadrupole complement the sensitivity and fast ion scanning of the Astral analyzer to enable narrow-bin data-independent analysis methods. Over a 30-min active chromatographic method consuming a total analysis time of 56 min, the Q-Orbitrap-Astral hybrid MS collects an average of 4319 MS1 scans and 438,062 tandem mass spectrometry scans per run, producing 235,916 peptide sequences (1% false discovery rate). On average, each 30-min analysis achieved detection of 10,411 protein groups (1% false discovery rate). We conclude, with these results and alongside other recent reports, that the 1-h human proteome is within reach.
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Affiliation(s)
- Lia R Serrano
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Eugen Damoc
- Thermo Fisher Scientific GmbH, Bremen, Germany
| | - Margaret Lea Robinson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Noah M Lancaster
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | - Corinne Moss
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Pavel Sinitcyn
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | | | - Scott T Quarmby
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | | | | | | | | | | | | | | | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA.
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Chen M, Zhang L, Yao Z, Cao X, Ma Q, Chen S, Zhang X, Zhao S. Integrated Transcriptome and Proteome Analysis Reveals That Cell Wall Activity Affects Phelipanche aegyptiaca Parasitism. Plants (Basel) 2024; 13:869. [PMID: 38592861 PMCID: PMC10974318 DOI: 10.3390/plants13060869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Phelipanche aegyptiaca can infect many crops, causing large agricultural production losses. It is important to study the parasitism mechanism of P. aegyptiaca to control its harm. In this experiment, the P. aegyptiaca HY13M and TE9M from Tacheng Prefecture and Hami City in Xinjiang, respectively, were used to analyze the parasitical mechanism of P. aegyptiaca by means of transcriptome and proteome analyses. The parasitic capacity of TE9M was significantly stronger than that of HY13M in Citrullus lanatus. The results showed that the DEGs and DEPs were prominently enriched in the cell wall metabolism pathways, including "cell wall organization or biogenesis", "cell wall organization", and "cell wall". Moreover, the functions of the pectinesterase enzyme gene (TR138070_c0_g), which is involved in the cell wall metabolism of P. aegyptiaca in its parasitism, were studied by means HIGS. The number and weight of P. aegyptiaca were significantly reduced when TR138070_c0_g1, which encodes a cell-wall-degrading protease, was silenced, indicating that it positively regulates P. aegyptiaca parasitism. Thus, these results suggest that the cell wall metabolism pathway is involved in P. aegyptiaca differentiation of the parasitic ability and that the TR138070_c0_g1 gene plays an important role in P. aegyptiaca's parasitism.
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Affiliation(s)
- Meixiu Chen
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Shihezi University, Shihezi 832003, China; (M.C.); (L.Z.)
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Lu Zhang
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Shihezi University, Shihezi 832003, China; (M.C.); (L.Z.)
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Zhaoqun Yao
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Xiaolei Cao
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Qianqian Ma
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Siyu Chen
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Xuekun Zhang
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Sifeng Zhao
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Shihezi University, Shihezi 832003, China; (M.C.); (L.Z.)
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
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Yang Q, Langston JC, Prosniak R, Pettigrew S, Zhao H, Perez E, Edelmann H, Mansoor N, Merali C, Merali S, Marchetti N, Prabhakarpandian B, Kiani MF, Kilpatrick LE. Distinct functional neutrophil phenotypes in sepsis patients correlate with disease severity. Front Immunol 2024; 15:1341752. [PMID: 38524125 PMCID: PMC10957777 DOI: 10.3389/fimmu.2024.1341752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/26/2024] Open
Abstract
Purpose Sepsis is a clinical syndrome defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. Sepsis is a highly heterogeneous syndrome with distinct phenotypes that impact immune function and response to infection. To develop targeted therapeutics, immunophenotyping is needed to identify distinct functional phenotypes of immune cells. In this study, we utilized our Organ-on-Chip assay to categorize sepsis patients into distinct phenotypes using patient data, neutrophil functional analysis, and proteomics. Methods Following informed consent, neutrophils and plasma were isolated from sepsis patients in the Temple University Hospital ICU (n=45) and healthy control donors (n=7). Human lung microvascular endothelial cells (HLMVEC) were cultured in the Organ-on-Chip and treated with buffer or cytomix ((TNF/IL-1β/IFNγ). Neutrophil adhesion and migration across HLMVEC in the Organ-on-Chip were used to categorize functional neutrophil phenotypes. Quantitative label-free global proteomics was performed on neutrophils to identify differentially expressed proteins. Plasma levels of sepsis biomarkers and neutrophil extracellular traps (NETs) were determined by ELISA. Results We identified three functional phenotypes in critically ill ICU sepsis patients based on ex vivo neutrophil adhesion and migration patterns. The phenotypes were classified as: Hyperimmune characterized by enhanced neutrophil adhesion and migration, Hypoimmune that was unresponsive to stimulation, and Hybrid with increased adhesion but blunted migration. These functional phenotypes were associated with distinct proteomic signatures and differentiated sepsis patients by important clinical parameters related to disease severity. The Hyperimmune group demonstrated higher oxygen requirements, increased mechanical ventilation, and longer ICU length of stay compared to the Hypoimmune and Hybrid groups. Patients with the Hyperimmune neutrophil phenotype had significantly increased circulating neutrophils and elevated plasma levels NETs. Conclusion Neutrophils and NETs play a critical role in vascular barrier dysfunction in sepsis and elevated NETs may be a key biomarker identifying the Hyperimmune group. Our results establish significant associations between specific neutrophil functional phenotypes and disease severity and identify important functional parameters in sepsis pathophysiology that may provide a new approach to classify sepsis patients for specific therapeutic interventions.
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Affiliation(s)
- Qingliang Yang
- Department of Mechanical Engineering, College of Engineering, Temple University, Philadelphia, PA, United States
| | - Jordan C. Langston
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, PA, United States
| | - Roman Prosniak
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Samantha Pettigrew
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Huaqing Zhao
- Department of Biomedical Education and Data Science, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Edwin Perez
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Hannah Edelmann
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Nadia Mansoor
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Carmen Merali
- School of Pharmacy, Temple University, Philadelphia, PA, United States
| | - Salim Merali
- School of Pharmacy, Temple University, Philadelphia, PA, United States
| | - Nathaniel Marchetti
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | | | - Mohammad F. Kiani
- Department of Mechanical Engineering, College of Engineering, Temple University, Philadelphia, PA, United States
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, PA, United States
| | - Laurie E. Kilpatrick
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
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5
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Shi M, Evans CA, McQuillan JL, Noirel J, Pandhal J. LFQRatio: A Normalization Method to Decipher Quantitative Proteome Changes in Microbial Coculture Systems. J Proteome Res 2024; 23:999-1013. [PMID: 38354288 PMCID: PMC10913063 DOI: 10.1021/acs.jproteome.3c00714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The value of synthetic microbial communities in biotechnology is gaining traction due to their ability to undertake more complex metabolic tasks than monocultures. However, a thorough understanding of strain interactions, productivity, and stability is often required to optimize growth and scale up cultivation. Quantitative proteomics can provide valuable insights into how microbial strains adapt to changing conditions in biomanufacturing. However, current workflows and methodologies are not suitable for simple artificial coculture systems where strain ratios are dynamic. Here, we established a workflow for coculture proteomics using an exemplar system containing two members, Azotobacter vinelandii and Synechococcus elongatus. Factors affecting the quantitative accuracy of coculture proteomics were investigated, including peptide physicochemical characteristics such as molecular weight, isoelectric point, hydrophobicity, and dynamic range as well as factors relating to protein identification such as varying proteome size and shared peptides between species. Different quantification methods based on spectral counts and intensity were evaluated at the protein and cell level. We propose a new normalization method, named "LFQRatio", to reflect the relative contributions of two distinct cell types emerging from cell ratio changes during cocultivation. LFQRatio can be applied to real coculture proteomics experiments, providing accurate insights into quantitative proteome changes in each strain.
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Affiliation(s)
- Mengxun Shi
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
| | - Caroline A Evans
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
| | - Josie L McQuillan
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
| | - Josselin Noirel
- GBCM Laboratory (EA7528), Conservatoire National des Arts et Métiers, HESAM Université, 2 rue Conté, Paris 75003, France
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
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6
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Radke J, Meinhardt J, Aschman T, Chua RL, Farztdinov V, Lukassen S, Ten FW, Friebel E, Ishaque N, Franz J, Huhle VH, Mothes R, Peters K, Thomas C, Schneeberger S, Schumann E, Kawelke L, Jünger J, Horst V, Streit S, von Manitius R, Körtvélyessy P, Vielhaber S, Reinhold D, Hauser AE, Osterloh A, Enghard P, Ihlow J, Elezkurtaj S, Horst D, Kurth F, Müller MA, Gassen NC, Melchert J, Jechow K, Timmermann B, Fernandez-Zapata C, Böttcher C, Stenzel W, Krüger E, Landthaler M, Wyler E, Corman V, Stadelmann C, Ralser M, Eils R, Heppner FL, Mülleder M, Conrad C, Radbruch H. Proteomic and transcriptomic profiling of brainstem, cerebellum and olfactory tissues in early- and late-phase COVID-19. Nat Neurosci 2024; 27:409-420. [PMID: 38366144 DOI: 10.1038/s41593-024-01573-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
Neurological symptoms, including cognitive impairment and fatigue, can occur in both the acute infection phase of coronavirus disease 2019 (COVID-19) and at later stages, yet the mechanisms that contribute to this remain unclear. Here we profiled single-nucleus transcriptomes and proteomes of brainstem tissue from deceased individuals at various stages of COVID-19. We detected an inflammatory type I interferon response in acute COVID-19 cases, which resolves in the late disease phase. Integrating single-nucleus RNA sequencing and spatial transcriptomics, we could localize two patterns of reaction to severe systemic inflammation, one neuronal with a direct focus on cranial nerve nuclei and a separate diffuse pattern affecting the whole brainstem. The latter reflects a bystander effect of the respiratory infection that spreads throughout the vascular unit and alters the transcriptional state of mainly oligodendrocytes, microglia and astrocytes, while alterations of the brainstem nuclei could reflect the connection of the immune system and the central nervous system via, for example, the vagus nerve. Our results indicate that even without persistence of severe acute respiratory syndrome coronavirus 2 in the central nervous system, local immune reactions are prevailing, potentially causing functional disturbances that contribute to neurological complications of COVID-19.
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Affiliation(s)
- Josefine Radke
- Institute of Pathology, Universitätsmedizin Greifswald, Greifswald, Germany.
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Jenny Meinhardt
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tom Aschman
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Robert Lorenz Chua
- Center of Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Vadim Farztdinov
- Core Facility High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sören Lukassen
- Center of Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Foo Wei Ten
- Center of Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ekaterina Friebel
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Naveed Ishaque
- Center of Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jonas Franz
- Department of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Valerie Helena Huhle
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ronja Mothes
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kristin Peters
- Institute of Pathology, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Carolina Thomas
- Department of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Shirin Schneeberger
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Elisa Schumann
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Leona Kawelke
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Julia Jünger
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Viktor Horst
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Simon Streit
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Regina von Manitius
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Péter Körtvélyessy
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Vielhaber
- Department of Neurology, Otto von Guerike University Magdeburg, Magdeburg, Germany
| | - Dirk Reinhold
- Institute of Molecular and Clinical Immunology, Otto von Guerike University Magdeburg, Magdeburg, Germany
| | - Anja E Hauser
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Immune Dynamics, Deutsches Rheuma-Forschungszentrum, a Leibniz Institute, Berlin, Germany
| | - Anja Osterloh
- Department of Pathology, University Medical Center Ulm, Ulm, Germany
| | - Philipp Enghard
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jana Ihlow
- Department of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sefer Elezkurtaj
- Department of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - David Horst
- Department of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Marcel A Müller
- Institute of Virology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nils C Gassen
- Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Julia Melchert
- Institute of Virology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Katharina Jechow
- Center of Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Camila Fernandez-Zapata
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Chotima Böttcher
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Werner Stenzel
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institut für Biologie, Humboldt Universität, Berlin, Germany
| | - Emanuel Wyler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Victor Corman
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), associated partner, Berlin, Germany
| | - Christine Stadelmann
- Department of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Markus Ralser
- Core Facility High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Roland Eils
- Center of Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frank L Heppner
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Cluster of Excellence NeuroCure, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Mülleder
- Core Facility High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Conrad
- Center of Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Helena Radbruch
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
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7
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Huang M, Zheng X, Zhang Y, Wang R, Wei X. Comparative proteomics analysis of kidney in chicken infected by infectious bronchitis virus. Poult Sci 2024; 103:103259. [PMID: 37992619 PMCID: PMC10700468 DOI: 10.1016/j.psj.2023.103259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023] Open
Abstract
The gamma coronavirus infectious bronchitis virus (IBV) is known to cause an acute and highly contagious infectious disease in poultry. Here, this study aimed to investigate the impact of virulent or avirulent IBV infection on the avian host by conducting proteomics with data-independent acquisition mass spectrometry (DIA-MS) in the kidneys of IBV-infected chickens. The results revealed 267, 489, and 510 differentially expressed proteins (DEPs) in the chicken kidneys at 3, 5, and 7 days postinfection (dpi), respectively, when infected with the GD17/04 strain, which is a highly nephrogenic strain and belongs to the 4/91 genotype. In contrast, the attenuated 4/91 vaccine resulted in the identification of 144, 175, and 258 DEPs at 3, 5, and 7 dpi, respectively. Functional enrichment analyses indicated distinct expression profiles between the 2 IBV strains. Upon GD17/04 infection, metabolic pathways respond initially in the early stage (3 dpi) and immune-related signaling pathways respond in the middle and late stages (5 and 7 dpi). The 4/91 vaccine elicited a completely opposite response compared to the GD17/04 infection. Among all DEPs, 62 immune-related DEPs were focused on and found to be mainly enriched in the type I interferon (IFN-I) signaling pathway and involved in humoral and cellular immunity. Notably, key molecules in the IFN-I signaling pathway including MDA5, LGP2, and TBK1 may serve as regulatory targets of IBV. Overall, this study highlights similarities and discrepancies in the patterns of protein expression at different stages of infection with virulent and avirulent IBV strains, with the IFN-I signaling pathway emerging as a critical response to IBV infection.
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Affiliation(s)
- Mengjiao Huang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, China.
| | - Xuewei Zheng
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Yunjing Zhang
- National Research Center for Veterinary Medicine, Luoyang 471000, China
| | - Ruohan Wang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Xiaona Wei
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
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8
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Madern M, Reiter W, Stanek F, Hartl N, Mechtler K, Hartl M. A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics. Mol Cell Proteomics 2024; 23:100694. [PMID: 38097181 PMCID: PMC10828822 DOI: 10.1016/j.mcpro.2023.100694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 01/29/2024] Open
Abstract
Multiplex proteomics using isobaric labeling tags has emerged as a powerful tool for the simultaneous relative quantification of peptides and proteins across multiple experimental conditions. However, the quantitative accuracy of the approach is largely compromised by ion interference, a phenomenon that causes fold changes to appear compressed. The degree of compression is generally unknown, and the contributing factors are poorly understood. In this study, we thoroughly characterized ion interference at the MS2 level using a defined two-proteome experimental system with known ground-truth. We discovered remarkably poor agreement between the apparent precursor purity in the isolation window and the actual level of observed reporter ion interference in MS2 scans-a discrepancy that we found resolved by considering cofragmentation of peptide ions hidden within the spectral "noise" of the MS1 isolation window. To address this issue, we developed a regression modeling strategy to accurately predict reporter ion interference in any dataset. Finally, we demonstrate the utility of our procedure for improved fold change estimation and unbiased PTM site-to-protein normalization. All computational tools and code required to apply this method to any MS2 TMT dataset are documented and freely available.
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Affiliation(s)
- Moritz Madern
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Vienna, Austria; Department for Biochemistry and Cell Biology, Center for Molecular Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Wolfgang Reiter
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Vienna, Austria; Department for Biochemistry and Cell Biology, Center for Molecular Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Florian Stanek
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Natascha Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Markus Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Vienna, Austria; Department for Biochemistry and Cell Biology, Center for Molecular Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria.
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9
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Krumbein M, Oberman F, Cinnamon Y, Golomb M, May D, Vainer G, Belzer V, Meir K, Fridman I, Haybaeck J, Poelzl G, Kehat I, Beeri R, Kessler SM, Yisraeli JK. RNA binding protein IGF2BP2 expression is induced by stress in the heart and mediates dilated cardiomyopathy. Commun Biol 2023; 6:1229. [PMID: 38052926 PMCID: PMC10698010 DOI: 10.1038/s42003-023-05547-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
The IGF2BP family of RNA binding proteins consists of three paralogs that regulate intracellular RNA localization, RNA stability, and translational control. Although IGF2BP1 and 3 are oncofetal proteins, IGF2BP2 expression is maintained in many tissues, including the heart, into adulthood. IGF2BP2 is upregulated in cardiomyocytes during cardiac stress and remodeling and returns to normal levels in recovering hearts. We wondered whether IGF2BP2 might play an adaptive role during cardiac stress and recovery. Enhanced expression of an IGF2BP2 transgene in a conditional, inducible mouse line leads to dilated cardiomyopathy (DCM) and death within 3-4 weeks in newborn or adult hearts. Downregulation of the transgene after 2 weeks, however, rescues these mice, with complete recovery by 12 weeks. Hearts overexpressing IGF2BP2 downregulate sarcomeric and mitochondrial proteins and have fragmented mitochondria and elongated, thinner sarcomeres. IGF2BP2 is also upregulated in DCM or myocardial infarction patients. These results suggest that IGF2BP2 may be an attractive target for therapeutic intervention in cardiomyopathies.
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Affiliation(s)
- Miriam Krumbein
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Froma Oberman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Cinnamon
- Institute of Animal Science, Agricultural Research Organization, The Volcani Institute, Rishon Lezion, Israel
| | | | - Dalit May
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Shaare Zedek Medical Center, Jerusalem, Israel
- Clalit Health Service, Jerusalem, Israel
| | - Gilad Vainer
- Department of Pathology, Hadassah Medical Center, Jerusalem, Israel
| | - Vitali Belzer
- Department of Pathology, Hadassah Medical Center, Jerusalem, Israel
| | - Karen Meir
- Department of Pathology, Hadassah Medical Center, Jerusalem, Israel
| | - Irina Fridman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Johannes Haybaeck
- Institut für Pathologie, Neuropathologie und Molekularpathologie, Medical University Innsbruck, Innsbruck, Austria
- Diagnostic and Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, 8010, Graz, Austria
| | - Gerhard Poelzl
- Department of Cardiology and Angiology, Medical University Innsbruck, Innsbruck, Austria
| | - Izhak Kehat
- Department of Physiology and Biophysics, The Ruth and Bruce Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Bat Galim, Haifa, Israel
| | - Ronen Beeri
- Department of Cardiology, Hadassah Medical Center, Jerusalem, Israel
| | - Sonja M Kessler
- Experimental Pharmacology for Natural Sciences, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany.
| | - Joel K Yisraeli
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
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10
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Stewart HI, Grinfeld D, Giannakopulos A, Petzoldt J, Shanley T, Garland M, Denisov E, Peterson AC, Damoc E, Zeller M, Arrey TN, Pashkova A, Renuse S, Hakimi A, Kühn A, Biel M, Kreutzmann A, Hagedorn B, Colonius I, Schütz A, Stefes A, Dwivedi A, Mourad D, Hoek M, Reitemeier B, Cochems P, Kholomeev A, Ostermann R, Quiring G, Ochmann M, Möhring S, Wagner A, Petker A, Kanngiesser S, Wiedemeyer M, Balschun W, Hermanson D, Zabrouskov V, Makarov AA, Hock C. Parallelized Acquisition of Orbitrap and Astral Analyzers Enables High-Throughput Quantitative Analysis. Anal Chem 2023; 95:15656-15664. [PMID: 37815927 PMCID: PMC10603608 DOI: 10.1021/acs.analchem.3c02856] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023]
Abstract
The growing trend toward high-throughput proteomics demands rapid liquid chromatography-mass spectrometry (LC-MS) cycles that limit the available time to gather the large numbers of MS/MS fragmentation spectra required for identification. Orbitrap analyzers scale performance with acquisition time and necessarily sacrifice sensitivity and resolving power to deliver higher acquisition rates. We developed a new mass spectrometer that combines a mass-resolving quadrupole, the Orbitrap, and the novel Asymmetric Track Lossless (Astral) analyzer. The new hybrid instrument enables faster acquisition of high-resolution accurate mass (HRAM) MS/MS spectra compared with state-of-the-art mass spectrometers. Accordingly, new proteomics methods were developed that leverage the strengths of each HRAM analyzer, whereby the Orbitrap analyzer performs full scans with a high dynamic range and resolution, synchronized with the Astral analyzer's acquisition of fast and sensitive HRAM MS/MS scans. Substantial improvements are demonstrated over previous methods using current state-of-the-art mass spectrometers.
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Affiliation(s)
- Hamish I. Stewart
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Dmitry Grinfeld
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | - Johannes Petzoldt
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Toby Shanley
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Matthew Garland
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Eduard Denisov
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | - Eugen Damoc
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Martin Zeller
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Tabiwang N. Arrey
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Anna Pashkova
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Santosh Renuse
- Thermo
Fisher Scientific, 355
River Oaks Pkwy, San Jose, California 95134, United States
| | - Amirmansoor Hakimi
- Thermo
Fisher Scientific, 355
River Oaks Pkwy, San Jose, California 95134, United States
| | - Andreas Kühn
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Matthias Biel
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Arne Kreutzmann
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Bernd Hagedorn
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Immo Colonius
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Adrian Schütz
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Arne Stefes
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Ankit Dwivedi
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Daniel Mourad
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Max Hoek
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | - Philipp Cochems
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
- Thermo
Fisher Scientific, 355
River Oaks Pkwy, San Jose, California 95134, United States
| | | | - Robert Ostermann
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Gregor Quiring
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | - Sascha Möhring
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Alexander Wagner
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - André Petker
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | | | - Wilko Balschun
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Daniel Hermanson
- Thermo
Fisher Scientific, 355
River Oaks Pkwy, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo
Fisher Scientific, 355
River Oaks Pkwy, San Jose, California 95134, United States
| | | | - Christian Hock
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
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11
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Rojas J, Oz T, Jonak K, Lyzak O, Massaad V, Biriuk O, Zachariae W. Spo13/MEIKIN ensures a Two-Division meiosis by preventing the activation of APC/C Ama1 at meiosis I. EMBO J 2023; 42:e114288. [PMID: 37728253 PMCID: PMC10577557 DOI: 10.15252/embj.2023114288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/21/2023] Open
Abstract
Genome haploidization at meiosis depends on two consecutive nuclear divisions, which are controlled by an oscillatory system consisting of Cdk1-cyclin B and the APC/C bound to the Cdc20 activator. How the oscillator generates exactly two divisions has been unclear. We have studied this question in yeast where exit from meiosis involves accumulation of the APC/C activator Ama1 at meiosis II. We show that inactivation of the meiosis I-specific protein Spo13/MEIKIN results in a single-division meiosis due to premature activation of APC/CAma1 . In the wild type, Spo13 bound to the polo-like kinase Cdc5 prevents Ama1 synthesis at meiosis I by stabilizing the translational repressor Rim4. In addition, Cdc5-Spo13 inhibits the activity of Ama1 by converting the B-type cyclin Clb1 from a substrate to an inhibitor of Ama1. Cdc20-dependent degradation of Spo13 at anaphase I unleashes a feedback loop that increases Ama1's synthesis and activity, leading to irreversible exit from meiosis at the second division. Thus, by repressing the exit machinery at meiosis I, Cdc5-Spo13 ensures that cells undergo two divisions to produce haploid gametes.
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Affiliation(s)
- Julie Rojas
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
Laboratory of GeneticsUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Tugce Oz
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Katarzyna Jonak
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Oleksii Lyzak
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Vinal Massaad
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Olha Biriuk
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Wolfgang Zachariae
- Laboratory of Chromosome BiologyMax Planck Institute of BiochemistryMartinsriedGermany
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12
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Bennike TB. Advances in proteomics: characterization of the innate immune system after birth and during inflammation. Front Immunol 2023; 14:1254948. [PMID: 37868984 PMCID: PMC10587584 DOI: 10.3389/fimmu.2023.1254948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/26/2023] [Indexed: 10/24/2023] Open
Abstract
Proteomics is the characterization of the protein composition, the proteome, of a biological sample. It involves the large-scale identification and quantification of proteins, peptides, and post-translational modifications. This review focuses on recent developments in mass spectrometry-based proteomics and provides an overview of available methods for sample preparation to study the innate immune system. Recent advancements in the proteomics workflows, including sample preparation, have significantly improved the sensitivity and proteome coverage of biological samples including the technically difficult blood plasma. Proteomics is often applied in immunology and has been used to characterize the levels of innate immune system components after perturbations such as birth or during chronic inflammatory diseases like rheumatoid arthritis (RA) and inflammatory bowel disease (IBD). In cancers, the tumor microenvironment may generate chronic inflammation and release cytokines to the circulation. In these situations, the innate immune system undergoes profound and long-lasting changes, the large-scale characterization of which may increase our biological understanding and help identify components with translational potential for guiding diagnosis and treatment decisions. With the ongoing technical development, proteomics will likely continue to provide increasing insights into complex biological processes and their implications for health and disease. Integrating proteomics with other omics data and utilizing multi-omics approaches have been demonstrated to give additional valuable insights into biological systems.
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Affiliation(s)
- Tue Bjerg Bennike
- Medical Microbiology and Immunology, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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13
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Topriceanu CC, Alfarih M, Hughes AD, Shiwani H, Chan F, Mohiddin SA, Moody W, Steeds RP, O’Brien B, Vowinckel J, Syrris P, Coats C, Pettit S, Arbustini E, Moon JC, Captur G. The atrial and ventricular myocardial proteome of end-stage lamin heart disease. Acta Myol 2023; 42:43-52. [PMID: 38090549 PMCID: PMC10712656 DOI: 10.36185/2532-1900-339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/02/2023] [Indexed: 12/18/2023]
Abstract
Lamins A/C (encoded by LMNA gene) can lead to dilated cardiomyopathy (DCM). This pilot study sought to explore the postgenomic phenotype of end-stage lamin heart disease. Consecutive patients with end-stage lamin heart disease (LMNA-group, n = 7) and ischaemic DCM (ICM-group, n = 7) undergoing heart transplantation were prospectively enrolled. Samples were obtained from left atrium (LA), left ventricle (LV), right atrium (RA), right ventricle (RV) and interventricular septum (IVS), avoiding the infarcted myocardial segments in the ICM-group. Samples were analysed using a discovery 'shotgun' proteomics approach. We found that 990 proteins were differentially abundant between LMNA and ICM samples with the LA being most perturbed (16-fold more than the LV). Abundance of lamin A/C protein was reduced, but lamin B increased in LMNA LA/RA tissue compared to ICM, but not in LV/RV. Carbonic anhydrase 3 (CA3) was over-abundant across all LMNA tissue samples (LA, LV, RA, RV, and IVS) when compared to ICM. Transthyretin was more abundant in the LV/RV of LMNA compared to ICM, while sarcomeric proteins such as titin and cardiac alpha-cardiac myosin heavy chain were generally less abundant in RA/LA of LMNA. Protein expression profiling and enrichment analysis pointed towards sarcopenia, extracellular matrix remodeling, deficient myocardial energetics, redox imbalances, and abnormal calcium handling in LMNA samples. Compared to ICM, end-stage lamin heart disease is a biventricular but especially a biatrial disease appearing to have an abundance of lamin B, CA3 and transthyretin, potentially hinting to compensatory responses.
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Affiliation(s)
- Constantin-Cristian Topriceanu
- UCL MRC Unit for Lifelong Health and Ageing, University College London, London, UK
- UCL Institute of Cardiovascular Science, University College London, London, UK
- Cardiac MRI Unit, Barts Heart Centre, London, UK
| | - Mashael Alfarih
- UCL MRC Unit for Lifelong Health and Ageing, University College London, London, UK
- UCL Institute of Cardiovascular Science, University College London, London, UK
| | - Alun D Hughes
- UCL MRC Unit for Lifelong Health and Ageing, University College London, London, UK
- UCL Institute of Cardiovascular Science, University College London, London, UK
| | | | - Fiona Chan
- UCL MRC Unit for Lifelong Health and Ageing, University College London, London, UK
- UCL Institute of Cardiovascular Science, University College London, London, UK
| | | | - William Moody
- Centre for Cardiovascular Sciences, University of Birmingham, Birmingham, UK
- Department of Cardiology, The Queen Elizabeth HospitalBirmingham, UK
| | - Richard P. Steeds
- Centre for Cardiovascular Sciences, University of Birmingham, Birmingham, UK
- Department of Cardiology, The Queen Elizabeth HospitalBirmingham, UK
| | - Benjamin O’Brien
- Department of Perioperative Medicine, St. Bartholomew’s Hospital, London, UK
- Department of Cardiac Anesthesiology and Intensive Care Medicine, German Heart Center, Berlin, Germany
- Department of Cardiac Anesthesiology and Intensive Care Medicine, Charité Berlin, Berlin, Germany
- Outcomes Research Consortium, Department of Outcomes Research, The Cleveland Clinic, Ohio, USA
| | | | - Petros Syrris
- UCL Institute of Cardiovascular Science, University College London, London, UK
| | | | - Stephen Pettit
- Advanced Heart Failure and Transplant Unit, Royal Papworth Hospital, Cambridge, UK
| | - Eloisa Arbustini
- Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Department of Medical Sciences and Infectious Diseases, IRCCS San Matteo Hospital Foundation, Pavia, Italy
| | - James C. Moon
- UCL Institute of Cardiovascular Science, University College London, London, UK
- Cardiac MRI Unit, Barts Heart Centre, London, UK
| | - Gabriella Captur
- UCL MRC Unit for Lifelong Health and Ageing, University College London, London, UK
- UCL Institute of Cardiovascular Science, University College London, London, UK
- The Royal Free Hospital, Centre for Inherited Heart Muscle Conditions, Cardiology Department, Pond Street, Hampstead, London, UK
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14
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Perchepied S, Zhou Z, Mitulović G, Eeltink S. Exploiting ion-mobility mass spectrometry for unraveling proteome complexity. J Sep Sci 2023; 46:e2300512. [PMID: 37746674 DOI: 10.1002/jssc.202300512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) is experiencing rapid growth in proteomic studies, driven by its enhancements in dynamic range and throughput, increasing the quantitation precision, and the depth of proteome coverage. The core principle of ion mobility spectrometry is to separate ions in an inert gas under the influence of an electric field based on differences in drift time. This minireview provides an introduction to IMS operation modes and a description of advantages and limitations is presented. Moreover, the principles of trapped IMS-MS (TIMS-MS), including parallel accumulation-serial fragmentation are discussed. Finally, emerging applications linked to TIMS focusing on sample throughput (in clinical proteomics) and sensitivity (single-cell proteomics) are reviewed, and the possibilities of intact protein analysis are discussed.
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Affiliation(s)
- Stan Perchepied
- Department of Chemical Engineering, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Zhuoheng Zhou
- Department of Chemical Engineering, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Sebastiaan Eeltink
- Department of Chemical Engineering, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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15
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Yehuda A, Malach E, Vanunu Ofri S, Slamti L, Kuo SH, Lau JZ, Oh MW, Adeoye J, Shlezinger N, Lereclus D, Lau GW, Hayouka Z. The quorum-sensing peptidic inhibitor rescues host immune system eradication: A novel infectivity mechanism. Proc Natl Acad Sci U S A 2023; 120:e2301045120. [PMID: 37607229 PMCID: PMC10469338 DOI: 10.1073/pnas.2301045120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/23/2023] [Indexed: 08/24/2023] Open
Abstract
Subverting the host immune system is a major task for any given pathogen to assure its survival and proliferation. For the opportunistic human pathogen Bacillus cereus (Bc), immune evasion enables the establishment of potent infections. In various species of the Bc group, the pleiotropic regulator PlcR and its cognate cell-cell signaling peptide PapR7 regulate virulence gene expression in response to fluctuations in population density, i.e., a quorum-sensing (QS) system. However, how QS exerts its effects during infections and whether PlcR confers the immune evading ability remain unclear. Herein, we report how interception of the QS communication in Bc obliterates the ability to affect the host immune system. Here, we designed a peptide-based QS inhibitor that suppresses PlcR-dependent virulence factor expression and attenuates Bc infectivity in mouse models. We demonstrate that the QS peptidic inhibitor blocks host immune system-mediated eradication by reducing the expression of PlcR-regulated major toxins similarly to the profile that was observed for isogenic strains. Our findings provide evidence that Bc infectivity is regulated by QS circuit-mediated destruction of host immunity, thus reveal a interesting strategy to limit Bc virulence and enhance host defense. This peptidic quorum-quenching agent constitutes a readily accessible chemical tool for studying how other pathogen QS systems modulate host immunity and forms a basis for development of anti-infective therapeutics.
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Affiliation(s)
- Avishag Yehuda
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agricultural, Food & Environment, The Hebrew University of Jerusalem, Rehovot76100, Israel
| | - Einav Malach
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agricultural, Food & Environment, The Hebrew University of Jerusalem, Rehovot76100, Israel
| | - Shahar Vanunu Ofri
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agricultural, Food & Environment, The Hebrew University of Jerusalem, Rehovot76100, Israel
| | - Leyla Slamti
- Unité Micalis, Domaine de La Minière, Unité Mixte de Recherche 1319, Institut National de la Recherche Agronomique, 78280Guyancourt, France
| | - Shanny Hsuan Kuo
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL61802
| | - Jonathan Z. Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL61802
| | - Myung Whan Oh
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL61802
| | - John Adeoye
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agricultural, Food & Environment, The Hebrew University of Jerusalem, Rehovot76100, Israel
| | - Neta Shlezinger
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agricultural, Food & Environment, The Hebrew University of Jerusalem, Rehovot76100, Israel
| | - Didier Lereclus
- Unité Micalis, Domaine de La Minière, Unité Mixte de Recherche 1319, Institut National de la Recherche Agronomique, 78280Guyancourt, France
| | - Gee W. Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL61802
| | - Zvi Hayouka
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agricultural, Food & Environment, The Hebrew University of Jerusalem, Rehovot76100, Israel
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16
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He Y, Shishkova E, Peters-Clarke TM, Brademan DR, Westphall MS, Bergen D, Huang J, Huguet R, Senko MW, Zabrouskov V, McAlister GC, Coon JJ. Evaluation of the Orbitrap Ascend Tribrid Mass Spectrometer for Shotgun Proteomics. Anal Chem 2023; 95:10655-10663. [PMID: 37389810 PMCID: PMC10528367 DOI: 10.1021/acs.analchem.3c01155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Mass spectrometry (MS)-based proteomics is a powerful technology to globally profile protein abundances, activities, interactions, and modifications. The extreme complexity of proteomics samples, which often contain hundreds of thousands of analytes, necessitates continuous development of MS techniques and instrumentation to improve speed, sensitivity, precision, and accuracy, among other analytical characteristics. Here, we systematically evaluated the Orbitrap Ascend Tribrid mass spectrometer in the context of shotgun proteomics, and we compared its performance to that of the previous generation of Tribrid instruments─the Orbitrap Eclipse. The updated architecture of the Orbitrap Ascend includes a second ion-routing multipole (IRM) in front of the redesigned C-trap/Orbitrap and a new ion funnel that allows gentler ion introduction, among other changes. These modifications in Ascend hardware configuration enabled an increase in parallelizable ion injection time during higher-energy collisional dissociation (HCD) Orbitrap tandem MS (FTMS2) analysis of ∼5 ms. This enhancement was particularly valuable in the analyses of limited sample amounts, where improvements in sensitivity resulted in up to 140% increase in the number of identified tryptic peptides. Further, analysis of phosphorylated peptides enriched from the K562 human cell line yielded up to ∼50% increase in the number of unique phosphopeptides and localized phosphosites. Strikingly, we also observed a ∼2-fold boost in the number of detected N-glycopeptides, likely owing to the improvements in ion transmission and sensitivity. In addition, we performed the multiplexed quantitative proteomics analyses of TMT11-plex labeled HEK293T tryptic peptides and observed 9-14% increase in the number of quantified peptides. In conclusion, the Orbitrap Ascend consistently outperformed its predecessor the Orbitrap Eclipse in various bottom-up proteomic analyses, and we anticipate that it will generate reproducible and in-depth datasets for numerous proteomic applications.
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Affiliation(s)
- Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | | | | | - Michael S. Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - David Bergen
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | | | | | | | | | | | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
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17
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Salignon J, Faridani OR, Miliotis T, Janssens GE, Chen P, Zarrouki B, Sandberg R, Davidsson P, Riedel CG. Age prediction from human blood plasma using proteomic and small RNA data: a comparative analysis. Aging (Albany NY) 2023; 15:5240-5265. [PMID: 37341993 PMCID: PMC10333066 DOI: 10.18632/aging.204787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/26/2023] [Indexed: 06/22/2023]
Abstract
Aging clocks, built from comprehensive molecular data, have emerged as promising tools in medicine, forensics, and ecological research. However, few studies have compared the suitability of different molecular data types to predict age in the same cohort and whether combining them would improve predictions. Here, we explored this at the level of proteins and small RNAs in 103 human blood plasma samples. First, we used a two-step mass spectrometry approach measuring 612 proteins to select and quantify 21 proteins that changed in abundance with age. Notably, proteins increasing with age were enriched for components of the complement system. Next, we used small RNA sequencing to select and quantify a set of 315 small RNAs that changed in abundance with age. Most of these were microRNAs (miRNAs), downregulated with age, and predicted to target genes related to growth, cancer, and senescence. Finally, we used the collected data to build age-predictive models. Among the different types of molecules, proteins yielded the most accurate model (R² = 0.59 ± 0.02), followed by miRNAs as the best-performing class of small RNAs (R² = 0.54 ± 0.02). Interestingly, the use of protein and miRNA data together improved predictions (R2 = 0.70 ± 0.01). Future work using larger sample sizes and a validation dataset will be necessary to confirm these results. Nevertheless, our study suggests that combining proteomic and miRNA data yields superior age predictions, possibly by capturing a broader range of age-related physiological changes. It will be interesting to determine if combining different molecular data types works as a general strategy to improve future aging clocks.
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Affiliation(s)
- Jérôme Salignon
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institutet, Huddinge 14157, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden
| | - Omid R. Faridani
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institutet, Huddinge 14157, Sweden
- Lowy Cancer Research Centre, School of Medical Sciences, University of New South Wales, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
| | - Tasso Miliotis
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Georges E. Janssens
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institutet, Huddinge 14157, Sweden
| | - Ping Chen
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institutet, Huddinge 14157, Sweden
| | - Bader Zarrouki
- Bioscience Metabolism, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Rickard Sandberg
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institutet, Huddinge 14157, Sweden
- Department of Cellular and Molecular Biology, Ludwig Institute for Cancer Research, Karolinska Institutet, Solna 17165, Sweden
| | - Pia Davidsson
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Christian G. Riedel
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institutet, Huddinge 14157, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden
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18
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Müller F, Bange T. Identification of N-degrons and N-recognins using peptide pull-downs combined with quantitative mass spectrometry. Methods Enzymol 2023; 686:67-97. [PMID: 37532409 DOI: 10.1016/bs.mie.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Regulated protein degradation controls protein levels of all short-lived proteins to ensure cellular homeostasis and also protects cells from misfolded or other abnormal proteins. The most important players in the degradation system are E3 ubiquitin ligases which recognize exposed sequence motifs, so-called degrons, of target proteins and mark them through the attachment of ubiquitin for degradation. N-terminal (Nt) sequences are extensively used as degrons (N-degrons) and all 20 amino acids are able to feed proteins in 1 of the 5 known N-degron pathways. Studies have mainly focused on characterizing systematically the role of the starting amino acid on protein stability and less on the identification of the E3 ligases involved. Recent data from our lab and literature suggest that there is an extensive interplay of N-recognins and Nt-modifying enzymes like Nt-acetyltransferases (NATs) or N-myristoyltransferases which only starts to be elucidated. It suggests that improperly modified or unexpectedly unmodified proteins become rapidly removed after synthesis ensuring protein maturation and quality control of specific subsets of proteins. Here, we describe a peptide pull-down and down-stream bioinformatics workflow conducted in the MaxQuant and Perseus computational environment to identify N-recognin candidates in an unbiased way using quantitative mass spectrometry (MS)-based proteomics. Our workflow allows the identification of N-recognin candidates for specific N-degrons, to determine their sequence specificity and it can be applied as well more general to identify binding partners of N-terminal modifications. This method paves the way to identify pathways involved in protein quality control and stability acting at the N-terminus.
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Affiliation(s)
- Franziska Müller
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Tanja Bange
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians University, Munich, Germany.
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19
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Tian X, Permentier HP, Bischoff R. Chemical isotope labeling for quantitative proteomics. Mass Spectrom Rev 2023; 42:546-576. [PMID: 34091937 PMCID: PMC10078755 DOI: 10.1002/mas.21709] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 05/05/2023]
Abstract
Advancements in liquid chromatography and mass spectrometry over the last decades have led to a significant development in mass spectrometry-based proteome quantification approaches. An increasingly attractive strategy is multiplex isotope labeling, which significantly improves the accuracy, precision and throughput of quantitative proteomics in the data-dependent acquisition mode. Isotope labeling-based approaches can be classified into MS1-based and MS2-based quantification. In this review, we give an overview of approaches based on chemical isotope labeling and discuss their principles, benefits, and limitations with the goal to give insights into fundamental questions and provide a useful reference for choosing a method for quantitative proteomics. As a perspective, we discuss the current possibilities and limitations of multiplex, isotope labeling approaches for the data-independent acquisition mode, which is increasing in popularity.
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Affiliation(s)
- Xiaobo Tian
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
| | - Hjalmar P. Permentier
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
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20
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Sha M, Li X, Liu Y, Tian H, Liang X, Li X, Gao W. Comparative chemical characters of Pseudostellaria heterophylla from geographical origins of China. Chinese Herbal Medicines 2023. [PMID: 37538864 PMCID: PMC10394325 DOI: 10.1016/j.chmed.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
Objective Pseudostellaria heterophylla has been paid more attention in recent years, mainly as a medicine food homology plant. The content determination of P. heterophylla is not specified in the Chinese Pharmacopoeia (version 2020). The environmental conditions in different production areas could exert an influence on the quality of P. heterophylla. The purpose of this study is to discriminate P. heterophylla collected from different geographical origins of China. Methods In this study, the content of polysaccharide in 28 batches of P. heterophylla was determined using phenol-sulfuric acid. HPLC fingerprints were established under optimised HPLC-PDA methods. Subsequently, the similarity analysis (SA) and the quantification of heterophyllin B were analyzed. The metabolites of P. heterophylla were identified and evaluated using UHPLC-Q Exactive HF orbitrap MS system. Principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), hierarchical cluster analysis (HCA) and orthogonal PLS-DA (OPLS-DA) were performed based on all peak areas. Results The polysaccharide content in Guizhou and Jiangsu was higher than that of other production areas, which varied significant from different origins. While the content of heterophyllin B in Anhui and Jiangsu was high. The correlation coefficients of HPLC fingerprints for 28 batches samples ranged from 0.877 to 0.990, and the characteristic map can be used to identify and evaluate the quality of P. heterophylla. The samples from Fujian, Guizhou, Jiangsu provinces can be relatively separated using multivariate statistical analysis including PCA, PLS-DA, HCA, OPLS-DA, indicating that their metabolic compositions were significantly different. Ultimately, a total of 15 metabolites which were filtrated by a VIP-value > 1 and a P-value < 0.05 associated with the separation of different origins were identified. Conclusion HPLC fingerprint was established to evaluate the quality and authenticity of P. heterophylla. The present work showed that the difference of geographic distributions had an influence on the internal chemical compositions. A sensitive and rapid untargeted metabolomics approach by UHPLC-Q Exactive HF orbitrap MS was utilized to evaluate P. heterophylla from different origins in China for the first time. Overall, this study provides insights to metabolomics of P. heterophylla and supplies important reference values for the development of functional foods.
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21
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Zeng HL, Hu L, Chen X, Han QQ, Li H, Cheng L, Li CX. DIA-MS Based Proteomics Combined with RNA-Seq Data to Unveil the Mitochondrial Dysfunction in Human Glioblastoma. Molecules 2023; 28. [PMID: 36838582 DOI: 10.3390/molecules28041595] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
Mitochondrial dysfunctions underlie the pathogenesis in glioblastoma multiforme (GBM). Comprehensive proteomic profiling of mitochondria-specific changes in human GBM is still insufficient. This study carried out a DIA-MS based proteomic analysis on the mitochondria isolated from human primary GBM and peritumoral tissue (as paired control), and further compared those findings with the transcriptomic datasets. A total of 538 mitochondrion-specific proteins were rigorously confirmed, among which 190 differentially expressed proteins were identified. Co-regulations of the mitochondrial dysfunction pathway networks were observed, including significant up-regulations of mitochondrial translation and apoptosis, as well as down-regulations of OXPHOS and mitochondrial dynamics. Proteins related to FA, AA metabolism and ROS also showed significant variations. Most of these alterations were consistent in trend when compared the proteomics findings with the RNA-Seq datasets, while the changes at protein levels appeared to be more dramatic. Potentially key proteins in GBM were identified, including up-regulated pro-apoptotic protein CASP3, BAX, fatty acid oxidation enzymes CPT1A, CPT2, ACADM, serine-glycine enzymes SHMT2, GATM, ROS-related protein SOD2, GPX1, and CAT; and down-regulated dynamin-related protein MFN1, MFN2, OPA1, and OXPHOS components; and also several differentially expressed ALDH isoforms. This study systematically profiled the mitochondrial dysfunctions by combining proteomic findings and mRNA datasets, which would be a valuable resource to the community for further thorough analyses.
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22
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Rotheneder M, Stakyte K, van de Logt E, Bartho JD, Lammens K, Fan Y, Alt A, Kessler B, Jung C, Roos WP, Steigenberger B, Hopfner KP. Cryo-EM structure of the Mre11-Rad50-Nbs1 complex reveals the molecular mechanism of scaffolding functions. Mol Cell 2023; 83:167-185.e9. [PMID: 36577401 DOI: 10.1016/j.molcel.2022.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/14/2022] [Accepted: 12/03/2022] [Indexed: 12/28/2022]
Abstract
The DNA double-strand break repair complex Mre11-Rad50-Nbs1 (MRN) detects and nucleolytically processes DNA ends, activates the ATM kinase, and tethers DNA at break sites. How MRN can act both as nuclease and scaffold protein is not well understood. The cryo-EM structure of MRN from Chaetomium thermophilum reveals a 2:2:1 complex with a single Nbs1 wrapping around the autoinhibited Mre11 nuclease dimer. MRN has two DNA-binding modes, one ATP-dependent mode for loading onto DNA ends and one ATP-independent mode through Mre11's C terminus, suggesting how it may interact with DSBs and intact DNA. MRNs two 60-nm-long coiled-coil domains form a linear rod structure, the apex of which is assembled by the two joined zinc-hook motifs. Apices from two MRN complexes can further dimerize, forming 120-nm spanning MRN-MRN structures. Our results illustrate the architecture of MRN and suggest how it mechanistically integrates catalytic and tethering functions.
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Affiliation(s)
- Matthias Rotheneder
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Kristina Stakyte
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Erik van de Logt
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Joseph D Bartho
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Katja Lammens
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Yilan Fan
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Aaron Alt
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Brigitte Kessler
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Christophe Jung
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Wynand P Roos
- Institute for Toxicology, Johannes-Gutenberg-Universität, Mainz, Germany
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany.
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23
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Smith EG, Surm JM, Macrander J, Simhi A, Amir G, Sachkova MY, Lewandowska M, Reitzel AM, Moran Y. Micro and macroevolution of sea anemone venom phenotype. Nat Commun 2023; 14:249. [PMID: 36646703 PMCID: PMC9842752 DOI: 10.1038/s41467-023-35794-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
Venom is a complex trait with substantial inter- and intraspecific variability resulting from strong selective pressures acting on the expression of many toxic proteins. However, understanding the processes underlying toxin expression dynamics that determine the venom phenotype remains unresolved. By interspecific comparisons we reveal that toxin expression in sea anemones evolves rapidly and that in each species different toxin family dictates the venom phenotype by massive gene duplication events. In-depth analysis of the sea anemone, Nematostella vectensis, revealed striking variation of the dominant toxin (Nv1) diploid copy number across populations (1-24 copies) resulting from independent expansion/contraction events, which generate distinct haplotypes. Nv1 copy number correlates with expression at both the transcript and protein levels with one population having a near-complete loss of Nv1 production. Finally, we establish the dominant toxin hypothesis which incorporates observations in other venomous lineages that animals have convergently evolved a similar strategy in shaping their venom.
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Affiliation(s)
- Edward G Smith
- University of North Carolina at Charlotte, Department of Biological Sciences, Charlotte, NC, USA. .,School of Life Sciences, University of Warwick, Coventry, United Kingdom.
| | - Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Jason Macrander
- University of North Carolina at Charlotte, Department of Biological Sciences, Charlotte, NC, USA.,Florida Southern College, Biology Department, Lakeland, FL, USA
| | - Adi Simhi
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Hebrew University of Jerusalem, The School of Computer Science & Engineering, Jerusalem, Israel
| | - Guy Amir
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Hebrew University of Jerusalem, The School of Computer Science & Engineering, Jerusalem, Israel
| | - Maria Y Sachkova
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Magda Lewandowska
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adam M Reitzel
- University of North Carolina at Charlotte, Department of Biological Sciences, Charlotte, NC, USA
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.
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24
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Liang Y, Zhang L, Zhang Y. Chromatographic separation of peptides and proteins for characterization of proteomes. Chem Commun (Camb) 2023; 59:270-281. [PMID: 36504223 DOI: 10.1039/d2cc05568f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Characterization of proteomes aims to comprehensively characterize proteins in cells or tissues via two main strategies: (1) bottom-up strategy based on the separation and identification of enzymatic peptides; (2) top-down strategy based on the separation and identification of intact proteins. However, it is challenged by the high complexity of proteomes. Consequently, the improvements in peptide and protein separation technologies for simplifying the sample should be critical. In this feature article, separation columns for peptide and protein separation were introduced, and peptide separation technologies for bottom-up proteomic analysis as well as protein separation technologies for top-down proteomic analysis were summarized. The achievement, recent development, limitation and future trends are discussed. Besides, the outlook on challenges and future directions of chromatographic separation in the field of proteomics was also presented.
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Affiliation(s)
- Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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25
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Carmon I, Zecharyahu L, Elayyan J, Meka SRK, Reich E, Kandel L, Bilkei-Gorzo A, Zimmer A, Mechoulam R, Kravchenko-Balasha N, Dvir-Ginzberg M. HU308 Mitigates Osteoarthritis by Stimulating Sox9-Related Networks of Carbohydrate Metabolism. J Bone Miner Res 2023; 38:154-170. [PMID: 36350089 PMCID: PMC10098743 DOI: 10.1002/jbmr.4741] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/11/2022]
Abstract
Osteoarthritis (OA) is characterized by progressive, irreversible erosion of articular cartilage accompanied by severe pain and immobility. This study aimed to assess the effect and mechanism of action of HU308, a selective cannabinoid receptor type 2 (CB2) agonist, in preventing OA-related joint damage. To test the assumption that HU308 could prevent OA-related joint damage, Cnr2 null mice and wild type (WT) mice were aged to reach 20 months and analyzed for joint structural features. OA was induced in WT mice via a post-traumatic procedure or aging, followed by HU308 local (intra-articular) or systemic (intraperitoneal) administration, respectively. Additional analyses of time and dose courses for HU308 were carried out in human primary chondrocytes, analyzed by RNA sequencing, RT-PCR, chromatin immunoprecipitation, and immunoblotting. Our results showed that Cnr2 null mice exhibited enhanced age-related OA severity and synovitis compared to age-matched WT mice. Systemic administration of HU308 to 16-month-old mice improved pain sensitivity and maintained joint integrity, which was consistent with the intra-articular administration of HU308 in post-traumatic OA mice. When assessing human chondrocytes treated with HU308, we uncovered a dose- and time-related increase in ACAN and COL2A1 expression, which was preceded by increased SOX9 expression due to pCREB transcriptional activity. Finally, transcriptomic analysis of patient-derived human chondrocytes identified patient subpopulations exhibiting HU308-responsive trends as judged by enhanced SOX9 expression, accompanied by enriched gene networks related to carbohydrate metabolism. Collectively, the results showed that HU308 reduced trauma and age-induced OA via CB2-pCREB dependent activation of SOX9, contributing to augmented gene networks related to carbohydrate metabolism. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Idan Carmon
- Multidisciplinary Center for Cannabinoid Research, Hebrew University of Jerusalem, Jerusalem, Israel.,Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lital Zecharyahu
- Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jinan Elayyan
- Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sai R K Meka
- Multidisciplinary Center for Cannabinoid Research, Hebrew University of Jerusalem, Jerusalem, Israel.,Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eli Reich
- Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Leonid Kandel
- Orthopedic Complex. Hebrew University- Hadassah Medical Center, Jerusalem, Israel
| | | | - Andreas Zimmer
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Raphael Mechoulam
- Multidisciplinary Center for Cannabinoid Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nataly Kravchenko-Balasha
- Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mona Dvir-Ginzberg
- Multidisciplinary Center for Cannabinoid Research, Hebrew University of Jerusalem, Jerusalem, Israel.,Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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26
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Orsburn BC, Yuan Y, Bumpus NN. Insights into protein post-translational modification landscapes of individual human cells by trapped ion mobility time-of-flight mass spectrometry. Nat Commun 2022; 13:7246. [PMID: 36433961 DOI: 10.1038/s41467-022-34919-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/11/2022] [Indexed: 11/26/2022] Open
Abstract
Single cell proteomics is a powerful tool with potential for markedly enhancing understanding of cellular processes. Here we report the development and application of multiplexed single cell proteomics using trapped ion mobility time-of-flight mass spectrometry. When employing a carrier channel to improve peptide signal, this method allows over 40,000 tandem mass spectra to be acquired in 30 min. Using a KRASG12C model human-derived cell line, we demonstrate the quantification of over 1200 proteins per cell with high relative sequence coverage permitting the detection of multiple classes of post-translational modifications in single cells. When cells were treated with a KRASG12C covalent inhibitor, this approach revealed cell-to-cell variability in the impact of the drug, providing insight missed by traditional proteomics. We provide multiple resources necessary for the application of single cell proteomics to drug treatment studies including tools to reduce cell cycle linked proteomic effects from masking pharmacological phenotypes.
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27
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Yin M, Kuang W, Wang Q, Wang X, Yuan C, Lin Z, Zhang H, Deng F, Jiang H, Gong P, Zou Z, Hu Z, Wang M. Dual roles and evolutionary implications of P26/poxin in antagonizing intracellular cGAS-STING and extracellular melanization immunity. Nat Commun 2022; 13:6934. [PMID: 36376305 PMCID: PMC9663721 DOI: 10.1038/s41467-022-34761-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
P26, a homolog of the viral-encoded nuclease poxin that neutralizes the cGAS-STING innate immunity, is widely distributed in various invertebrate viruses, lepidopteran insects, and parasitoid wasps. P26/poxin from certain insect viruses also retains protease activity, though its biological role remains unknown. Given that many P26s contain a signal peptide, it is surmised that P26 may possess certain extracellular functions. Here, we report that a secretory baculoviral P26 suppresses melanization, a prominent insect innate immunity against pathogen invasion. P26 targets the cofactor of a prophenoloxidase-activating protease, and its inhibitory function is independent of nuclease activity. The analysis of P26/poxin homologs from different origins suggests that the ability to inhibit the extracellular melanization pathway is limited to P26s with a signal peptide and not shared by the homologs without it. These findings highlight the independent evolution of a single viral suppressor to perform dual roles in modulating immunity during virus-host adaptation.
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Affiliation(s)
- Mengyi Yin
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Wenhua Kuang
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Qianran Wang
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xi Wang
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Chuanfei Yuan
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zhe Lin
- grid.9227.e0000000119573309State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Huanyu Zhang
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Fei Deng
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Haobo Jiang
- grid.65519.3e0000 0001 0721 7331Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK USA
| | - Peng Gong
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zhen Zou
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.9227.e0000000119573309State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhihong Hu
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Manli Wang
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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Stejskal K, Jeff ODB, Matzinger M, Dürnberger G, Boychenko A, Jacobs P, Mechtler K. Deep Proteome Profiling with Reduced Carryover Using Superficially Porous Microfabricated nanoLC Columns. Anal Chem 2022; 94:15930-15938. [PMID: 36356180 PMCID: PMC9685595 DOI: 10.1021/acs.analchem.2c01196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
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In the field of liquid chromatography–mass spectrometry
(LC–MS)-based proteomics, increases in the sampling depth and
proteome coverage have mainly been accomplished by rapid advances
in mass spectrometer technology. The comprehensiveness and quality
of the data that can be generated do, however, also depend on the
performance provided by nano-liquid chromatography (nanoLC) separations.
Proper selection of reversed-phase separation columns can be important
to provide the MS instrument with peptides at the highest possible
concentration and separated at the highest possible resolution. In
the current contribution, we evaluate the use of the prototype generation
2 μPAC nanoLC columns, which use C18-functionalized superficially
porous micropillars as a stationary phase. When compared to traditionally
used fully porous silica stationary phases, more precursors could
be characterized when performing single shot data-dependent LC–MS/MS
analyses of a human cell line tryptic digest. Up to 30% more protein
groups and 60% more unique peptides were identified for short gradients
(10 min) and limited sample amounts (10–100 ng of cell lysate
digest). With LC–MS gradient times of 10, 60, 120, and 180
min, respectively, we identified 2252, 6513, 7382, and 8174 protein
groups with 25, 500, 1000, and 2000 ng of the sample loaded on the
column. Reduction of sample carryover to the next run (up to 2 to
3%) and decreased levels of methionine oxidation (up to 3-fold) were
identified as additional figures of merit. When analyzing a disuccinimidyl
dibutyric urea-crosslinked synthetic library, 29 to 59 more unique
crosslinked peptides could be identified at an experimentally validated
false discovery rate of 1–2%.
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Affiliation(s)
- Karel Stejskal
- IMBA─Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | - Op de Beeck Jeff
- Thermo Fisher Scientific, Technologiepark-Zwijnaarde 82, B-9052 Gent, Belgium
| | - Manuel Matzinger
- IMP─Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
| | - Gerhard Dürnberger
- Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | | | - Paul Jacobs
- Thermo Fisher Scientific, Technologiepark-Zwijnaarde 82, B-9052 Gent, Belgium
| | - Karl Mechtler
- IMP─Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
- IMBA─Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
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29
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Adetunji A, Casey T, Franco J, Shah D, Fasina Y. Proteomic Analysis of the Effect of Salmonella Challenge on Broiler Chicken. Molecules 2022; 27. [PMID: 36364100 DOI: 10.3390/molecules27217277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 11/29/2022] Open
Abstract
Salmonella enteritidis is a foodborne pathogen that causes high morbidity in poultry. Proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to study the effects of Salmonella infection on spleen proteome in broiler chickens. Day-old broilers were assigned to control (CON; n = 60) or Salmonella challenge (CON−SE; n = 60), and gavaged with Tryptic soy agar broth or SE. A subset of chicks was euthanized on D3 and D7 (n = 4/group/day) and the spleen was removed, and rapidly frozen, subsequently proteome was measured using label-free LC-MS/MS. Protein spectra were mapped to Gallus gallus Uniprot database. Differentially abundant proteins (DAP; FDR < 0.05) between days and treatments were identified using ANOVA. Cecal content of Salmonella in CON−SE was 3.37 log10 CFU/g and CON were negative. Across the 16 samples, 2625 proteins were identified. Proteins that decreased in abundance between days mediated cell cycle progression, while those that increased in abundance function in cytoskeleton and mRNA processing. SE infection caused an increase in proteins that mediated redox homeostasis, lysosomal activities, and energy production, while proteins decreased in abundance-mediated developmental progression. Proteomic signatures of spleen suggest SE infection was metabolically costly, and energy was diverted from normal developmental processes to potentiate disease resistance mechanisms.
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30
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Fremdling P, Esser TK, Saha B, Makarov AA, Fort KL, Reinhardt-Szyba M, Gault J, Rauschenbach S. A Preparative Mass Spectrometer to Deposit Intact Large Native Protein Complexes. ACS Nano 2022; 16:14443-14455. [PMID: 36037396 PMCID: PMC9527803 DOI: 10.1021/acsnano.2c04831] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Electrospray ion-beam deposition (ES-IBD) is a versatile tool to study the structure and reactivity of molecules from small metal clusters to large protein assemblies. It brings molecules gently into the gas phase, where they can be accurately manipulated and purified, followed by controlled deposition onto various substrates. In combination with imaging techniques, direct structural information on well-defined molecules can be obtained, which is essential to test and interpret results from indirect mass spectrometry techniques. To date, ion-beam deposition experiments are limited to a small number of custom instruments worldwide, and there are no commercial alternatives. Here we present a module that adds ion-beam deposition capabilities to a popular commercial MS platform (Thermo Scientific Q Exactive UHMR mass spectrometer). This combination significantly reduces the overhead associated with custom instruments, while benefiting from established high performance and reliability. We present current performance characteristics including beam intensity, landing-energy control, and deposition spot size for a broad range of molecules. In combination with atomic force microscopy (AFM) and transmission electron microscopy (TEM), we distinguish near-native from unfolded proteins and show retention of the native shape of protein assemblies after dehydration and deposition. Further, we use an enzymatic assay to quantify the activity of a noncovalent protein complex after deposition on a dry surface. Together, these results not only indicate a great potential of ES-IBD for applications in structural biology, but also outline the challenges that need to be solved for it to reach its full potential.
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Affiliation(s)
- Paul Fremdling
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tim K. Esser
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Bodhisattwa Saha
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Alexander A. Makarov
- Thermo
Fisher Scientific, Bremen 28199, Germany
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
| | | | | | - Joseph Gault
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Stephan Rauschenbach
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart 70569, Germany
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31
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Manes NP, Calzola JM, Kaplan PR, Fraser IDC, Germain RN, Meier-Schellersheim M, Nita-Lazar A. Absolute protein quantitation of the mouse macrophage Toll-like receptor and chemotaxis pathways. Sci Data 2022; 9:491. [PMID: 35961990 PMCID: PMC9374760 DOI: 10.1038/s41597-022-01612-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022] Open
Abstract
The Toll-like receptor (TLR) and chemotaxis pathways are key components of the innate immune system. Subtle variation in the concentration, timing, and molecular structure of the ligands are known to affect downstream signaling and the resulting immune response. Computational modeling and simulation at the molecular interaction level can be used to study complex biological pathways, but such simulations require protein concentration values as model parameters. Here we report the development and application of targeted mass spectrometry assays to measure the absolute abundance of proteins of the mouse macrophage Toll-like receptor 4 (TLR4) and chemotaxis pathways. Two peptides per protein were quantified, if possible. The protein abundance values ranged from 1,332 to 227,000,000 copies per cell. They moderately correlated with transcript abundance values from a previously published mouse macrophage RNA-seq dataset, and these two datasets were combined to make proteome-wide abundance estimates. The datasets produced during this investigation can be used for pathway modeling and simulation, as well as for other studies of the TLR and chemotaxis pathways. Measurement(s) | molecules per cell | Technology Type(s) | nanoflow high-performance liquid chromatography-electrospray ionisation tandem mass spectrometry | Sample Characteristic - Organism | Mus musculus |
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Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jessica M Calzola
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Pauline R Kaplan
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Iain D C Fraser
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Ronald N Germain
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Martin Meier-Schellersheim
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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32
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Rossi MT, Langston JC, Singh N, Merali C, Yang Q, Merali S, Prabhakarpandian B, Kilpatrick LE, Kiani MF. Molecular Framework of Mouse Endothelial Cell Dysfunction during Inflammation: A Proteomics Approach. Int J Mol Sci 2022; 23:8399. [PMID: 35955534 PMCID: PMC9369400 DOI: 10.3390/ijms23158399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 02/01/2023] Open
Abstract
A key aspect of cytokine-induced changes as observed in sepsis is the dysregulated activation of endothelial cells (ECs), initiating a cascade of inflammatory signaling leading to leukocyte adhesion/migration and organ damage. The therapeutic targeting of ECs has been hampered by concerns regarding organ-specific EC heterogeneity and their response to inflammation. Using in vitro and in silico analysis, we present a comprehensive analysis of the proteomic changes in mouse lung, liver and kidney ECs following exposure to a clinically relevant cocktail of proinflammatory cytokines. Mouse lung, liver and kidney ECs were incubated with TNF-α/IL-1β/IFN-γ for 4 or 24 h to model the cytokine-induced changes. Quantitative label-free global proteomics and bioinformatic analysis performed on the ECs provide a molecular framework for the EC response to inflammatory stimuli over time and organ-specific differences. Gene Ontology and PANTHER analysis suggest why some organs are more susceptible to inflammation early on, and show that, as inflammation progresses, some protein expression patterns become more uniform while additional organ-specific proteins are expressed. These findings provide an in-depth understanding of the molecular changes involved in the EC response to inflammation and can support the development of drugs targeting ECs within different organs. Data are available via ProteomeXchange (identifier PXD031804).
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33
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Li M, Fan W, Xu Y. Comprehensive Identification of Short and Medium-Sized Peptides from Pixian Broad Bean Paste Protein Hydrolysates Using UPLC-Q-TOF-MS and UHPLC-Q Exactive HF-X. J Agric Food Chem 2022; 70:8288-8299. [PMID: 35785966 DOI: 10.1021/acs.jafc.2c02487] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Pixian broad bean paste (PBBP) is an indispensable food widely used in many East Asian countries, yet the knowledge about bioactive peptides released from parent proteins by enzymatic hydrolysis is limited. A total of 5867 low-molecular weight peptides were identified in the highly bioactive subfractions of the PBBP alcalase hydrolysates using traditional and peptidomics approaches. 19 short peptides (3-5 amino acids) were identified by ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry, including 5 tripeptides, 8 tetrapeptides, and 6 pentapeptides. 5848 medium-sized peptides (6-10 amino acids) were characterized using the peptidomics approach, including 1484 hexapeptides, 1217 heptapeptides, 1634 octapeptides, 927 nonapeptides, and 586 decapeptides. The comprehensive method can be used for the investigation of bioactive peptides in complex food matrices.
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Affiliation(s)
- Mingyang Li
- Lab of Brewing Microbiology and Applied Enzymology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
| | - Wenlai Fan
- Lab of Brewing Microbiology and Applied Enzymology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
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34
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Androschuk AM, Carleton MM, Talior-volodarsky I, Sefton MV. Methacrylic Acid-Based Regenerative Biomaterials: Explorations into the MAAgic. Regen Eng Transl Med . [DOI: 10.1007/s40883-022-00263-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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35
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Li S, Wang Y, Dun W, Han W, Zhang X, Guo N, Wang M. Phosphoproteomic analysis of FAC overload-triggered human hepatic cells reveals G2/M phase arrest. Biochem Biophys Res Commun 2022; 619:62-7. [PMID: 35738066 DOI: 10.1016/j.bbrc.2022.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/23/2022]
Abstract
Hepatic iron overload is a universal phenomenon in patients with myelodysplastic syndromes (MDS) who undergo bone marrow transplantation and may experience the toxicity of peri- and post-bone marrow transplantation. To clarify the mechanisms of iron overload-triggered liver injury, we determined the effects of iron overload on changes in protein phosphorylation in human hepatocyte cell line HH4 in vitro by using a phosphoproteomics approach. The hepatocytes were exposed to high concentrations of ferric ammonium citrate (FAC) to build up an iron overload model in vitro. Changes in protein phosphorylation initiated by iron overloading were studied by 2D-LC/MS. We identified 335 differentially expressed phosphorylated proteins under the condition of excess hepatocyte iron, 11% of which were related to cell cycle progression. The results of phosphoproteomics showed that iron overload induced 10.9 times increase in Thr 14/Tyr 15-phosphorylated Cdk1 in HH4 cells. Flow cytometry analysis revealed that FAC-treated HH4 cells showed significant G2/M phase arrest. Our subsequent RT-PCR and Western blot experiments indicated that FAC-induced G2/M phase arrest was related to the activation of p53-p21-Cdk1, p53-14-3-3 sigma-Cdk1, and 14-3-3 gamma pathway. Our findings demonstrate the first evidence that iron overload causes G2/M arrest in HH4 hepatocytes.
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36
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Laloum D, Magen S, Soroka Y, Avin-Wittenberg T. Exploring the Contribution of Autophagy to the Excess-Sucrose Response in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23073891. [PMID: 35409249 PMCID: PMC8999498 DOI: 10.3390/ijms23073891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/13/2022] [Accepted: 03/29/2022] [Indexed: 01/18/2023] Open
Abstract
Autophagy is an essential intracellular eukaryotic recycling mechanism, functioning in, among others, carbon starvation. Surprisingly, although autophagy-deficient plants (atg mutants) are hypersensitive to carbon starvation, metabolic analysis revealed that they accumulate sugars under such conditions. In plants, sugars serve as both an energy source and as signaling molecules, affecting many developmental processes, including root and shoot formation. We thus set out to understand the interplay between autophagy and sucrose excess, comparing wild-type and atg mutant seedlings. The presented work showed that autophagy contributes to primary root elongation arrest under conditions of exogenous sucrose and glucose excess but not during fructose or mannitol treatment. Minor or no alterations in starch and primary metabolites were observed between atg mutants and wild-type plants, indicating that the sucrose response relates to its signaling and not its metabolic role. Extensive proteomic analysis of roots performed to further understand the mechanism found an accumulation of proteins essential for ROS reduction and auxin maintenance, which are necessary for root elongation, in atg plants under sucrose excess. The analysis also suggested mitochondrial and peroxisomal involvement in the autophagy-mediated sucrose response. This research increases our knowledge of the complex interplay between autophagy and sugar signaling in plants.
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37
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Morawietz CM, Peter Ventura AM, Grevelding CG, Haeberlein S, Spengler B. Spatial visualization of drug uptake and distribution in Fasciola hepatica using high-resolution AP-SMALDI mass spectrometry imaging. Parasitol Res 2022; 121:1145-1153. [PMID: 35067744 PMCID: PMC8986696 DOI: 10.1007/s00436-021-07388-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022]
Abstract
Understanding drug penetration, distribution, and metabolization is fundamental for understanding drug efficacy. This also accounts for parasites during antiparasitic treatment. Recently, we established matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) in blood flukes and liver flukes. This label-free technique is capable of visualizing the molecular distribution of endogenous and exogenous molecules, such as drug compounds. Here, we conducted atmospheric-pressure scanning microprobe MALDI MSI (AP-SMALDI MSI) of tissue sections of adult Fasciola hepatica that have been treated in vitro with 100 µM of triclabendazole (TCBZ), the drug of choice for treatment of fasciolosis, and its main metabolite triclabendazole sulfoxide (TCBZ-SO). Measurements covered an m/z mass range of 250–1,000 and provided a high spatial resolution using a pixel size of 10 µm. To support the interpretation of drug distribution, we first identified endogenous lipids that mark characteristic tissues such as the gastrodermis, the tegument, and the parenchyma. The obtained results suggested an early tegumental route of TCBZ uptake within 20 min, followed by spreading throughout the parasite after 4 h, and an even distribution in most tissues after 12 h. This coincided with a strong reduction of parasite vitality. TCBZ-SO treatment demonstrated the accumulation of this metabolite in the same tissues as the parent drug compound. These data demonstrate the auspicious potential of MALDI MSI to visualize uptake and distribution patterns of drugs or drug-candidate compounds in parasites, which might contribute to preclinical drug discovery in liver fluke research and beyond.
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Affiliation(s)
- Carolin M Morawietz
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | | | - Christoph G Grevelding
- Institute of Parasitology, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Giessen, Giessen, Germany
| | - Simone Haeberlein
- Institute of Parasitology, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Giessen, Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany.
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38
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Wiseman CL, Kharazi A, Sunkari VG, Galeas JL, Dozio V, Hashwah H, Macúchová E, Williams WV, Lacher MD. Regression of Breast Cancer Metastases Following Treatment with Irradiated SV-BR-1-GM, a GM-CSF Overexpressing Breast Cancer Cell Line: Intellectual Property and Immune Markers of Response. Recent Pat Anticancer Drug Discov 2022; 18:224-240. [PMID: 35593340 PMCID: PMC10009895 DOI: 10.2174/1574892817666220518123331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/28/2022] [Accepted: 03/06/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND SV-BR-1-GM, derived from a patient with grade 2 (moderately differentiated) breast cancer, is a GM-CSF-secreting breast cancer cell line with properties of antigen-presenting cells. SV-BR-1-GM and next-generation versions are covered by several pending and granted patents. METHODS We report findings from an open-label phase I, single-arm pilot study with irradiated SV-BR-1-GM cells in 3 breast and 1 ovarian cancer subjects. Inoculations were preceded by lowdose intravenous cyclophosphamide and followed by interferon-alpha2b injections into the SVBR- 1-GM inoculation sites. We assessed both cellular and humoral immune responses, and measured expression levels of SV-BR-1-GM HLA alleles. RESULTS Treatment was generally safe and well tolerated. Immune responses were elicited universally. Overall survival was more than 33 months for three of the four patients. As previously reported, one patient had prompt regression of metastases in lung, breast, and soft tissue. Following cessation of treatment, the patient relapsed widely, including in the brain. Upon retreatment, rapid tumor response was again seen, including complete regression of brain metastases. Consistent with a role of Class II HLA in contributing to SV-BR-1-GM's mechanism of action, this patient allele-matched SV-BR-1-GM at the HLA-DRB1 and HLA-DRB3 loci. We are in the process of developing next-generation SV-BR-1-GM, expressing patient-specific HLAs. Patent applications were filed in various jurisdictions. Thus far, one is granted, in Japan. CONCLUSION A whole-cell immunotherapy regimen with SV-BR-1-GM cells induced regression of metastatic breast cancer. We develop intellectual property based on SV-BR-1-GM's predicted mechanism of action to develop additional whole-cell immunotherapies for cancer patients.
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Affiliation(s)
- Charles L. Wiseman
- BriaCell Therapeutics Corporation, 2929 Arch Street, 3 Floor, Philadelphia, PA, 19104, USA
| | - Alexander Kharazi
- Immunotherapy Laboratory, St. Vincent Medical Center, Los Angeles, CA, USA
| | - Vivekananda G. Sunkari
- BriaCell Therapeutics Corporation, 2929 Arch Street, 3 Floor, Philadelphia, PA, 19104, USA
| | - Jacqueline L. Galeas
- BriaCell Therapeutics Corporation, 2929 Arch Street, 3 Floor, Philadelphia, PA, 19104, USA
| | - Vito Dozio
- Operations Department, Biognosys AG, Wagistrasse 21, 8952, Schlieren, Switzerland
| | - Hind Hashwah
- Sales and Marketing Nebion AG, Hohlstrasse 515, 8048, Zurich, Switzerland
| | - Eva Macúchová
- Sales and Marketing Nebion AG, Hohlstrasse 515, 8048, Zurich, Switzerland
| | - William V. Williams
- BriaCell Therapeutics Corporation, 2929 Arch Street, 3 Floor, Philadelphia, PA, 19104, USA
| | - Markus D. Lacher
- BriaCell Therapeutics Corporation, 2929 Arch Street, 3 Floor, Philadelphia, PA, 19104, USA
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39
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Iannetta AA, Hicks LM. Maximizing Depth of PTM Coverage: Generating Robust MS Datasets for Computational Prediction Modeling. Methods Mol Biol 2022; 2499:1-41. [PMID: 35696073 DOI: 10.1007/978-1-0716-2317-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Post-translational modifications (PTMs) regulate complex biological processes through the modulation of protein activity, stability, and localization. Insights into the specific modification type and localization within a protein sequence can help ascertain functional significance. Computational models are increasingly demonstrated to offer a low-cost, high-throughput method for comprehensive PTM predictions. Algorithms are optimized using existing experimental PTM data, thus accurate prediction performance relies on the creation of robust datasets. Herein, advancements in mass spectrometry-based proteomics technologies to maximize PTM coverage are reviewed. Further, requisite experimental validation approaches for PTM predictions are explored to ensure that follow-up mechanistic studies are focused on accurate modification sites.
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Affiliation(s)
- Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Manz KE, Yamada K, Scheidl L, La Merrill MA, Lind L, Pennell KD. Targeted and Nontargeted Detection and Characterization of Trace Organic Chemicals in Human Serum and Plasma Using QuEChERS Extraction. Toxicol Sci 2021; 185:77-88. [PMID: 34668567 PMCID: PMC8714361 DOI: 10.1093/toxsci/kfab121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Humans are exposed to a broad range of organic chemicals. Although targeted gas chromatography mass spectrometry techniques are used to quantify a limited number of persistent organic pollutants and trace organic contaminants in biological samples, nontargeted, high-resolution mass spectrometry (HRMS) methods assess the human exposome more extensively. We present a QuEChERS extraction for targeted and nontargeted analysis of trace organic contaminants using HRMS and compare this method to a traditional, cartridge-based solid-phase extraction (SPE). Following validation using reference and spiked serum samples, the method was applied to plasma samples (n = 75) from the Prospective investigation of Obesity, Energy, and Metabolism (POEM) study. We quantified 44 analytes using targeted analysis and 6247 peaks were detected using the nontargeted approach. Over 90% of targeted analytes were at least 90% recovered using the QuEChERS method in spiked serum samples. In nontargeted analysis, 84% of the peaks were above the method detection limit with area counts up to 3.0 × 105 times greater using the QuEChERS method. Of the targeted compounds, 88% were also identified in the nontargeted analysis. We categorized the 4212 chemicals assigned an identity in using EPA's CompTox Dashboard and 1076 chemicals were found in at least one list. The category with the highest number of chemicals was "androgen or estrogen receptor activity." The findings demonstrate that a QuEChERS technique is suitable for both targeted and nontargeted analysis of trace organic contaminants in biological samples.
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Affiliation(s)
- Katherine E Manz
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Kyle Yamada
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Lukas Scheidl
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Michele A La Merrill
- Department of Environmental Toxicology, University of California, Davis, Davis, California 95616, USA
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala 752 36, Sweden
| | - Kurt D Pennell
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
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41
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Zhang Z, Zheng M, Zhao Y, Wang PG. Technique development of high-throughput and high-sensitivity sample preparation and separation for proteomics. Bioanalysis 2022; 14:101-11. [PMID: 34854341 DOI: 10.4155/bio-2021-0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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42
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Murgia M, Nogara L, Baraldo M, Reggiani C, Mann M, Schiaffino S. Protein profile of fiber types in human skeletal muscle: a single-fiber proteomics study. Skelet Muscle 2021; 11:24. [PMID: 34727990 PMCID: PMC8561870 DOI: 10.1186/s13395-021-00279-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/19/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Human skeletal muscle is composed of three major fiber types, referred to as type 1, 2A, and 2X fibers. This heterogeneous cellular composition complicates the interpretation of studies based on whole skeletal muscle lysate. A single-fiber proteomics approach is required to obtain a fiber-type resolved quantitative information on skeletal muscle pathophysiology. METHODS Single fibers were dissected from vastus lateralis muscle biopsies of young adult males and processed for mass spectrometry-based single-fiber proteomics. We provide and analyze a resource dataset based on relatively pure fibers, containing at least 80% of either MYH7 (marker of slow type 1 fibers), MYH2 (marker of fast 2A fibers), or MYH1 (marker of fast 2X fibers). RESULTS In a dataset of more than 3800 proteins detected by single-fiber proteomics, we selected 404 proteins showing a statistically significant difference among fiber types. We identified numerous type 1 or 2X fiber type-specific protein markers, defined as proteins present at 3-fold or higher levels in these compared to other fiber types. In contrast, we could detect only two 2A-specific protein markers in addition to MYH2. We observed three other major patterns: proteins showing a differential distribution according to the sequence 1 > 2A > 2X or 2X > 2A > 1 and type 2-specific proteins expressed in 2A and 2X fibers at levels 3 times greater than in type 1 fibers. In addition to precisely quantifying known fiber type-specific protein patterns, our study revealed several novel features of fiber type specificity, including the selective enrichment of components of the dystrophin and integrin complexes, as well as microtubular proteins, in type 2X fibers. The fiber type-specific distribution of some selected proteins revealed by proteomics was validated by immunofluorescence analyses with specific antibodies. CONCLUSION We here show that numerous muscle proteins, including proteins whose function is unknown, are selectively enriched in specific fiber types, pointing to potential implications in muscle pathophysiology. This reinforces the notion that single-fiber proteomics, together with recently developed approaches to single-cell proteomics, will be instrumental to explore and quantify muscle cell heterogeneity.
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Affiliation(s)
- Marta Murgia
- Department of Biomedical Science, University of Padova, 35121, Padova, Italy.
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany.
| | - Leonardo Nogara
- Department of Biomedical Science, University of Padova, 35121, Padova, Italy
- Venetian Institute of Molecular Medicine (VIMM), 35121, Padova, Italy
| | - Martina Baraldo
- Department of Biomedical Science, University of Padova, 35121, Padova, Italy
- Venetian Institute of Molecular Medicine (VIMM), 35121, Padova, Italy
| | - Carlo Reggiani
- Department of Biomedical Science, University of Padova, 35121, Padova, Italy
- Science and Research Center Koper, Institute for Kinesiology Research, 6000, Koper, Slovenia
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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Krane M, Dreßen M, Santamaria G, My I, Schneider CM, Dorn T, Laue S, Mastantuono E, Berutti R, Rawat H, Gilsbach R, Schneider P, Lahm H, Schwarz S, Doppler SA, Paige S, Puluca N, Doll S, Neb I, Brade T, Zhang Z, Abou-Ajram C, Northoff B, Holdt LM, Sudhop S, Sahara M, Goedel A, Dendorfer A, Tjong FVY, Rijlaarsdam ME, Cleuziou J, Lang N, Kupatt C, Bezzina C, Lange R, Bowles NE, Mann M, Gelb BD, Crotti L, Hein L, Meitinger T, Wu S, Sinnecker D, Gruber PJ, Laugwitz KL, Moretti A. Sequential Defects in Cardiac Lineage Commitment and Maturation Cause Hypoplastic Left Heart Syndrome. Circulation 2021; 144:1409-1428. [PMID: 34694888 PMCID: PMC8542085 DOI: 10.1161/circulationaha.121.056198] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND Complex molecular programs in specific cell lineages govern human heart development. Hypoplastic left heart syndrome (HLHS) is the most common and severe manifestation within the spectrum of left ventricular outflow tract obstruction defects occurring in association with ventricular hypoplasia. The pathogenesis of HLHS is unknown, but hemodynamic disturbances are assumed to play a prominent role. METHODS To identify perturbations in gene programs controlling ventricular muscle lineage development in HLHS, we performed whole-exome sequencing of 87 HLHS parent-offspring trios, nuclear transcriptomics of cardiomyocytes from ventricles of 4 patients with HLHS and 15 controls at different stages of heart development, single cell RNA sequencing, and 3D modeling in induced pluripotent stem cells from 3 patients with HLHS and 3 controls. RESULTS Gene set enrichment and protein network analyses of damaging de novo mutations and dysregulated genes from ventricles of patients with HLHS suggested alterations in specific gene programs and cellular processes critical during fetal ventricular cardiogenesis, including cell cycle and cardiomyocyte maturation. Single-cell and 3D modeling with induced pluripotent stem cells demonstrated intrinsic defects in the cell cycle/unfolded protein response/autophagy hub resulting in disrupted differentiation of early cardiac progenitor lineages leading to defective cardiomyocyte subtype differentiation/maturation in HLHS. Premature cell cycle exit of ventricular cardiomyocytes from patients with HLHS prevented normal tissue responses to developmental signals for growth, leading to multinucleation/polyploidy, accumulation of DNA damage, and exacerbated apoptosis, all potential drivers of left ventricular hypoplasia in absence of hemodynamic cues. CONCLUSIONS Our results highlight that despite genetic heterogeneity in HLHS, many mutations converge on sequential cellular processes primarily driving cardiac myogenesis, suggesting novel therapeutic approaches.
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Affiliation(s)
- Markus Krane
- Department of Cardiovascular Surgery, Institute Insure (M.K., M.D., H.L., S.A.D., N.P., I.N., Z.Z., C.A.-A., R.L.),Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research)-partner site Munich Heart Alliance, Germany (M.K., A.D., C.K., R.L., T.M., D.S., K.-L.L., A.M.)
| | - Martina Dreßen
- Department of Cardiovascular Surgery, Institute Insure (M.K., M.D., H.L., S.A.D., N.P., I.N., Z.Z., C.A.-A., R.L.),Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Gianluca Santamaria
- Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Ilaria My
- Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Christine M Schneider
- Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Tatjana Dorn
- Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Svenja Laue
- Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Elisa Mastantuono
- German Heart Center Munich, and Institute of Human Genetics (E.M., R.B., T.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany.,Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany.,Helmholtz Zentrum München, Neuherberg, Germany (E.M., R.B., T.M.)
| | - Riccardo Berutti
- German Heart Center Munich, and Institute of Human Genetics (E.M., R.B., T.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany.,Helmholtz Zentrum München, Neuherberg, Germany (E.M., R.B., T.M.)
| | - Hilansi Rawat
- Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Ralf Gilsbach
- Institute of Experimental and Clinical Pharmacology and Toxicology (R.G., P.S., L.H.), University of Freiburg, Germany.,Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany (R.G.).,DZHK (German Centre for Cardiovascular Research)-partner site RheinMain, Frankfurt am Main, Germany (R.G.)
| | - Pedro Schneider
- Institute of Experimental and Clinical Pharmacology and Toxicology (R.G., P.S., L.H.), University of Freiburg, Germany
| | - Harald Lahm
- Department of Cardiovascular Surgery, Institute Insure (M.K., M.D., H.L., S.A.D., N.P., I.N., Z.Z., C.A.-A., R.L.),Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Sascha Schwarz
- Center for Applied Tissue Engineering and Regenerative Medicine (CANTER), Munich University of Applied Sciences, Germany (S. Schwarz, S. Sudhop)
| | - Stefanie A Doppler
- Department of Cardiovascular Surgery, Institute Insure (M.K., M.D., H.L., S.A.D., N.P., I.N., Z.Z., C.A.-A., R.L.),Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Sharon Paige
- Cardiovascular Institute, Stanford University School of Medicine, CA (S.P., S.W.)
| | - Nazan Puluca
- Department of Cardiovascular Surgery, Institute Insure (M.K., M.D., H.L., S.A.D., N.P., I.N., Z.Z., C.A.-A., R.L.),Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Sophia Doll
- Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany (S.D., M.M.)
| | - Irina Neb
- Department of Cardiovascular Surgery, Institute Insure (M.K., M.D., H.L., S.A.D., N.P., I.N., Z.Z., C.A.-A., R.L.),Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Thomas Brade
- Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Zhong Zhang
- Department of Cardiovascular Surgery, Institute Insure (M.K., M.D., H.L., S.A.D., N.P., I.N., Z.Z., C.A.-A., R.L.),Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Claudia Abou-Ajram
- Department of Cardiovascular Surgery, Institute Insure (M.K., M.D., H.L., S.A.D., N.P., I.N., Z.Z., C.A.-A., R.L.),Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Bernd Northoff
- Institute of Laboratory Medicine (B.N., L.M.H.), University Hospital, LMU Munich, Germany
| | - Lesca M Holdt
- Institute of Laboratory Medicine (B.N., L.M.H.), University Hospital, LMU Munich, Germany
| | - Stefanie Sudhop
- Center for Applied Tissue Engineering and Regenerative Medicine (CANTER), Munich University of Applied Sciences, Germany (S. Schwarz, S. Sudhop)
| | - Makoto Sahara
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden (M.S.)
| | - Alexander Goedel
- Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Andreas Dendorfer
- DZHK (German Centre for Cardiovascular Research)-partner site Munich Heart Alliance, Germany (M.K., A.D., C.K., R.L., T.M., D.S., K.-L.L., A.M.).,Walter-Brendel-Centre of Experimental Medicine (A.D.), University Hospital, LMU Munich, Germany
| | - Fleur V Y Tjong
- Heart Centre, Department of Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, The Netherlands (F.V.Y.T., C.B.)
| | - Maria E Rijlaarsdam
- Department of Pediatric Cardiology, Leiden University Medical Center, The Netherlands (M.E.R.)
| | - Julie Cleuziou
- Department of Congenital and Paediatric Heart Surgery, Institute Insure (J.C.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Nora Lang
- Department of Paediatric Cardiology and Congenital Heart Defects (N.L.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
| | - Christian Kupatt
- Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research)-partner site Munich Heart Alliance, Germany (M.K., A.D., C.K., R.L., T.M., D.S., K.-L.L., A.M.)
| | - Connie Bezzina
- Heart Centre, Department of Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, The Netherlands (F.V.Y.T., C.B.)
| | - Rüdiger Lange
- Department of Cardiovascular Surgery, Institute Insure (M.K., M.D., H.L., S.A.D., N.P., I.N., Z.Z., C.A.-A., R.L.),Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research)-partner site Munich Heart Alliance, Germany (M.K., A.D., C.K., R.L., T.M., D.S., K.-L.L., A.M.)
| | - Neil E Bowles
- Department of Pediatrics (Division of Cardiology), University of Utah School of Medicine, Salt Lake City (N.E.B.)
| | - Matthias Mann
- Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany (S.D., M.M.)
| | - Bruce D Gelb
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York (B.D.G.)
| | - Lia Crotti
- Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Istituto Auxologico Italiano, IRCCS, Milan, Italy (L.C.).,Cardiomyopathies Unit, Department of Cardiovascular, Neural and Metabolic Sciences, Istituto Auxologico Italiano, IRCCS, San Luca Hospital, Milan, Italy (L.C.).,Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy (L.C.)
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology (R.G., P.S., L.H.), University of Freiburg, Germany.,BIOSS, Center for Biological Signaling Studies (L.H.), University of Freiburg, Germany
| | - Thomas Meitinger
- German Heart Center Munich, and Institute of Human Genetics (E.M., R.B., T.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research)-partner site Munich Heart Alliance, Germany (M.K., A.D., C.K., R.L., T.M., D.S., K.-L.L., A.M.).,Helmholtz Zentrum München, Neuherberg, Germany (E.M., R.B., T.M.)
| | - Sean Wu
- Cardiovascular Institute, Stanford University School of Medicine, CA (S.P., S.W.)
| | - Daniel Sinnecker
- Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research)-partner site Munich Heart Alliance, Germany (M.K., A.D., C.K., R.L., T.M., D.S., K.-L.L., A.M.)
| | - Peter J Gruber
- Department of Surgery, Yale University, New Haven, CT (P.J.G.)
| | - Karl-Ludwig Laugwitz
- Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research)-partner site Munich Heart Alliance, Germany (M.K., A.D., C.K., R.L., T.M., D.S., K.-L.L., A.M.)
| | - Alessandra Moretti
- Department of Internal Medicine I, Cardiology (G.S., I.M., C.M.S., T.D., S.L., E.M., H.R., T.B., A.G., C.K., D.S., K.-L.L., A.M.), Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research)-partner site Munich Heart Alliance, Germany (M.K., A.D., C.K., R.L., T.M., D.S., K.-L.L., A.M.)
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Canale FP, Basso C, Antonini G, Perotti M, Li N, Sokolovska A, Neumann J, James MJ, Geiger S, Jin W, Theurillat JP, West KA, Leventhal DS, Lora JM, Sallusto F, Geiger R. Metabolic modulation of tumours with engineered bacteria for immunotherapy. Nature 2021; 598:662-666. [PMID: 34616044 DOI: 10.1038/s41586-021-04003-2] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/07/2021] [Indexed: 11/09/2022]
Abstract
The availability of L-arginine in tumours is a key determinant of an efficient anti-tumour T cell response1-4. Consequently, increases of typically low L-arginine concentrations within the tumour may greatly potentiate the anti-tumour responses of immune checkpoint inhibitors, such as programmed death-ligand 1 (PD-L1)-blocking antibodies5. However, currently no means are available to locally increase intratumoural L-arginine levels. Here we used a synthetic biology approach to develop an engineered probiotic Escherichia coli Nissle 1917 strain that colonizes tumours and continuously converts ammonia, a metabolic waste product that accumulates in tumours6, to L-arginine. Colonization of tumours with these bacteria increased intratumoural L-arginine concentrations, increased the number of tumour-infiltrating T cells and had marked synergistic effects with PD-L1 blocking antibodies in the clearance of tumours. The anti-tumour effect of these bacteria was mediated by L-arginine and was dependent on T cells. These results show that engineered microbial therapies enable metabolic modulation of the tumour microenvironment leading to enhanced efficacy of immunotherapies.
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Affiliation(s)
- Fernando P Canale
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Camilla Basso
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Ente Ospedaliero Cantonale, Department of Surgery, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Gaia Antonini
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Michela Perotti
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Ning Li
- Synlogic, Cambridge, MA, USA
| | | | - Julia Neumann
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | | | - Stefania Geiger
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Wenjie Jin
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | | | | | | | - Jose M Lora
- Synlogic, Cambridge, MA, USA.,Intergalactic Therapeutics, Boston, MA, USA
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Roger Geiger
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland. .,Institute of Oncology Research, Università della Svizzera italiana, Bellinzona, Switzerland.
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Kakhlon O, Vaknin H, Mishra K, D’Souza J, Marisat M, Sprecher U, Wald‐Altman S, Dukhovny A, Raviv Y, Da’adoosh B, Engel H, Benhamron S, Nitzan K, Sweetat S, Permyakova A, Mordechai A, Akman HO, Rosenmann H, Lossos A, Tam J, Minassian BA, Weil M. Alleviation of a polyglucosan storage disorder by enhancement of autophagic glycogen catabolism. EMBO Mol Med 2021; 13:e14554. [PMID: 34486811 PMCID: PMC8495453 DOI: 10.15252/emmm.202114554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/09/2022] Open
Abstract
This work employs adult polyglucosan body disease (APBD) models to explore the efficacy and mechanism of action of the polyglucosan-reducing compound 144DG11. APBD is a glycogen storage disorder (GSD) caused by glycogen branching enzyme (GBE) deficiency causing accumulation of poorly branched glycogen inclusions called polyglucosans. 144DG11 improved survival and motor parameters in a GBE knockin (Gbeys/ys ) APBD mouse model. 144DG11 reduced polyglucosan and glycogen in brain, liver, heart, and peripheral nerve. Indirect calorimetry experiments revealed that 144DG11 increases carbohydrate burn at the expense of fat burn, suggesting metabolic mobilization of pathogenic polyglucosan. At the cellular level, 144DG11 increased glycolytic, mitochondrial, and total ATP production. The molecular target of 144DG11 is the lysosomal membrane protein LAMP1, whose interaction with the compound, similar to LAMP1 knockdown, enhanced autolysosomal degradation of glycogen and lysosomal acidification. 144DG11 also enhanced mitochondrial activity and modulated lysosomal features as revealed by bioenergetic, image-based phenotyping and proteomics analyses. As an effective lysosomal targeting therapy in a GSD model, 144DG11 could be developed into a safe and efficacious glycogen and lysosomal storage disease therapy.
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Affiliation(s)
- Or Kakhlon
- Department of NeurologyHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | - Hilla Vaknin
- Laboratory for Neurodegenerative Diseases and Personalized MedicineThe Cell Screening Facility for Personalized MedicineThe Shmunis School of Biomedicine and Cancer ResearchThe George S. Wise Faculty for Life SciencesSagol School of NeurosciencesTel Aviv UniversityTel AvivIsrael
| | - Kumudesh Mishra
- Department of NeurologyHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | - Jeevitha D’Souza
- Laboratory for Neurodegenerative Diseases and Personalized MedicineThe Cell Screening Facility for Personalized MedicineThe Shmunis School of Biomedicine and Cancer ResearchThe George S. Wise Faculty for Life SciencesSagol School of NeurosciencesTel Aviv UniversityTel AvivIsrael
| | - Monzer Marisat
- Laboratory for Neurodegenerative Diseases and Personalized MedicineThe Cell Screening Facility for Personalized MedicineThe Shmunis School of Biomedicine and Cancer ResearchThe George S. Wise Faculty for Life SciencesSagol School of NeurosciencesTel Aviv UniversityTel AvivIsrael
| | - Uri Sprecher
- Laboratory for Neurodegenerative Diseases and Personalized MedicineThe Cell Screening Facility for Personalized MedicineThe Shmunis School of Biomedicine and Cancer ResearchThe George S. Wise Faculty for Life SciencesSagol School of NeurosciencesTel Aviv UniversityTel AvivIsrael
| | - Shane Wald‐Altman
- Laboratory for Neurodegenerative Diseases and Personalized MedicineThe Cell Screening Facility for Personalized MedicineThe Shmunis School of Biomedicine and Cancer ResearchThe George S. Wise Faculty for Life SciencesSagol School of NeurosciencesTel Aviv UniversityTel AvivIsrael
| | - Anna Dukhovny
- Laboratory for Neurodegenerative Diseases and Personalized MedicineThe Cell Screening Facility for Personalized MedicineThe Shmunis School of Biomedicine and Cancer ResearchThe George S. Wise Faculty for Life SciencesSagol School of NeurosciencesTel Aviv UniversityTel AvivIsrael
| | - Yuval Raviv
- Laboratory for Neurodegenerative Diseases and Personalized MedicineThe Cell Screening Facility for Personalized MedicineThe Shmunis School of Biomedicine and Cancer ResearchThe George S. Wise Faculty for Life SciencesSagol School of NeurosciencesTel Aviv UniversityTel AvivIsrael
| | - Benny Da’adoosh
- Blavatnik Center for Drug DiscoveryTel Aviv UniversityTel AvivIsrael
| | - Hamutal Engel
- Blavatnik Center for Drug DiscoveryTel Aviv UniversityTel AvivIsrael
| | - Sandrine Benhamron
- Department of NeurologyHadassah‐Hebrew University Medical CenterJerusalemIsrael
- Hadassah BrainLabs – National Knowledge Center for Research on Brain DiseasesHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | - Keren Nitzan
- Department of NeurologyHadassah‐Hebrew University Medical CenterJerusalemIsrael
- Hadassah BrainLabs – National Knowledge Center for Research on Brain DiseasesHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | - Sahar Sweetat
- Department of NeurologyHadassah‐Hebrew University Medical CenterJerusalemIsrael
- Hadassah BrainLabs – National Knowledge Center for Research on Brain DiseasesHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | - Anna Permyakova
- Obesity and Metabolism LaboratoryInstitute for Drug ResearchSchool of PharmacyFaculty of MedicineThe Hebrew University of JerusalemJerusalemIsrael
| | - Anat Mordechai
- Department of NeurologyHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | - Hasan Orhan Akman
- Department of NeurologyColumbia University Medical CenterNew YorkNew YorkUSA
| | - Hanna Rosenmann
- Department of NeurologyHadassah‐Hebrew University Medical CenterJerusalemIsrael
- Hadassah BrainLabs – National Knowledge Center for Research on Brain DiseasesHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | - Alexander Lossos
- Department of NeurologyHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | - Joseph Tam
- Obesity and Metabolism LaboratoryInstitute for Drug ResearchSchool of PharmacyFaculty of MedicineThe Hebrew University of JerusalemJerusalemIsrael
| | - Berge A. Minassian
- Division of NeurologyDepartment of PediatricsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Miguel Weil
- Laboratory for Neurodegenerative Diseases and Personalized MedicineThe Cell Screening Facility for Personalized MedicineThe Shmunis School of Biomedicine and Cancer ResearchThe George S. Wise Faculty for Life SciencesSagol School of NeurosciencesTel Aviv UniversityTel AvivIsrael
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Gritti F, Wahab F. Extraction of intrinsic column peak profiles of narrow-bore and microbore columns by peak deconvolution methods. Anal Chim Acta 2021; 1180:338851. [PMID: 34538318 DOI: 10.1016/j.aca.2021.338851] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/07/2021] [Accepted: 07/11/2021] [Indexed: 11/19/2022]
Abstract
The intrinsic peak profiles (free from the delay and dispersion caused by state-of-the art UHPLC systems) generated by narrow-bore and microbore chromatographic columns used in liquid chromatography-mass spectrometry (LC-MS) proteomic analyses are extracted from two different deconvolution methods. The first method is based on the classical discrete Fourier transform (DFT) while the second method refers to the Taylor expansion of the continuous Fourier transform (FT). The two numerical methods are compared regarding the accurate determination of the intrinsic peak profiles of the non-retained compound (toluene) expected on a narrow-bore 2.1 mm × 100 mm column packed with 1.6 μm CORTECS-C18 superficially porous particles and installed on three different LC systems (ACQUITY i-class UPLC, ACQUITY H-class UPLC, and Arc LC systems). The DFT-based method is most relevant when the low-frequency band of the chromatographic peak does not overlap with the high-frequency bands related to the experimental baseline noise (pump/detector). The Taylor expansion-based method is successful for the extraction of the intrinsic peak profiles of narrow-bore 2.1 mm i.d. columns packed with sub-2 μm particles installed on standard UHPLC systems. When the LC system dispersion significantly exceeds that of the column, the DFT-based method is preferred over the Taylor expansion-based method and is successfully applied to extract the intrinsic peak profiles generated by a microbore 1.0 mm × 100 mm column packed with 1.8 μm HSS-C18 fully porous particles (volume variance ∼ 0.15 μL2 for the non-retained compound toluene) run on the low-dispersion ACQUITY i-class UPLC system (∼ 1 μL2 volume variance). This result opens up promising avenues for the development, quality control, and LC-MS analyses of microbore 1 mm i.d. columns using the state-of-the-art UHPLC instruments at flow rates larger than 0.1 mL/min.
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Affiliation(s)
- Fabrice Gritti
- Waters Corporation, Instrument/Core Research/Fundamental, 34 Maple Street, Milford, MA, 01757, USA.
| | - Farooq Wahab
- Department of Chemistry and Biochemistry, University of Texas at Arlington, USA.
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47
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Assis A, Camargo S, Margalit R, Mitrani E. Creation of a vascular inducing device using mesenchymal stem cells to induce angiogenesis. J Biosci Bioeng 2021; 132:408-416. [PMID: 34326013 DOI: 10.1016/j.jbiosc.2021.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/14/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022]
Abstract
Conventional treatments of peripheral vascular disease and coronary artery disease have partial success but are still limited. Methods to deliver angiogenic factors into ischemic areas using gene, protein and cell therapies are faced with difficult issues such a delivery, effective concentration and duration of action. Tissue engineering offers the possibility of creating a functional self-contained three-dimensional (3D) unit that works as a coordinated biological pump that can secrete a whole range of angiogenic factors. We report a tissue engineering approach using decellularized micro-fragments and mesenchymal stem cells (MSCs) to create a vascular inducing device (VID). Proteomic analysis of the decellularized micro-fragments and of the VIDs reveals a large number of extracellular-matrix (ECM) proteins. Moreover, the VIDs were found to transcribe and secrete a whole repertoire of angiogenic factors in a sustained manner. Furthermore, preliminary results of implantation VIDs into non-obese diabetic/severe combined immunodeficiency (NOD/SCID) mice indicate formation of vascular network at the site within a week. We propose that those VIDs could serve as a safe, localized, simple and powerful method for the treatment of certain types of vascular diseases.
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Affiliation(s)
- Assaf Assis
- Department of Cell and Developmental Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Givat Ram Campus, Jerusalem 91904, Israel
| | - Sandra Camargo
- Department of Cell and Developmental Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Givat Ram Campus, Jerusalem 91904, Israel
| | | | - Eduardo Mitrani
- Department of Cell and Developmental Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Givat Ram Campus, Jerusalem 91904, Israel.
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48
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Walsh AN, Reddy CM, Niles SF, McKenna AM, Hansel CM, Ward CP. Plastic Formulation is an Emerging Control of Its Photochemical Fate in the Ocean. Environ Sci Technol 2021; 55:12383-12392. [PMID: 34494430 DOI: 10.1021/acs.est.1c02272] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Sunlight exposure is a control of long-term plastic fate in the environment that converts plastic into oxygenated products spanning the polymer, dissolved, and gas phases. However, our understanding of how plastic formulation influences the amount and composition of these photoproducts remains incomplete. Here, we characterized the initial formulations and resulting dissolved photoproducts of four single-use consumer polyethylene (PE) bags from major retailers and one pure PE film. Consumer PE bags contained 15-36% inorganic additives, primarily calcium carbonate (13-34%) and titanium dioxide (TiO2; 1-2%). Sunlight exposure consistently increased production of dissolved organic carbon (DOC) relative to leaching in the dark (3- to 80-fold). All consumer PE bags produced more DOC during sunlight exposure than the pure PE (1.2- to 2.0-fold). The DOC leached after sunlight exposure increasingly reflected the 13C and 14C isotopic composition of the plastic. Ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry revealed that sunlight exposure substantially increased the number of DOC formulas detected (1.1- to 50-fold). TiO2-containing bags photochemically degraded into the most compositionally similar DOC, with 68-94% of photoproduced formulas in common with at least one other TiO2-containing bag. Conversely, only 28% of photoproduced formulas from the pure PE were detected in photoproduced DOC from the consumer PE. Overall, these findings suggest that plastic formulation, especially TiO2, plays a determining role in the amount and composition of DOC generated by sunlight. Consequently, studies on pure, unweathered polymers may not accurately represent the fates and impacts of the plastics entering the ocean.
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Affiliation(s)
- Anna N Walsh
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher M Reddy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Sydney F Niles
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310-4005, United States
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310-4005, United States
- Department of Chemistry, Colorado State University, 1872 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Collin P Ward
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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Mai L, He G, Chen J, Zhu J, Chen S, Hou X, Yang H, Zhang M, Wu Y, Lin Q, Yang M, Li X. Proteomic Analysis of Hypoxia-Induced Senescence of Human Bone Marrow Mesenchymal Stem Cells. Stem Cells Int 2021; 2021:5555590. [PMID: 34484348 DOI: 10.1155/2021/5555590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/29/2021] [Accepted: 07/28/2021] [Indexed: 12/18/2022] Open
Abstract
Methods Hypoxia in hBMSCs was induced for 0, 4, and 12 hours, and cellular senescence was evaluated by senescence-associated β-galactosidase (SA-β-gal) staining. Tandem mass tag (TMT) labeling was combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) for differential proteomic analysis of hypoxia in hBMSCs. Parallel reaction monitoring (PRM) analysis was used to validate the candidate proteins. Verifications of signaling pathways were evaluated by western blotting. Cell apoptosis was evaluated using Annexin V/7-AAD staining by flow cytometry. The production of reactive oxygen species (ROS) was detected by the fluorescent probe 2,7-dichlorodihydrofluorescein diacetate (DCFH-DA). Results Cell senescence detected by SA-β-gal activity was higher in the 12-hour hypoxia-induced group. TMT analysis of 12-hour hypoxia-induced cells identified over 6000 proteins, including 686 differentially expressed proteins. Based on biological pathway analysis, we found that the senescence-associated proteins were predominantly enriched in the cancer pathways, PI3K-Akt pathway, and cellular senescence signaling pathways. CDK1, CDK2, and CCND1 were important nodes in PPI analyses. Moreover, the CCND1, UQCRH, and COX7C expressions were verified by PRM. Hypoxia induction for 12 hours in hBMSCs reduced CCND1 expression but promoted ROS production and cell apoptosis. Such effects were markedly reduced by the PI3K agonist, 740 Y-P, and attenuated by LY294002. Conclusions Hypoxia of hBMSCs inhibited CCND1 expression but promoted ROS production and cell apoptosis through activating the PI3K-dependent signaling pathway. These findings provided a detailed characterization of the proteomic profiles related to hypoxia-induced senescence of hBMSCs and facilitated our understanding of the molecular mechanisms leading to stem cell senescence.
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50
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Gardner ML, Freitas MA. Multiple Imputation Approaches Applied to the Missing Value Problem in Bottom-Up Proteomics. Int J Mol Sci 2021; 22:ijms22179650. [PMID: 34502557 PMCID: PMC8431783 DOI: 10.3390/ijms22179650] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/28/2021] [Accepted: 08/31/2021] [Indexed: 01/15/2023] Open
Abstract
Analysis of differential abundance in proteomics data sets requires careful application of missing value imputation. Missing abundance values widely vary when performing comparisons across different sample treatments. For example, one would expect a consistent rate of “missing at random” (MAR) across batches of samples and varying rates of “missing not at random” (MNAR) depending on the inherent difference in sample treatments within the study. The missing value imputation strategy must thus be selected that best accounts for both MAR and MNAR simultaneously. Several important issues must be considered when deciding the appropriate missing value imputation strategy: (1) when it is appropriate to impute data; (2) how to choose a method that reflects the combinatorial manner of MAR and MNAR that occurs in an experiment. This paper provides an evaluation of missing value imputation strategies used in proteomics and presents a case for the use of hybrid left-censored missing value imputation approaches that can handle the MNAR problem common to proteomics data.
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Affiliation(s)
- Miranda L. Gardner
- Ohio State Biochemistry Program, Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA;
- Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
| | - Michael A. Freitas
- Ohio State Biochemistry Program, Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA;
- Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
- Correspondence: or
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