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Bielow C, Hoffmann N, Jimenez-Morales D, Van Den Bossche T, Vizcaíno JA, Tabb DL, Bittremieux W, Walzer M. Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 38918936 DOI: 10.1021/jasms.4c00174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Mass spectrometry is a powerful technique for analyzing molecules in complex biological samples. However, inter- and intralaboratory variability and bias can affect the data due to various factors, including sample handling and preparation, instrument calibration and performance, and data acquisition and processing. To address this issue, the Quality Control (QC) working group of the Human Proteome Organization's Proteomics Standards Initiative has established the standard mzQC file format for reporting and exchanging information relating to data quality. mzQC is based on the JavaScript Object Notation (JSON) format and provides a lightweight yet versatile file format that can be easily implemented in software. Here, we present open-source software libraries to process mzQC data in three programming languages: Python, using pymzqc; R, using rmzqc; and Java, using jmzqc. The libraries follow a common data model and provide shared functionalities, including the (de)serialization and validation of mzQC files. We demonstrate use of the software libraries in a workflow for extracting, analyzing, and visualizing QC metrics from different sources. Additionally, we show how these libraries can be integrated with each other, with existing software tools, and in automated workflows for the QC of mass spectrometry data. All software libraries are available as open source under the MS-Quality-Hub organization on GitHub (https://github.com/MS-Quality-Hub).
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Affiliation(s)
- Chris Bielow
- Bioinformatics Solution Center, Institut für Mathematik und Informatik, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany
| | - Nils Hoffmann
- Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - David Jimenez-Morales
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Tim Van Den Bossche
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David L Tabb
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Wout Bittremieux
- Department of Computer Science, University of Antwerp, Antwerpen 2020, Belgium
| | - Mathias Walzer
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
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Schauer A, Adams V, Kämmerer S, Langner E, Augstein A, Barthel P, Männel A, Fabig G, Alves PKN, Günscht M, El-Armouche A, Müller-Reichert T, Linke A, Winzer EB. Empagliflozin Improves Diastolic Function in HFpEF by Restabilizing the Mitochondrial Respiratory Chain. Circ Heart Fail 2024; 17:e011107. [PMID: 38847102 PMCID: PMC11177604 DOI: 10.1161/circheartfailure.123.011107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Clinical studies demonstrated beneficial effects of sodium-glucose-transporter 2 inhibitors on the risk of cardiovascular death in patients with heart failure with preserved ejection fraction (HFpEF). However, underlying processes for cardioprotection remain unclear. The present study focused on the impact of empagliflozin (Empa) on myocardial function in a rat model with established HFpEF and analyzed underlying molecular mechanisms. METHODS Obese ZSF1 (Zucker fatty and spontaneously hypertensive) rats were randomized to standard care (HFpEF, n=18) or Empa (HFpEF/Empa, n=18). ZSF1 lean rats (con, n=18) served as healthy controls. Echocardiography was performed at baseline and after 4 and 8 weeks, respectively. After 8 weeks of treatment, hemodynamics were measured invasively, mitochondrial function was assessed and myocardial tissue was collected for either molecular and histological analyses or transmission electron microscopy. RESULTS In HFpEF Empa significantly improved diastolic function (E/é: con: 17.5±2.8; HFpEF: 24.4±4.6; P<0.001 versus con; HFpEF/Empa: 19.4±3.2; P<0.001 versus HFpEF). This was accompanied by improved hemodynamics and calcium handling and by reduced inflammation, hypertrophy, and fibrosis. Proteomic analysis demonstrated major changes in proteins involved in mitochondrial oxidative phosphorylation. Cardiac mitochondrial respiration was significantly impaired in HFpEF but restored by Empa (Vmax complex IV: con: 0.18±0.07 mmol O2/s/mg; HFpEF: 0.13±0.05 mmol O2/s/mg; P<0.041 versus con; HFpEF/Empa: 0.21±0.05 mmol O2/s/mg; P=0.012 versus HFpEF) without alterations of mitochondrial content. The expression of cardiolipin, an essential stability/functionality-mediating phospholipid of the respiratory chain, was significantly decreased in HFpEF but reverted by Empa (con: 15.9±1.7 nmol/mg protein; HFpEF: 12.5±1.8 nmol/mg protein; P=0.002 versus con; HFpEF/Empa: 14.5±1.8 nmol/mg protein; P=0.03 versus HFpEF). Transmission electron microscopy revealed a reduced size of mitochondria in HFpEF, which was restored by Empa. CONCLUSIONS The study demonstrates beneficial effects of Empa on diastolic function, hemodynamics, inflammation, and cardiac remodeling in a rat model of HFpEF. These effects were mediated by improved mitochondrial respiratory capacity due to modulated cardiolipin and improved calcium handling.
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Affiliation(s)
- Antje Schauer
- Department of Internal Medicine and Cardiology, Heart Center Dresden - Laboratory of Experimental and Molecular Cardiology, Technische Universität Dresden, Germany (A.S., V.A., E.L., A.A., P.B., A.M., P.K.N.A., A.L., E.B.W.)
| | - Volker Adams
- Department of Internal Medicine and Cardiology, Heart Center Dresden - Laboratory of Experimental and Molecular Cardiology, Technische Universität Dresden, Germany (A.S., V.A., E.L., A.A., P.B., A.M., P.K.N.A., A.L., E.B.W.)
| | - Susanne Kämmerer
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Germany (S.K., M.G., A.E.-A.)
| | - Erik Langner
- Department of Internal Medicine and Cardiology, Heart Center Dresden - Laboratory of Experimental and Molecular Cardiology, Technische Universität Dresden, Germany (A.S., V.A., E.L., A.A., P.B., A.M., P.K.N.A., A.L., E.B.W.)
| | - Antje Augstein
- Department of Internal Medicine and Cardiology, Heart Center Dresden - Laboratory of Experimental and Molecular Cardiology, Technische Universität Dresden, Germany (A.S., V.A., E.L., A.A., P.B., A.M., P.K.N.A., A.L., E.B.W.)
| | - Peggy Barthel
- Department of Internal Medicine and Cardiology, Heart Center Dresden - Laboratory of Experimental and Molecular Cardiology, Technische Universität Dresden, Germany (A.S., V.A., E.L., A.A., P.B., A.M., P.K.N.A., A.L., E.B.W.)
| | - Anita Männel
- Department of Internal Medicine and Cardiology, Heart Center Dresden - Laboratory of Experimental and Molecular Cardiology, Technische Universität Dresden, Germany (A.S., V.A., E.L., A.A., P.B., A.M., P.K.N.A., A.L., E.B.W.)
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Germany (G.F., T.M.-R.)
| | - Paula Ketilly Nascimento Alves
- Department of Internal Medicine and Cardiology, Heart Center Dresden - Laboratory of Experimental and Molecular Cardiology, Technische Universität Dresden, Germany (A.S., V.A., E.L., A.A., P.B., A.M., P.K.N.A., A.L., E.B.W.)
- Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, Brazil (P.K.N.A.)
| | - Mario Günscht
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Germany (S.K., M.G., A.E.-A.)
| | - Ali El-Armouche
- Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Germany (S.K., M.G., A.E.-A.)
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Germany (G.F., T.M.-R.)
| | - Axel Linke
- Department of Internal Medicine and Cardiology, Heart Center Dresden - Laboratory of Experimental and Molecular Cardiology, Technische Universität Dresden, Germany (A.S., V.A., E.L., A.A., P.B., A.M., P.K.N.A., A.L., E.B.W.)
| | - Ephraim B. Winzer
- Department of Internal Medicine and Cardiology, Heart Center Dresden - Laboratory of Experimental and Molecular Cardiology, Technische Universität Dresden, Germany (A.S., V.A., E.L., A.A., P.B., A.M., P.K.N.A., A.L., E.B.W.)
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Ramsbottom KA, Prakash A, Perez-Riverol Y, Camacho OM, Sun Z, Kundu DJ, Bowler-Barnett E, Martin M, Fan J, Chebotarov D, McNally KL, Deutsch EW, Vizcaíno JA, Jones AR. Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome. J Proteome Res 2024. [PMID: 38810119 DOI: 10.1021/acs.jproteome.4c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have reanalyzed publicly available mass spectrometry proteomics data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we identified 15,565 phosphosites on serine, threonine, and tyrosine residues on rice proteins. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation likely caused by different kinase groups. We cross-referenced phosphosites against the rice 3,000 genomes, to identify single amino acid variations (SAAVs) within or proximal to phosphosites that could cause loss of a site in a given rice variety and clustered the data to identify groups of sites with similar patterns across rice family groups. The data has been loaded into UniProt Knowledge-Base─enabling researchers to visualize sites alongside other data on rice proteins, e.g., structural models from AlphaFold2, PeptideAtlas, and the PRIDE database─enabling visualization of source evidence, including scores and supporting mass spectra.
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Affiliation(s)
- Kerry A Ramsbottom
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, United Kingdom
| | - Ananth Prakash
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Oscar Martin Camacho
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, United Kingdom
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Deepti J Kundu
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Emily Bowler-Barnett
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Maria Martin
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Jun Fan
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Dmytro Chebotarov
- International Rice Research Institute, DAPO Box 7777, Manila 1301, Philippines
| | - Kenneth L McNally
- International Rice Research Institute, DAPO Box 7777, Manila 1301, Philippines
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, United Kingdom
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Caller T, Rotem I, Shaihov-Teper O, Lendengolts D, Schary Y, Shai R, Glick-Saar E, Dominissini D, Motiei M, Katzir I, Popovtzer R, Nahmoud M, Boomgarden A, D'Souza-Schorey C, Naftali-Shani N, Leor J. Small Extracellular Vesicles From Infarcted and Failing Heart Accelerate Tumor Growth. Circulation 2024; 149:1729-1748. [PMID: 38487879 DOI: 10.1161/circulationaha.123.066911] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/20/2024] [Indexed: 05/24/2024]
Abstract
BACKGROUND Myocardial infarction (MI) and heart failure are associated with an increased incidence of cancer. However, the mechanism is complex and unclear. Here, we aimed to test our hypothesis that cardiac small extracellular vesicles (sEVs), particularly cardiac mesenchymal stromal cell-derived sEVs (cMSC-sEVs), contribute to the link between post-MI left ventricular dysfunction (LVD) and cancer. METHODS We purified and characterized sEVs from post-MI hearts and cultured cMSCs. Then, we analyzed cMSC-EV cargo and proneoplastic effects on several lines of cancer cells, macrophages, and endothelial cells. Next, we modeled heterotopic and orthotopic lung and breast cancer tumors in mice with post-MI LVD. We transferred cMSC-sEVs to assess sEV biodistribution and its effect on tumor growth. Finally, we tested the effects of sEV depletion and spironolactone treatment on cMSC-EV release and tumor growth. RESULTS Post-MI hearts, particularly cMSCs, produced more sEVs with proneoplastic cargo than nonfailing hearts did. Proteomic analysis revealed unique protein profiles and higher quantities of tumor-promoting cytokines, proteins, and microRNAs in cMSC-sEVs from post-MI hearts. The proneoplastic effects of cMSC-sEVs varied with different types of cancer, with lung and colon cancers being more affected than melanoma and breast cancer cell lines. Post-MI cMSC-sEVs also activated resting macrophages into proangiogenic and protumorigenic states in vitro. At 28-day follow-up, mice with post-MI LVD developed larger heterotopic and orthotopic lung tumors than did sham-MI mice. Adoptive transfer of cMSC-sEVs from post-MI hearts accelerated the growth of heterotopic and orthotopic lung tumors, and biodistribution analysis revealed accumulating cMSC-sEVs in tumor cells along with accelerated tumor cell proliferation. sEV depletion reduced the tumor-promoting effects of MI, and adoptive transfer of cMSC-sEVs from post-MI hearts partially restored these effects. Finally, spironolactone treatment reduced the number of cMSC-sEVs and suppressed tumor growth during post-MI LVD. CONCLUSIONS Cardiac sEVs, specifically cMSC-sEVs from post-MI hearts, carry multiple protumorigenic factors. Uptake of cMSC-sEVs by cancer cells accelerates tumor growth. Treatment with spironolactone significantly reduces accelerated tumor growth after MI. Our results provide new insight into the mechanism connecting post-MI LVD to cancer and propose a translational option to mitigate this deadly association.
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Affiliation(s)
- Tal Caller
- Neufeld and Tamman Cardiovascular Research Institutes, School of Medicine, Tel Aviv University, Israel (T.C., I.R., O.S.-T., D.L., Y.S., R.S., M.N., N.N.-S., J.L.)
- Lev Leviev Cardiovascular and Thoracic Center (T.C., I.R., O.S.-T., D.L., Y.S., N.N.-S., J.L.), Sheba Medical Center, Tel Hashomer, Israel
| | - Itai Rotem
- Neufeld and Tamman Cardiovascular Research Institutes, School of Medicine, Tel Aviv University, Israel (T.C., I.R., O.S.-T., D.L., Y.S., R.S., M.N., N.N.-S., J.L.)
- Lev Leviev Cardiovascular and Thoracic Center (T.C., I.R., O.S.-T., D.L., Y.S., N.N.-S., J.L.), Sheba Medical Center, Tel Hashomer, Israel
| | - Olga Shaihov-Teper
- Neufeld and Tamman Cardiovascular Research Institutes, School of Medicine, Tel Aviv University, Israel (T.C., I.R., O.S.-T., D.L., Y.S., R.S., M.N., N.N.-S., J.L.)
- Lev Leviev Cardiovascular and Thoracic Center (T.C., I.R., O.S.-T., D.L., Y.S., N.N.-S., J.L.), Sheba Medical Center, Tel Hashomer, Israel
| | - Daria Lendengolts
- Neufeld and Tamman Cardiovascular Research Institutes, School of Medicine, Tel Aviv University, Israel (T.C., I.R., O.S.-T., D.L., Y.S., R.S., M.N., N.N.-S., J.L.)
- Lev Leviev Cardiovascular and Thoracic Center (T.C., I.R., O.S.-T., D.L., Y.S., N.N.-S., J.L.), Sheba Medical Center, Tel Hashomer, Israel
| | - Yeshai Schary
- Neufeld and Tamman Cardiovascular Research Institutes, School of Medicine, Tel Aviv University, Israel (T.C., I.R., O.S.-T., D.L., Y.S., R.S., M.N., N.N.-S., J.L.)
- Lev Leviev Cardiovascular and Thoracic Center (T.C., I.R., O.S.-T., D.L., Y.S., N.N.-S., J.L.), Sheba Medical Center, Tel Hashomer, Israel
| | - Ruty Shai
- Neufeld and Tamman Cardiovascular Research Institutes, School of Medicine, Tel Aviv University, Israel (T.C., I.R., O.S.-T., D.L., Y.S., R.S., M.N., N.N.-S., J.L.)
- Pediatric Hemato-Oncology, Edmond and Lilly Safra Children's Hospital, Cancer Research Center (R.S.), Sheba Medical Center, Tel Hashomer, Israel
| | - Efrat Glick-Saar
- Cancer Research Center and Wohl Centre for Translational Medicine (E.G.-S., D.D.), Sheba Medical Center, Tel Hashomer, Israel
| | - Dan Dominissini
- Cancer Research Center and Wohl Centre for Translational Medicine (E.G.-S., D.D.), Sheba Medical Center, Tel Hashomer, Israel
| | - Menachem Motiei
- Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel (M.M., I.K., R.P.)
| | - Idan Katzir
- Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel (M.M., I.K., R.P.)
| | - Rachela Popovtzer
- Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel (M.M., I.K., R.P.)
| | | | - Alex Boomgarden
- Department of Biological Sciences, University of Notre Dame, IN (A.B., C.D'S.-S.)
| | | | - Nili Naftali-Shani
- Neufeld and Tamman Cardiovascular Research Institutes, School of Medicine, Tel Aviv University, Israel (T.C., I.R., O.S.-T., D.L., Y.S., R.S., M.N., N.N.-S., J.L.)
- Lev Leviev Cardiovascular and Thoracic Center (T.C., I.R., O.S.-T., D.L., Y.S., N.N.-S., J.L.), Sheba Medical Center, Tel Hashomer, Israel
| | - Jonathan Leor
- Neufeld and Tamman Cardiovascular Research Institutes, School of Medicine, Tel Aviv University, Israel (T.C., I.R., O.S.-T., D.L., Y.S., R.S., M.N., N.N.-S., J.L.)
- Lev Leviev Cardiovascular and Thoracic Center (T.C., I.R., O.S.-T., D.L., Y.S., N.N.-S., J.L.), Sheba Medical Center, Tel Hashomer, Israel
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Tam YB, Low K, Ps H, Chadha M, Burns J, Wilding CP, Arthur A, Chen TW, Thway K, Sadanandam A, Jones RL, Huang PH. Proteomic features of soft tissue tumours in adolescents and young adults. COMMUNICATIONS MEDICINE 2024; 4:93. [PMID: 38762630 PMCID: PMC11102500 DOI: 10.1038/s43856-024-00522-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 05/07/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND Adolescents and young adult (AYA) patients with soft tissue tumours including sarcomas are an underserved group with disparities in treatment outcomes. METHODS To define the molecular features between AYA and older adult (OA) patients, we analysed the proteomic profiles of a large cohort of soft tissue tumours across 10 histological subtypes (AYA n = 66, OA n = 243), and also analysed publicly available functional genomic data from soft tissue tumour cell lines (AYA n = 5, OA n = 8). RESULTS Biological hallmarks analysis demonstrates that OA tumours are significantly enriched in MYC targets compared to AYA tumours. By comparing the patient-level proteomic data with functional genomic profiles from sarcoma cell lines, we show that the mRNA splicing pathway is an intrinsic vulnerability in cell lines from OA patients and that components of the spliceosome complex are independent prognostic factors for metastasis free survival in AYA patients. CONCLUSIONS Our study highlights the importance of performing age-specific molecular profiling studies to identify risk stratification tools and targeted agents tailored for the clinical management of AYA patients.
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Affiliation(s)
- Yuen Bun Tam
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Kaan Low
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Hari Ps
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Madhumeeta Chadha
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Jessica Burns
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Christopher P Wilding
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Amani Arthur
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Tom W Chen
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Khin Thway
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Robin L Jones
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom.
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Li Y, Wang Z, Yang J, Sun Y, He Y, Wang Y, Chen X, Liang Y, Zhang N, Wang X, Zhao W, Hu G, Yang Q. CircTRIM1 encodes TRIM1-269aa to promote chemoresistance and metastasis of TNBC via enhancing CaM-dependent MARCKS translocation and PI3K/AKT/mTOR activation. Mol Cancer 2024; 23:102. [PMID: 38755678 PMCID: PMC11097450 DOI: 10.1186/s12943-024-02019-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024] Open
Abstract
Peptides and proteins encoded by noncanonical open reading frames (ORFs) of circRNAs have recently been recognized to play important roles in disease progression, but the biological functions and mechanisms of these peptides and proteins are largely unknown. Here, we identified a potential coding circular RNA, circTRIM1, that was upregulated in doxorubicin-resistant TNBC cells by intersecting transcriptome and translatome RNA-seq data, and its expression was correlated with clinicopathological characteristics and poor prognosis in patients with TNBC. CircTRIM1 possesses a functional IRES element along with an 810 nt ORF that can be translated into a novel endogenously expressed protein termed TRIM1-269aa. Functionally, we demonstrated that TRIM1-269aa, which is involved in the biological functions of circTRIM1, promoted chemoresistance and metastasis in TNBC cells both in vitro and in vivo. In addition, we found that TRIM1-269aa can be packaged into exosomes and transmitted between TNBC cells. Mechanistically, TRIM1-269aa enhanced the interaction between MARCKS and calmodulin, thus promoting the calmodulin-dependent translocation of MARCKS, which further initiated the activation of the PI3K/AKT/mTOR pathway. Overall, circTRIM1, which encodes TRIM1-269aa, promoted TNBC chemoresistance and metastasis by enhancing MARCKS translocation and PI3K/AKT/mTOR activation. Our investigation has yielded novel insights into the roles of protein-coding circRNAs and supported circTRIM1/TRIM1-269aa as a novel promising prognostic and therapeutic target for patients with TNBC.
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Affiliation(s)
- Yaming Li
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Zekun Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Jingwen Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yuhan Sun
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yinqiao He
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yuping Wang
- School of Basic Medicine, Jining Medical College, Jining, Shandong, 272067, China
| | - Xi Chen
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yiran Liang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Ning Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Xiaolong Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Wenjing Zhao
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Guohong Hu
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China.
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China.
- Research Institute of Breast Cancer, Shandong University, Jinan, Shandong, 250012, China.
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7
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Habeck T, Brown KA, Des Soye B, Lantz C, Zhou M, Alam N, Hossain MA, Jung W, Keener JE, Volny M, Wilson JW, Ying Y, Agar JN, Danis PO, Ge Y, Kelleher NL, Li H, Loo JA, Marty MT, Paša-Tolić L, Sandoval W, Lermyte F. Top-down mass spectrometry of native proteoforms and their complexes: a community study. Nat Methods 2024:10.1038/s41592-024-02279-6. [PMID: 38744918 DOI: 10.1038/s41592-024-02279-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
The combination of native electrospray ionization with top-down fragmentation in mass spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and cofactors. Although this approach is powerful, both native MS and top-down MS are not yet well standardized, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics initiated a study to develop and test protocols for native MS combined with top-down fragmentation of proteins and protein complexes across 11 instruments in nine laboratories. Here we report the summary of the outcomes to provide robust benchmarks and a valuable entry point for the scientific community.
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Affiliation(s)
- Tanja Habeck
- Technische Universität Darmstadt, Darmstadt, Germany
| | - Kyle A Brown
- University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Mowei Zhou
- Pacific Northwest National Laboratory, Richland, WA, USA
- Zhejiang University, Zhejiang, China
| | | | | | | | | | | | - Jesse W Wilson
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yujia Ying
- Sun Yat-sen University, Guangzhou, China
| | - Jeffrey N Agar
- Northeastern University, Boston, MA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Paul O Danis
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Ying Ge
- University of Wisconsin-Madison, Madison, WI, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Neil L Kelleher
- Northwestern University, Evanston, IL, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Huilin Li
- Sun Yat-sen University, Guangzhou, China
| | - Joseph A Loo
- University of California, Los Angeles, CA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | | | - Ljiljana Paša-Tolić
- Pacific Northwest National Laboratory, Richland, WA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
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8
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Gentry-Torfer D, Murillo E, Barrington CL, Nie S, Leeming MG, Suwanchaikasem P, Williamson NA, Roessner U, Boughton BA, Kopka J, Martinez-Seidel F. Streamlining Protein Fractional Synthesis Rates Using SP3 Beads and Stable Isotope Mass Spectrometry: A Case Study on the Plant Ribosome. Bio Protoc 2024; 14:e4981. [PMID: 38737506 PMCID: PMC11082790 DOI: 10.21769/bioprotoc.4981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024] Open
Abstract
Ribosomes are an archetypal ribonucleoprotein assembly. Due to ribosomal evolution and function, r-proteins share specific physicochemical similarities, making the riboproteome particularly suited for tailored proteome profiling methods. Moreover, the structural proteome of ribonucleoprotein assemblies reflects context-dependent functional features. Thus, characterizing the state of riboproteomes provides insights to uncover the context-dependent functionality of r-protein rearrangements, as they relate to what has been termed the ribosomal code, a concept that parallels that of the histone code, in which chromatin rearrangements influence gene expression. Compared to high-resolution ribosomal structures, omics methods lag when it comes to offering customized solutions to close the knowledge gap between structure and function that currently exists in riboproteomes. Purifying the riboproteome and subsequent shot-gun proteomics typically involves protein denaturation and digestion with proteases. The results are relative abundances of r-proteins at the ribosome population level. We have previously shown that, to gain insight into the stoichiometry of individual proteins, it is necessary to measure by proteomics bound r-proteins and normalize their intensities by the sum of r-protein abundances per ribosomal complex, i.e., 40S or 60S subunits. These calculations ensure that individual r-protein stoichiometries represent the fraction of each family/paralog relative to the complex, effectively revealing which r-proteins become substoichiometric in specific physiological scenarios. Here, we present an optimized method to profile the riboproteome of any organism as well as the synthesis rates of r-proteins determined by stable isotope-assisted mass spectrometry. Our method purifies the r-proteins in a reversibly denatured state, which offers the possibility for combined top-down and bottom-up proteomics. Our method offers a milder native denaturation of the r-proteome via a chaotropic GuHCl solution as compared with previous studies that use irreversible denaturation under highly acidic conditions to dissociate rRNA and r-proteins. As such, our method is better suited to conserve post-translational modifications (PTMs). Subsequently, our method carefully considers the amino acid composition of r-proteins to select an appropriate protease for digestion. We avoid non-specific protease cleavage by increasing the pH of our standardized r-proteome dilutions that enter the digestion pipeline and by using a digestion buffer that ensures an optimal pH for a reliable protease digestion process. Finally, we provide the R package ProtSynthesis to study the fractional synthesis rates of r-proteins. The package uses physiological parameters as input to determine peptide or protein fractional synthesis rates. Once the physiological parameters are measured, our equations allow a fair comparison between treatments that alter the biological equilibrium state of the system under study. Our equations correct peptide enrichment using enrichments in soluble amino acids, growth rates, and total protein accumulation. As a means of validation, our pipeline fails to find "false" enrichments in non-labeled samples while also filtering out proteins with multiple unique peptides that have different enrichment values, which are rare in our datasets. These two aspects reflect the accuracy of our tool. Our method offers the possibility of elucidating individual r-protein family/paralog abundances, PTM status, fractional synthesis rates, and dynamic assembly into ribosomal complexes if top-down and bottom-up proteomic approaches are used concomitantly, taking one step further into mapping the native and dynamic status of the r-proteome onto high-resolution ribosome structures. In addition, our method can be used to study the proteomes of all macromolecular assemblies that can be purified, although purification is the limiting step, and the efficacy and accuracy of the proteases may be limited depending on the digestion requirements. Key features • Efficient purification of the ribosomal proteome: streamlined procedure for the specific purification of the ribosomal proteome or complex Ome. • Accurate calculation of fractional synthesis rates: robust method for calculating fractional protein synthesis rates in macromolecular complexes under different physiological steady states. • Holistic ribosome methodology focused on plants: comprehensive approach that provides insights into the ribosomes and translational control of plants, demonstrated using cold acclimation [1]. • Tailored strategies for stable isotope labeling in plants: methodology focusing on materials and labeling considerations specific to free and proteinogenic amino acid analysis [2].
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Affiliation(s)
- Dione Gentry-Torfer
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- School of Biosciences, The University of Melbourne, Parkville, Australia
| | - Ester Murillo
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Chloe L. Barrington
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Shuai Nie
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
| | - Michael G. Leeming
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
- School of Chemistry, The University of Melbourne, Parkville, Australia
| | | | - Nicholas A. Williamson
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Australia
| | - Ute Roessner
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Research School of Biology, The Australian National University, Acton, Australia
| | - Berin A. Boughton
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
| | - Joachim Kopka
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Federico Martinez-Seidel
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
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9
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Ballmer D, Akiyoshi B. Dynamic localization of the chromosomal passenger complex in trypanosomes is controlled by the orphan kinesins KIN-A and KIN-B. eLife 2024; 13:RP93522. [PMID: 38564240 PMCID: PMC10987093 DOI: 10.7554/elife.93522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
The chromosomal passenger complex (CPC) is an important regulator of cell division, which shows dynamic subcellular localization throughout mitosis, including kinetochores and the spindle midzone. In traditional model eukaryotes such as yeasts and humans, the CPC consists of the catalytic subunit Aurora B kinase, its activator INCENP, and the localization module proteins Borealin and Survivin. Intriguingly, Aurora B and INCENP as well as their localization pattern are conserved in kinetoplastids, an evolutionarily divergent group of eukaryotes that possess unique kinetochore proteins and lack homologs of Borealin or Survivin. It is not understood how the kinetoplastid CPC assembles nor how it is targeted to its subcellular destinations during the cell cycle. Here, we identify two orphan kinesins, KIN-A and KIN-B, as bona fide CPC proteins in Trypanosoma brucei, the kinetoplastid parasite that causes African sleeping sickness. KIN-A and KIN-B form a scaffold for the assembly of the remaining CPC subunits. We show that the C-terminal unstructured tail of KIN-A interacts with the KKT8 complex at kinetochores, while its N-terminal motor domain promotes CPC translocation to spindle microtubules. Thus, the KIN-A:KIN-B complex constitutes a unique 'two-in-one' CPC localization module, which directs the CPC to kinetochores from S phase until metaphase and to the central spindle in anaphase. Our findings highlight the evolutionary diversity of CPC proteins and raise the possibility that kinesins may have served as the original transport vehicles for Aurora kinases in early eukaryotes.
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Affiliation(s)
- Daniel Ballmer
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological SciencesEdinburghUnited Kingdom
| | - Bungo Akiyoshi
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological SciencesEdinburghUnited Kingdom
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10
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Abdul Rehman SA, Cazzaniga C, Di Nisio E, Antico O, Knebel A, Johnson C, Şahin AT, Ibrahim PEGF, Lamoliatte F, Negri R, Muqit MMK, De Cesare V. Discovery and characterization of noncanonical E2-conjugating enzymes. SCIENCE ADVANCES 2024; 10:eadh0123. [PMID: 38536929 PMCID: PMC10971424 DOI: 10.1126/sciadv.adh0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 02/20/2024] [Indexed: 04/10/2024]
Abstract
E2-conjugating enzymes (E2s) play a central role in the enzymatic cascade that leads to the attachment of ubiquitin to a substrate. This process, termed ubiquitylation, is required to maintain cellular homeostasis and affects almost all cellular process. By interacting with multiple E3 ligases, E2s dictate the ubiquitylation landscape within the cell. Since its discovery, ubiquitylation has been regarded as a posttranslational modification that specifically targets lysine side chains (canonical ubiquitylation). We used Matrix-Assisted Laser Desorption/Ionization-Time Of Flight Mass Spectrometry to identify and characterize a family of E2s that are instead able to conjugate ubiquitin to serine and/or threonine. We used structural modeling and prediction tools to identify the key activity determinants that these E2s use to interact with ubiquitin as well as their substrates. Our results unveil the missing E2s necessary for noncanonical ubiquitylation, underscoring the adaptability and versatility of ubiquitin modifications.
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Affiliation(s)
- Syed Arif Abdul Rehman
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Chiara Cazzaniga
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Elena Di Nisio
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
- MRCPPU Reagents and Services, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi, 70 00185 Rome, Italy
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Clare Johnson
- MRCPPU Reagents and Services, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Alp T Şahin
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Peter E G F Ibrahim
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dow St, Dundee DD1 5EH, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Rodolfo Negri
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi, 70 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, CNR, Via degli Apuli 4, 00185 Rome, Italy
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
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11
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Rosario-Rodríguez LJ, Cantres-Rosario YM, Carrasquillo-Carrión K, Rodríguez-De Jesús AE, Cartagena-Isern LJ, García-Requena LA, Roche-Lima A, Meléndez LM. Quantitative Proteomics Reveal That CB2R Agonist JWH-133 Downregulates NF-κB Activation, Oxidative Stress, and Lysosomal Exocytosis from HIV-Infected Macrophages. Int J Mol Sci 2024; 25:3246. [PMID: 38542221 PMCID: PMC10970132 DOI: 10.3390/ijms25063246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/13/2024] Open
Abstract
HIV-associated neurocognitive disorders (HAND) affect 15-55% of HIV-positive patients and effective therapies are unavailable. HIV-infected monocyte-derived macrophages (MDM) invade the brain of these individuals, promoting neurotoxicity. We demonstrated an increased expression of cathepsin B (CATB), a lysosomal protease, in monocytes and post-mortem brain tissues of women with HAND. Increased CATB release from HIV-infected MDM leads to neurotoxicity, and their secretion is associated with NF-κB activation, oxidative stress, and lysosomal exocytosis. Cannabinoid receptor 2 (CB2R) agonist, JWH-133, decreases HIV-1 replication, CATB secretion, and neurotoxicity from HIV-infected MDM, but the mechanisms are not entirely understood. We hypothesized that HIV-1 infection upregulates the expression of proteins associated with oxidative stress and that a CB2R agonist could reverse these effects. MDM were isolated from healthy women donors (n = 3), infected with HIV-1ADA, and treated with JWH-133. After 13 days post-infection, cell lysates were labeled by Tandem Mass Tag (TMT) and analyzed by LC/MS/MS quantitative proteomics bioinformatics. While HIV-1 infection upregulated CATB, NF-κB signaling, Nrf2-mediated oxidative stress response, and lysosomal exocytosis, JWH-133 treatment downregulated the expression of the proteins involved in these pathways. Our results suggest that JWH-133 is a potential alternative therapy against HIV-induced neurotoxicity and warrant in vivo studies to test its potential against HAND.
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Affiliation(s)
- Lester J. Rosario-Rodríguez
- Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan 00935, Puerto Rico;
| | - Yadira M. Cantres-Rosario
- Translational Proteomics Center, Center for Collaborative Research in Health Disparities, University of Puerto Rico-Medical Sciences Campus, San Juan 00935, Puerto Rico; (Y.M.C.-R.); (A.E.R.-D.J.)
| | - Kelvin Carrasquillo-Carrión
- Integrated Informatics Core, Center for Collaborative Research in Health Disparities, University of Puerto Rico-Medical Sciences Campus, San Juan 00935, Puerto Rico; (K.C.-C.); (A.R.-L.)
| | - Ana E. Rodríguez-De Jesús
- Translational Proteomics Center, Center for Collaborative Research in Health Disparities, University of Puerto Rico-Medical Sciences Campus, San Juan 00935, Puerto Rico; (Y.M.C.-R.); (A.E.R.-D.J.)
| | - Luz J. Cartagena-Isern
- Department of Biology, University of Puerto Rico-Río Piedras Campus, San Juan 00925, Puerto Rico; (L.J.C.-I.); (L.A.G.-R.)
| | - Luis A. García-Requena
- Department of Biology, University of Puerto Rico-Río Piedras Campus, San Juan 00925, Puerto Rico; (L.J.C.-I.); (L.A.G.-R.)
| | - Abiel Roche-Lima
- Integrated Informatics Core, Center for Collaborative Research in Health Disparities, University of Puerto Rico-Medical Sciences Campus, San Juan 00935, Puerto Rico; (K.C.-C.); (A.R.-L.)
| | - Loyda M. Meléndez
- Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan 00935, Puerto Rico;
- Translational Proteomics Center, Center for Collaborative Research in Health Disparities, University of Puerto Rico-Medical Sciences Campus, San Juan 00935, Puerto Rico; (Y.M.C.-R.); (A.E.R.-D.J.)
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12
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Tavis S, Hettich RL. Multi-Omics integration can be used to rescue metabolic information for some of the dark region of the Pseudomonas putida proteome. BMC Genomics 2024; 25:267. [PMID: 38468234 PMCID: PMC10926591 DOI: 10.1186/s12864-024-10082-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/02/2024] [Indexed: 03/13/2024] Open
Abstract
In every omics experiment, genes or their products are identified for which even state of the art tools are unable to assign a function. In the biotechnology chassis organism Pseudomonas putida, these proteins of unknown function make up 14% of the proteome. This missing information can bias analyses since these proteins can carry out functions which impact the engineering of organisms. As a consequence of predicting protein function across all organisms, function prediction tools generally fail to use all of the types of data available for any specific organism, including protein and transcript expression information. Additionally, the release of Alphafold predictions for all Uniprot proteins provides a novel opportunity for leveraging structural information. We constructed a bespoke machine learning model to predict the function of recalcitrant proteins of unknown function in Pseudomonas putida based on these sources of data, which annotated 1079 terms to 213 proteins. Among the predicted functions supplied by the model, we found evidence for a significant overrepresentation of nitrogen metabolism and macromolecule processing proteins. These findings were corroborated by manual analyses of selected proteins which identified, among others, a functionally unannotated operon that likely encodes a branch of the shikimate pathway.
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Affiliation(s)
- Steven Tavis
- Genome Science and Technology Graduate Program, University of Tennessee Knoxville, Knoxville, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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13
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Pandi B, Brenman S, Black A, Ng DCM, Lau E, Lam MPY. Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart. J Proteome Res 2024. [PMID: 38456420 DOI: 10.1021/acs.jproteome.3c00789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
A computational analysis of mass spectrometry data was performed to uncover alternative splicing derived protein variants across chambers of the human heart. Evidence for 216 non-canonical isoforms was apparent in the atrium and the ventricle, including 52 isoforms not documented on SwissProt and recovered using an RNA sequencing derived database. Among non-canonical isoforms, 29 show signs of regulation based on statistically significant preferences in tissue usage, including a ventricular enriched protein isoform of tensin-1 (TNS1) and an atrium-enriched PDZ and LIM Domain 3 (PDLIM3) isoform 2 (PDLIM3-2/ALP-H). Examined variant regions that differ between alternative and canonical isoforms are highly enriched with intrinsically disordered regions. Moreover, over two-thirds of such regions are predicted to function in protein binding and RNA binding. The analysis here lends further credence to the notion that alternative splicing diversifies the proteome by rewiring intrinsically disordered regions, which are increasingly recognized to play important roles in the generation of biological function from protein sequences.
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14
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Henze H, Hüttner SS, Koch P, Schüler SC, Groth M, von Eyss B, von Maltzahn J. Denervation alters the secretome of myofibers and thereby affects muscle stem cell lineage progression and functionality. NPJ Regen Med 2024; 9:10. [PMID: 38424446 PMCID: PMC10904387 DOI: 10.1038/s41536-024-00353-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
Skeletal muscle function crucially depends on innervation while repair of skeletal muscle relies on resident muscle stem cells (MuSCs). However, it is poorly understood how innervation affects MuSC properties and thereby regeneration of skeletal muscle. Here, we report that loss of innervation causes precocious activation of MuSCs concomitant with the expression of markers of myogenic differentiation. This aberrant activation of MuSCs after loss of innervation is accompanied by profound alterations on the mRNA and protein level. Combination of muscle injury with loss of innervation results in impaired regeneration of skeletal muscle including shifts in myogenic populations concomitant with delayed maturation of regenerating myofibers. We further demonstrate that loss of innervation leads to alterations in myofibers and their secretome, which then affect MuSC behavior. In particular, we identify an increased secretion of Osteopontin and transforming growth factor beta 1 (Tgfb1) by myofibers isolated from mice which had undergone sciatic nerve transection. The altered secretome results in the upregulation of early activating transcription factors, such as Junb, and their target genes in MuSCs. However, the combination of different secreted factors from myofibers after loss of innervation is required to cause the alterations observed in MuSCs after loss of innervation. These data demonstrate that loss of innervation first affects myofibers causing alterations in their secretome which then affect MuSCs underscoring the importance of proper innervation for MuSC functionality and regeneration of skeletal muscle.
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Affiliation(s)
- Henriette Henze
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
| | - Sören S Hüttner
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
| | - Philipp Koch
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
| | - Svenja C Schüler
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
| | - Björn von Eyss
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany
| | - Julia von Maltzahn
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745, Jena, Germany.
- Faculty of Health Sciences Brandenburg, Brandenburg University of Technology Cottbus - Senftenberg, Universitätsplatz 1, 01968, Senftenberg, Germany.
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15
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Reed TJ, Tyl MD, Tadych A, Troyanskaya OG, Cristea IM. Tapioca: a platform for predicting de novo protein-protein interactions in dynamic contexts. Nat Methods 2024; 21:488-500. [PMID: 38361019 DOI: 10.1038/s41592-024-02179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/12/2024] [Indexed: 02/17/2024]
Abstract
Protein-protein interactions (PPIs) drive cellular processes and responses to environmental cues, reflecting the cellular state. Here we develop Tapioca, an ensemble machine learning framework for studying global PPIs in dynamic contexts. Tapioca predicts de novo interactions by integrating mass spectrometry interactome data from thermal/ion denaturation or cofractionation workflows with protein properties and tissue-specific functional networks. Focusing on the thermal proximity coaggregation method, we improved the experimental workflow. Finely tuned thermal denaturation afforded increased throughput, while cell lysis optimization enhanced protein detection from different subcellular compartments. The Tapioca workflow was next leveraged to investigate viral infection dynamics. Temporal PPIs were characterized during the reactivation from latency of the oncogenic Kaposi's sarcoma-associated herpesvirus. Together with functional assays, NUCKS was identified as a proviral hub protein, and a broader role was uncovered by integrating PPI networks from alpha- and betaherpesvirus infections. Altogether, Tapioca provides a web-accessible platform for predicting PPIs in dynamic contexts.
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Affiliation(s)
- Tavis J Reed
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew D Tyl
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Alicja Tadych
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Olga G Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ, USA.
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
- Flatiron Institute, Simons Foundation, New York City, NY, USA.
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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16
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Vringer E, Heilig R, Riley JS, Black A, Cloix C, Skalka G, Montes-Gómez AE, Aguado A, Lilla S, Walczak H, Gyrd-Hansen M, Murphy DJ, Huang DT, Zanivan S, Tait SW. Mitochondrial outer membrane integrity regulates a ubiquitin-dependent and NF-κB-mediated inflammatory response. EMBO J 2024; 43:904-930. [PMID: 38337057 PMCID: PMC10943237 DOI: 10.1038/s44318-024-00044-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Mitochondrial outer membrane permeabilisation (MOMP) is often essential for apoptosis, by enabling cytochrome c release that leads to caspase activation and rapid cell death. Recently, MOMP has been shown to be inherently pro-inflammatory with emerging cellular roles, including its ability to elicit anti-tumour immunity. Nonetheless, how MOMP triggers inflammation and how the cell regulates this remains poorly defined. We find that upon MOMP, many proteins localised either to inner or outer mitochondrial membranes are ubiquitylated in a promiscuous manner. This extensive ubiquitylation serves to recruit the essential adaptor molecule NEMO, leading to the activation of pro-inflammatory NF-κB signalling. We show that disruption of mitochondrial outer membrane integrity through different means leads to the engagement of a similar pro-inflammatory signalling platform. Therefore, mitochondrial integrity directly controls inflammation, such that permeabilised mitochondria initiate NF-κB signalling.
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Affiliation(s)
- Esmee Vringer
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Rosalie Heilig
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Joel S Riley
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Annabel Black
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Catherine Cloix
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - George Skalka
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Alfredo E Montes-Gómez
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Aurore Aguado
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Sergio Lilla
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Henning Walczak
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
- CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
- Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Mads Gyrd-Hansen
- Department of Immunology and Microbiology, LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Murphy
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Danny T Huang
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Sara Zanivan
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Stephen Wg Tait
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK.
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK.
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17
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Gupta R, Kaushik N, Negi M, Kaushik NK, Choi EH. Molecular insights: Proteomic and metabolomic dissection of plasma-induced growth and functional compound accumulation in Raphanus sativus. Food Chem 2024; 435:137548. [PMID: 37804729 DOI: 10.1016/j.foodchem.2023.137548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 10/09/2023]
Abstract
This study investigated the impact of plasma-activated water (PAW) on Raphanus sativus (radish) roots at the level of proteins and metabolites. PAW treatment induced the accumulation of reactive oxygen species (ROS) and nitrogen oxide species (NOx) in radish and enhanced the activities of antioxidant enzymes. Proteomic analysis resulted in the identification of 6054 proteins, including 1845 PAW-modulated proteins that were majorly associated with energy metabolism, ROS-detoxification, phytohormones signaling, and biosynthesis of glucosinolates. Subsequent metabolomics analysis identified 314 metabolites, of which 194 showed significant differences in response to PAW treatment. In particular, PAW treatment triggered the accumulation of functional compounds such as vitamin C, vitamin B5, glutathione, and glucosinolates, the well-known characteristic compounds of the Brassicaceae family. Further, integrating proteomics and metabolomics data provided novel insights into the molecular mechanism governing plasma-induced growth and the accumulation of these functional compounds in radish plants.
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Affiliation(s)
- Ravi Gupta
- College of General Education, Kookmin University, Seoul, South Korea.
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong,18323, South Korea.
| | - Manorma Negi
- Plasma Bioscience Research Center, Department of Plasma Bio Display, Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 01897, South Korea.
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Plasma Bio Display, Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 01897, South Korea.
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Plasma Bio Display, Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 01897, South Korea.
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18
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Wang B, Li Z, Shi Y, Zhu Z, Fields L, Shelef MA, Li L. Mass Spectrometry-Based Precise Identification of Citrullinated Histones via Limited Digestion and Biotin Derivative Tag Enrichment. Anal Chem 2024; 96:2309-2317. [PMID: 38285917 DOI: 10.1021/acs.analchem.3c02646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Histone citrullination is an essential epigenetic post-translational modification (PTM) that affects many important physiological and pathological processes, but effective tools to study histone citrullination are greatly limited due to several challenges, including the small mass shift caused by this PTM and its low abundance in biological systems. Although previous studies have reported frequent occurrences of histone citrullination, these methods failed to provide a high-throughput and site-specific strategy to detect histone citrullination. Recently, we developed a biotin thiol tag that enabled precise identification of protein citrullination coupled with mass spectrometry. However, very few histone citrullination sites were identified, likely due to the highly basic nature of these proteins. In this study, we develop a novel method utilizing limited digestion and biotin derivative tag enrichment to facilitate direct in vivo identification of citrullination sites on histones. We achieve improved coverage of histone identification via partial enzymatic digestion and lysine block by dimethylation. With biotin tag-assisted chemical derivatization and enrichment, we also achieve precise annotation of histone citrullination sites with high confidence. We further compare different fragmentation methods and find that the electron-transfer-dissociation-based approach enables the most in-depth analysis and characterization. In total, we unambiguously identify 18 unique citrullination sites on histones in human astrocytoma U87 cells, including 15 citrullinated sites being detected for the first time. Some of these citrullination sites are observed to exhibit noticeable alterations in response to DNA damage, which demonstrates the superiority of our strategy in understanding the roles of histone citrullination in critical biological processes.
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Affiliation(s)
- Bin Wang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Zihui Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Yatao Shi
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Zexin Zhu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Miriam A Shelef
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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19
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Jang GM, Sudarsan AKA, Shayeganmehr A, Munhoz EP, Lao R, Gaba A, Rodríguez MG, Love RP, Polacco BJ, Zhou Y, Krogan NJ, Kaake RM, Chelico L. Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579137. [PMID: 38370690 PMCID: PMC10871184 DOI: 10.1101/2024.02.06.579137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Human APOBEC3 enzymes are a family of single-stranded (ss)DNA and RNA cytidine deaminases that act as part of the intrinsic immunity against viruses and retroelements. These enzymes deaminate cytosine to form uracil which can functionally inactivate or cause degradation of viral or retroelement genomes. In addition, APOBEC3s have deamination independent antiviral activity through protein and nucleic acid interactions. If expression levels are misregulated, some APOBEC3 enzymes can access the human genome leading to deamination and mutagenesis, contributing to cancer initiation and evolution. While APOBEC3 enzymes are known to interact with large ribonucleoprotein complexes, the function and RNA dependence is not entirely understood. To further understand their cellular roles, we determined by affinity purification mass spectrometry (AP-MS) the protein interaction network for the human APOBEC3 enzymes and map a diverse set of protein-protein and protein-RNA mediated interactions. Our analysis identified novel RNA-mediated interactions between APOBEC3C, APOBEC3H Haplotype I and II, and APOBEC3G with spliceosome proteins, and APOBEC3G and APOBEC3H Haplotype I with proteins involved in tRNA methylation and ncRNA export from the nucleus. In addition, we identified RNA-independent protein-protein interactions with APOBEC3B, APOBEC3D, and APOBEC3F and the prefoldin family of protein folding chaperones. Interaction between prefoldin 5 (PFD5) and APOBEC3B disrupted the ability of PFD5 to induce degradation of the oncogene cMyc, implicating the APOBEC3B protein interaction network in cancer. Altogether, the results uncover novel functions and interactions of the APOBEC3 family and suggest they may have fundamental roles in cellular RNA biology, their protein-protein interactions are not redundant, and there are protein-protein interactions with tumor suppressors, suggesting a role in cancer biology.
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Affiliation(s)
- Gwendolyn M. Jang
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Arun Kumar Annan Sudarsan
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
- Current Address: Centre for Commercialization of Regenerative Medicine (CCRM), 661 University Ave #1002, Toronto, ON M5G 1M1
| | - Arzhang Shayeganmehr
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
| | - Erika Prando Munhoz
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
- Current Address: Department of Medicine, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW Calgary, AB T2N 4N1
| | - Reanna Lao
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Amit Gaba
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
| | - Milaid Granadillo Rodríguez
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
| | - Robin P. Love
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
- Current Address: Faculty of Medicine & Dentistry, Department of Medicine, TB Program Evaluation & Research Unit, University of Alberta, 11402 University Avenue NW, Edmonton, AB, T6G 2J3
| | - Benjamin J. Polacco
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
| | - Yuan Zhou
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Robyn M. Kaake
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Linda Chelico
- University of Saskatchewan, College of Medicine, Biochemistry, Microbiology & Immunology, Saskatoon, Saskatchewan, Canada
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20
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Lermyte F. The need for open and FAIR data in top-down proteomics. Proteomics 2024; 24:e2300354. [PMID: 38088481 DOI: 10.1002/pmic.202300354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 02/15/2024]
Abstract
In recent years, there has been a tremendous evolution in the high-throughput, tandem mass spectrometry-based analysis of intact proteins, also known as top-down proteomics (TDP). Both hardware and software have developed to the point that the technique has largely entered the mainstream, and large-scale, ambitious, multi-laboratory initiatives have started to make their appearance in the literature. For this, however, more convenient and robust data sharing and reuse will be required. Walzer et al. have created TopDownApp, a customisable, open platform for visualisation and analysis of TDP data, which they hope will be a step in this direction. As they point out, other benefits of such data sharing and interoperability would include reanalysis of published datasets, as well as the prospect of using large amounts of data to train machine learning algorithms. In time, this work could prove to be a valuable resource in the move towards a future of greater TDP data findability, accessibility, interoperability and reusability.
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Affiliation(s)
- Frederik Lermyte
- Department of Chemistry, Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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21
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Lee SY, Choi SH, Kim Y, Ahn HS, Ko YG, Kim K, Chi SW, Kim H. Migrasomal autophagosomes relieve endoplasmic reticulum stress in glioblastoma cells. BMC Biol 2024; 22:23. [PMID: 38287397 PMCID: PMC10826056 DOI: 10.1186/s12915-024-01829-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Glioblastoma (GBM) is more difficult to treat than other intractable adult tumors. The main reason that GBM is so difficult to treat is that it is highly infiltrative. Migrasomes are newly discovered membrane structures observed in migrating cells. Thus, they can be generated from GBM cells that have the ability to migrate along the brain parenchyma. However, the function of migrasomes has not yet been elucidated in GBM cells. RESULTS Here, we describe the composition and function of migrasomes generated along with GBM cell migration. Proteomic analysis revealed that LC3B-positive autophagosomes were abundant in the migrasomes of GBM cells. An increased number of migrasomes was observed following treatment with chloroquine (CQ) or inhibition of the expression of STX17 and SNAP29, which are involved in autophagosome/lysosome fusion. Furthermore, depletion of ITGA5 or TSPAN4 did not relieve endoplasmic reticulum (ER) stress in cells, resulting in cell death. CONCLUSIONS Taken together, our study suggests that increasing the number of autophagosomes, through inhibition of autophagosome/lysosome fusion, generates migrasomes that have the capacity to alleviate cellular stress.
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Affiliation(s)
- Seon Yong Lee
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Sang-Hun Choi
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Yoonji Kim
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
| | - Hee-Sung Ahn
- Convergence Medicine Research Center, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Young-Gyu Ko
- Department of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Kyunggon Kim
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sung Wook Chi
- Department of Life Sciences, Korea University, Seoul, Republic of Korea
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Hyunggee Kim
- Department of Biotechnology, Korea University, Seoul, Republic of Korea.
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea.
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22
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VenkataKrishna LM, Balasubramaniam B, Sushmitha TJ, Ravichandiran V, Balamurugan K. Cronobacter sakazakii infection implicates multifaceted neuro-immune regulatory pathways of Caenorhabditis elegans. Mol Omics 2024; 20:48-63. [PMID: 37818754 DOI: 10.1039/d3mo00167a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The neural pathways of Caenorhabditis elegans play a crucial role in regulating host immunity and inflammation during pathogenic infections. To understand the major neuro-immune signaling pathways, this study aimed to identify the key regulatory proteins in the host C. elegans during C. sakazakii infection. We used high-throughput label-free quantitative proteomics and identified 69 differentially expressed proteins. KEGG analysis revealed that C. sakazakii elicited host immune signaling cascades primarily including mTOR signaling, axon regeneration, metabolic pathways (let-363 and acox-1.4), calcium signaling (mlck-1), and longevity regulating pathways (ddl-2), respectively. The abrogation in functional loss of mTOR-associated players deciphered that C. sakazakii infection negatively regulated the lifespan of mutant worms (akt-1, let-363 and dlk-1), including physiological aberrations, such as reduced pharyngeal pumping and egg production. Additionally, the candidate pathway proteins were validated by transcriptional profiling of their corresponding genes. Furthermore, immunoblotting showed the downregulation of mTORC2/SGK-1 during the later hours of pathogen exposure. Overall, our findings profoundly provide an understanding of the specificity of proteome imbalance in affecting neuro-immune regulations during C. sakazakii infection.
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Affiliation(s)
| | | | - T J Sushmitha
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - V Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
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23
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Stener-Victorin E, Eriksson G, Mohan Shrestha M, Rodriguez Paris V, Lu H, Banks J, Samad M, Perian C, Jude B, Engman V, Boi R, Nilsson E, Ling C, Nyström J, Wernstedt Asterholm I, Turner N, Lanner J, Benrick A. Proteomic analysis shows decreased type I fibers and ectopic fat accumulation in skeletal muscle from women with PCOS. eLife 2024; 12:RP87592. [PMID: 38180081 PMCID: PMC10945439 DOI: 10.7554/elife.87592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
Background Polycystic ovary syndrome's (PCOS) main feature is hyperandrogenism, which is linked to a higher risk of metabolic disorders. Gene expression analyses in adipose tissue and skeletal muscle reveal dysregulated metabolic pathways in women with PCOS, but these differences do not necessarily lead to changes in protein levels and biological function. Methods To advance our understanding of the molecular alterations in PCOS, we performed global proteomic and phosphorylation site analysis using tandem mass spectrometry, and analyzed gene expression and methylation. Adipose tissue and skeletal muscle were collected at baseline from 10 women with and without PCOS, and in women with PCOS after 5 weeks of treatment with electrical stimulation. Results Perilipin-1, a protein that typically coats the surface of lipid droplets in adipocytes, was increased whereas proteins involved in muscle contraction and type I muscle fiber function were downregulated in PCOS muscle. Proteins in the thick and thin filaments had many altered phosphorylation sites, indicating differences in protein activity and function. A mouse model was used to corroborate that androgen exposure leads to a shift in muscle fiber type in controls but not in skeletal muscle-specific androgen receptor knockout mice. The upregulated proteins in muscle post treatment were enriched in pathways involved in extracellular matrix organization and wound healing, which may reflect a protective adaptation to repeated contractions and tissue damage due to needling. A similar, albeit less pronounced, upregulation in extracellular matrix organization pathways was also seen in adipose tissue. Conclusions Our results suggest that hyperandrogenic women with PCOS have higher levels of extra-myocellular lipids and fewer oxidative insulin-sensitive type I muscle fibers. These could be key factors leading to insulin resistance in PCOS muscle while electric stimulation-induced tissue remodeling may be protective. Funding Swedish Research Council (2020-02485, 2022-00550, 2020-01463), Novo Nordisk Foundation (NNF22OC0072904), and IngaBritt and Arne Lundberg Foundation. Clinical trial number NTC01457209.
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Affiliation(s)
| | - Gustaw Eriksson
- Department of Physiology and Pharmacology, Karolinska InstituteStockholmSweden
| | - Man Mohan Shrestha
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | | | - Haojiang Lu
- Department of Physiology and Pharmacology, Karolinska InstituteStockholmSweden
| | - Jasmine Banks
- School of Biomedical Sciences, University of New South WalesSydneyAustralia
- Victor Chang Cardiac Research Institute, DarlinghurstSydneyAustralia
| | - Manisha Samad
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Charlène Perian
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Baptiste Jude
- Department of Physiology and Pharmacology, Karolinska InstituteStockholmSweden
| | - Viktor Engman
- Department of Physiology and Pharmacology, Karolinska InstituteStockholmSweden
| | - Roberto Boi
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Emma Nilsson
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund UniversityMalmöSweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund UniversityMalmöSweden
| | - Jenny Nyström
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Ingrid Wernstedt Asterholm
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Nigel Turner
- School of Biomedical Sciences, University of New South WalesSydneyAustralia
- Victor Chang Cardiac Research Institute, DarlinghurstSydneyAustralia
| | - Johanna Lanner
- Department of Physiology and Pharmacology, Karolinska InstituteStockholmSweden
| | - Anna Benrick
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of GothenburgGothenburgSweden
- School of Health Sciences, University of SkövdeSkövdeSweden
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24
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Wang X, Wang Y, Hou J, Liu H, Zeng R, Li X, Han M, Li Q, Ji L, Pan D, Jia W, Zhong W, Xu T. Plasma proteome profiling reveals the therapeutic effects of the PPAR pan-agonist chiglitazar on insulin sensitivity, lipid metabolism, and inflammation in type 2 diabetes. Sci Rep 2024; 14:638. [PMID: 38182717 PMCID: PMC10770401 DOI: 10.1038/s41598-024-51210-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024] Open
Abstract
Chiglitazar is a novel peroxisome proliferator-activated receptor (PPAR) pan-agonist, which passed phase III clinical trials and was newly approved in China for use as an adjunct to diet and exercise in glycemic control in adult patients with Type 2 Diabetes (T2D). To explore the circulating protein signatures associated with the administration of chiglitazar in T2D patients, we conducted a comparative longitudinal study using plasma proteome profiling. Of the 157 T2D patients included in the study, we administered chiglitazar to a specific group, while the controls were given either placebo or sitagliptin. The plasma proteomes were profiled at baseline and 12 and 24 weeks post-treatment using data-independent acquisition mass spectrometry (DIA-MS). Our study indicated that 13 proteins were associated with chiglitazar treatment in T2D patients, including 10 up-regulated proteins (SHBG, TF, APOA2, APOD, GSN, MBL2, CFD, PGLYRP2, A2M, and APOA1) and 3 down-regulated proteins (PRG4, FETUB, and C2) after treatment, which were implicated in the regulation of insulin sensitivity, lipid metabolism, and inflammation response. Our study provides insight into the response of chiglitazar treatment from a proteome perspective and demonstrates the multi-faceted effects of chiglitazar in T2D patients, which will help the clinical application of chiglitazar and further study of its action mechanism.
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Affiliation(s)
- Xingyue Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - You Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Junjie Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hongyang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Rong Zeng
- CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xiangyu Li
- Guangzhou National Laboratory, Guangzhou, China
| | - Mei Han
- Guangzhou National Laboratory, Guangzhou, China
| | - Qingrun Li
- CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Linong Ji
- Department of Endocrinology and Metabolism, Peking University People's Hospital, Beijing, China
| | - Desi Pan
- Shenzhen Chipscreen Biosciences Co., Ltd, Shenzhen, China
| | - Weiping Jia
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Wen Zhong
- Guangzhou National Laboratory, Guangzhou, China.
| | - Tao Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Guangzhou National Laboratory, Guangzhou, China.
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
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25
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Ma M, Yu Q, Delafield DG, Cui Y, Li Z, Li M, Wu W, Shi X, Westmark PR, Gutierrez A, Ma G, Gao A, Xu M, Xu W, Westmark CJ, Li L. On-Tissue Spatial Proteomics Integrating MALDI-MS Imaging with Shotgun Proteomics Reveals Soy Consumption-Induced Protein Changes in a Fragile X Syndrome Mouse Model. ACS Chem Neurosci 2024; 15:119-133. [PMID: 38109073 PMCID: PMC11127747 DOI: 10.1021/acschemneuro.3c00497] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Fragile X syndrome (FXS), the leading cause of inherited intellectual disability and autism, is caused by the transcriptional silencing of the FMR1 gene, which encodes the fragile X messenger ribonucleoprotein (FMRP). FMRP interacts with numerous brain mRNAs that are involved in synaptic plasticity and implicated in autism spectrum disorders. Our published studies indicate that single-source, soy-based diets are associated with increased seizures and autism. Thus, there is an acute need for an unbiased protein marker identification in FXS in response to soy consumption. Herein, we present a spatial proteomics approach integrating mass spectrometry imaging with label-free proteomics in the FXS mouse model to map the spatial distribution and quantify levels of proteins in the hippocampus and hypothalamus brain regions. In total, 1250 unique peptides were spatially resolved, demonstrating the diverse array of peptidomes present in the tissue slices and the broad coverage of the strategy. A group of proteins that are known to be involved in glycolysis, synaptic transmission, and coexpression network analysis suggest a significant association between soy proteins and metabolic and synaptic processes in the Fmr1KO brain. Ultimately, this spatial proteomics work represents a crucial step toward identifying potential candidate protein markers and novel therapeutic targets for FXS.
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Affiliation(s)
- Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Daniel G. Delafield
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Zihui Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Miyang Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Wenxin Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Xudong Shi
- Division of Otolaryngology, Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Pamela R. Westmark
- Department of Neurology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Alejandra Gutierrez
- Department of Neurology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
- Molecular Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Gui Ma
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Ang Gao
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Meng Xu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Cara J. Westmark
- Department of Neurology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
- Molecular Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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26
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Ben Toumia I, Bachetti T, Chekir-Ghedira L, Profumo A, Ponassi M, Di Domizio A, Izzotti A, Sciacca S, Puglisi C, Forte S, Giuffrida R, Colarossi C, Milardi D, Grasso G, Lanza V, Fiordoro S, Drago G, Tkachenko K, Cardinali B, Romano P, Iervasi E, Vargas GC, Barboro P, Kohnke FH, Rosano C. Fraisinib: a calixpyrrole derivative reducing A549 cell-derived NSCLC tumor in vivo acts as a ligand of the glycine-tRNA synthase, a new molecular target in oncology. Front Pharmacol 2024; 14:1258108. [PMID: 38235113 PMCID: PMC10791888 DOI: 10.3389/fphar.2023.1258108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/17/2023] [Indexed: 01/19/2024] Open
Abstract
Background and purpose: Lung cancer is the leading cause of death in both men and women, constituting a major public health problem worldwide. Non-small-cell lung cancer accounts for 85%-90% of all lung cancers. We propose a compound that successfully fights tumor growth in vivo by targeting the enzyme GARS1. Experimental approach: We present an in-depth investigation of the mechanism through which Fraisinib [meso-(p-acetamidophenyl)-calix(4)pyrrole] affects the human lung adenocarcinoma A549 cell line. In a xenografted model of non-small-cell lung cancer, Fraisinib was found to reduce tumor mass volume without affecting the vital parameters or body weight of mice. Through a computational approach, we uncovered that glycyl-tRNA synthetase is its molecular target. Differential proteomics analysis further confirmed that pathways regulated by Fraisinib are consistent with glycyl-tRNA synthetase inhibition. Key results: Fraisinib displays a strong anti-tumoral potential coupled with limited toxicity in mice. Glycyl-tRNA synthetase has been identified and validated as a protein target of this compound. By inhibiting GARS1, Fraisinib modulates different key biological processes involved in tumoral growth, aggressiveness, and invasiveness. Conclusion and implications: The overall results indicate that Fraisinib is a powerful inhibitor of non-small-cell lung cancer growth by exerting its action on the enzyme GARS1 while displaying marginal toxicity in animal models. Together with the proven ability of this compound to cross the blood-brain barrier, we can assess that Fraisinib can kill two birds with one stone: targeting the primary tumor and its metastases "in one shot." Taken together, we suggest that inhibiting GARS1 expression and/or GARS1 enzymatic activity may be innovative molecular targets for cancer treatment.
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Affiliation(s)
| | | | - Leila Chekir-Ghedira
- Unit of Bioactive Natural Substances and Biotechnology, Faculty of Dental Medicine of Monastir, University of Monastir, Monastir, Tunisia
| | - Aldo Profumo
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Marco Ponassi
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Alberto Izzotti
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | | | | | - Stefano Forte
- Istituto Oncologico del Mediterraneo, Viagrande, Italy
| | | | | | - Danilo Milardi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Giuseppe Grasso
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Valeria Lanza
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Stefano Fiordoro
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Giacomo Drago
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | | | | | - Paolo Romano
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Erika Iervasi
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Paola Barboro
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Franz Heinrich Kohnke
- Dipartimento di Scienze Chimiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), University of Messina, Messina, Italy
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27
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Pandit AK, Misra S, Sengupta S, Chakraborty R, Singh P, Singh GP, Phuljhele S, Srivastava AK, Vibha D, Garg A, Shankar V, Mohania D, Shukla G, Prasad K. Cerebrospinal fluid proteins in idiopathic intracranial hypertension: An exploratory SWATH proteomics analysis. Proteomics Clin Appl 2024; 18:e2300021. [PMID: 37551060 DOI: 10.1002/prca.202300021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/17/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023]
Abstract
PURPOSE The pathogenesis of idiopathic intracranial hypertension (IIH) is currently poorly understood. This exploratory study aimed to identify potential cerebrospinal fluid (CSF) biomarkers in IIH cases compared to controls using SWATH-MS proteomics approach. EXPERIMENTAL DESIGN CSF samples were collected prospectively from IIH cases and control subjects which were subjected to SWATH-MS based untargeted proteomics. Proteins with fold change > 1.5 or < 0.67 and p-value < 0.05 were considered significantly differentially expressed. Data are available via ProteomeXchange with identifier PXD027751. Statistical analysis was conducted in R version 3.6.2. RESULTS We included CSF samples from 33 subjects, consisting of 13 IIH cases and 20 controls. A total of 262 proteins were identified in Proteinpilot search. Through SWATH analysis, we quantified 232 proteins. We observed 37 differentially expressed proteins between the two groups with 24 upregulated and 13 downregulated proteins. There were two differential proteins among overweight versus non-overweight IIH cases. Network for 23 proteins was highly connected in the interaction analysis. CONCLUSIONS AND CLINICAL RELEVANCE Neurosecretory, neuroendocrine, and inflammatory proteins were predominantly involved in causing IIH. This exploratory study served as a platform to identify 37 differentially expressed proteins in IIH and also showed significant differences between overweight and non-overweight IIH patients.
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Affiliation(s)
- Awadh Kishor Pandit
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Shubham Misra
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Department of Neurology, Yale University, New Haven, USA
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rahul Chakraborty
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Praveen Singh
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Gyaninder Pal Singh
- Department of Neuroanesthesiology and Critical Care, All India Institute of Medical Sciences, New Delhi, India
| | - Swati Phuljhele
- Department of Ophthalmology, Dr R.P. Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Achal K Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Deepti Vibha
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Ajay Garg
- Department of Neuroradiology, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Shankar
- Department of Orthopedics, All India Institute of Medical Sciences, New Delhi, India
| | - Dheeraj Mohania
- Dr R.P. Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Garima Shukla
- Department of Neurology (Epilepsy & Sleep Medicine), Department of Medicine, Queen's University, Kingston, Canada
| | - Kameshwar Prasad
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Department of Neurology, Rajendra Institute of Medical Sciences, Ranchi, India
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28
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Rossio V, Paulo JA, Liu X, Gygi SP, King RW. Substrate identification and specificity profiling of deubiquitylases against endogenously-generated ubiquitin-protein conjugates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572581. [PMID: 38187689 PMCID: PMC10769257 DOI: 10.1101/2023.12.20.572581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Deubiquitylating enzymes (DUBs) remove ubiquitin from proteins thereby regulating their stability or activity. Our understanding of DUB-substrate specificity is limited because DUBs are typically not compared to each other against many physiological substrates. By broadly inhibiting DUBs in Xenopus egg extract, we generated hundreds of ubiquitylated proteins and compared the ability of 30 DUBs to deubiquitylate them using quantitative proteomics. We identified five high impact DUBs (USP7, USP9X, USP36, USP15 and USP24) that each reduced ubiquitylation of over ten percent of the isolated proteins. Candidate substrates of high impact DUBs showed substantial overlap and were enriched for disordered regions, suggesting this feature may promote substrate recognition. Other DUBs showed lower impact and non-overlapping specificity, targeting distinct non-disordered proteins including complexes such as the ribosome or the proteasome. Altogether our study identifies candidate DUB substrates and defines patterns of functional redundancy and specificity, revealing substrate characteristics that may influence DUB-substrate recognition.
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29
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Shimpi AA, Williams ED, Ling L, Tamir T, White FM, Fischbach C. Phosphoproteomic Changes Induced by Cell-Derived Matrix and Their Effect on Tumor Cell Migration and Cytoskeleton Remodeling. ACS Biomater Sci Eng 2023; 9:6835-6848. [PMID: 38015076 DOI: 10.1021/acsbiomaterials.3c01034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Increased fibrotic extracellular matrix (ECM) deposition promotes tumor invasion, which is the first step of the metastatic cascade. Yet, the underlying mechanisms are poorly understood as conventional studies of tumor cell migration are often performed in 2D cultures lacking the compositional and structural complexity of native ECM. Moreover, these studies frequently focus on select candidate pathways potentially overlooking other relevant changes in cell signaling. Here, we combine a cell-derived matrix (CDM) model with phosphotyrosine phosphoproteomic analysis to investigate tumor cell migration on fibrotic ECM relative to standard tissue culture plastic (TCP). Our results suggest that tumor cells cultured on CDMs migrate faster and in a more directional manner than their counterparts on TCP. These changes in migration correlate with decreased cell spreading and increased cell elongation. While the formation of phosphorylated focal adhesion kinase (pFAK)+ adhesion complexes did not vary between TCP and CDMs, time-dependent phosphoproteomic analysis identified that the SRC family kinase LYN may be differentially regulated. Pharmacological inhibition of LYN decreased tumor cell migration and cytoskeletal rearrangement on CDMs and also on TCP, suggesting that LYN regulates tumor cell migration on CDMs in combination with other mechanisms. These data highlight how the combination of physicochemically complex in vitro systems with phosphoproteomics can help identify signaling mechanisms by which the fibrotic ECM regulates tumor cell migration.
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Affiliation(s)
- Adrian A Shimpi
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Erik D Williams
- Department of Information Science, Cornell University, Ithaca, New York 14853, United States
| | - Lu Ling
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Tigist Tamir
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 023139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 023139, United States
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 023139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 023139, United States
| | - Claudia Fischbach
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, United States
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30
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Claushuis B, de Ru AH, Rotman SA, van Veelen PA, Dawson LF, Wren BW, Corver J, Smits WK, Hensbergen PJ. Revised Model for the Type A Glycan Biosynthetic Pathway in Clostridioides difficile Strain 630Δ erm Based on Quantitative Proteomics of cd0241- cd0244 Mutant Strains. ACS Infect Dis 2023; 9:2665-2674. [PMID: 37965964 PMCID: PMC10714395 DOI: 10.1021/acsinfecdis.3c00485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/20/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
The bacterial flagellum is involved in a variety of processes including motility, adherence, and immunomodulation. In the Clostridioides difficile strain 630Δerm, the main filamentous component, FliC, is post-translationally modified with an O-linked Type A glycan structure. This modification is essential for flagellar function, since motility is seriously impaired in gene mutants with improper biosynthesis of the Type A glycan. The cd0240-cd0244 gene cluster encodes the Type A biosynthetic proteins, but the role of each gene, and the corresponding enzymatic activity, have not been fully elucidated. Using quantitative mass spectrometry-based proteomics analyses, we determined the relative abundance of the observed glycan variations of the Type A structure in cd0241, cd0242, cd0243, and cd0244 mutant strains. Our data not only confirm the importance of CD0241, CD0242, and CD0243 but, in contrast to previous data, also show that CD0244 is essential for the biosynthesis of the Type A modification. Combined with additional bioinformatic analyses, we propose a revised model for Type A glycan biosynthesis.
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Affiliation(s)
- Bart Claushuis
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Arnoud H. de Ru
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Sarah A. Rotman
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Peter A. van Veelen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Lisa F. Dawson
- Faculty
of Infectious and Tropical Diseases, London
School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Brendan W. Wren
- Faculty
of Infectious and Tropical Diseases, London
School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Jeroen Corver
- Department
of Medical Microbiology, Leiden University
Medical Center, Leiden 2333 ZA, The Netherlands
| | - Wiep Klaas Smits
- Department
of Medical Microbiology, Leiden University
Medical Center, Leiden 2333 ZA, The Netherlands
| | - Paul J. Hensbergen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
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31
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Ramsbottom KA, Prakash A, Riverol YP, Camacho OM, Sun Z, Kundu DJ, Bowler-Barnett E, Martin M, Fan J, Chebotarov D, McNally KL, Deutsch EW, Vizcaíno JA, Jones AR. A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.17.567512. [PMID: 38014076 PMCID: PMC10680829 DOI: 10.1101/2023.11.17.567512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have re-analysed publicly available mass spectrometry proteomics datasets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we identified 15,522 phosphosites on serine, threonine and tyrosine residues on rice proteins. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation likely caused by different kinase groups. We cross-referenced phosphosites against the rice 3,000 genomes, to identify single amino acid variations (SAAVs) within or proximal to phosphosites that could cause loss of a site in a given rice variety. The data was clustered to identify groups of sites with similar patterns across rice family groups, for example those highly conserved in Japonica, but mostly absent in Aus type rice varieties - known to have different responses to drought. These resources can assist rice researchers to discover alleles with significantly different functional effects across rice varieties. The data has been loaded into UniProt Knowledge-Base - enabling researchers to visualise sites alongside other data on rice proteins e.g. structural models from AlphaFold2, PeptideAtlas and the PRIDE database - enabling visualisation of source evidence, including scores and supporting mass spectra.
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Affiliation(s)
- Kerry A Ramsbottom
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, United Kingdom
| | - Ananth Prakash
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Yasset Perez Riverol
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Oscar Martin Camacho
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, United Kingdom
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Deepti J. Kundu
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Emily Bowler-Barnett
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Maria Martin
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Jun Fan
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Dmytro Chebotarov
- International Rice Research Institute, DAPO 7777, Manila 1301, Philippines
| | - Kenneth L McNally
- International Rice Research Institute, DAPO 7777, Manila 1301, Philippines
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, United Kingdom
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32
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Issara-Amphorn J, Sjoelund VH, Smelkinson M, Montalvo S, Yoon SH, Manes NP, Nita-Lazar A. Myristoylated, alanine-rich C-kinase substrate (MARCKS) regulates toll-like receptor 4 signaling in macrophages. Sci Rep 2023; 13:19562. [PMID: 37949888 PMCID: PMC10638260 DOI: 10.1038/s41598-023-46266-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
MARCKS (myristoylated alanine-rich C-kinase substrate) is a membrane-associated protein expressed in many cell types, including macrophages. MARCKS is functionally implicated in cell adhesion, phagocytosis, and inflammation. LPS (lipopolysaccharide) triggers inflammation via TLR4 (toll-like receptor 4).The presence of MARCKS and the formation of phospho-MARCKS in various cell types have been described, but the role(s) of MARCKS in regulating macrophage functions remain unclear. We investigated the role of MARCKS in inflammation. Confocal microscopy revealed that MARCKS and phospho-MARCKS increased localization to endosomes and the Golgi apparatus upon LPS stimulation.CRISPR-CAS9 mediated knockout of MARCKS in macrophages downregulated the production of TNF and IL6, suggesting a role for MARCKS in inflammatory responses. Our comprehensive proteomics analysis together with real-time metabolic assays comparing LPS-stimulation of WT and MARCKS knock-out macrophages provided insights into the involvement of MARCKS in specific biological processes including innate immune response, inflammatory response, cytokine production, and molecular functions such as extracellularly ATP-gated cation channel activity, electron transfer activity and oxidoreductase activity, uncovering specific proteins involved in regulating MARCKS activity upon LPS stimulation. MARCKS appears to be a key regulator of inflammation whose inhibition might be beneficial for therapeutic intervention in inflammatory diseases.
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Affiliation(s)
- Jiraphorn Issara-Amphorn
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892-1892, USA
| | - Virginie H Sjoelund
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892-1892, USA
- Barnett Institute, Northeastern University, Boston, MA, 02115, USA
| | - Margery Smelkinson
- Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sebastian Montalvo
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892-1892, USA
| | - Sung Hwan Yoon
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892-1892, USA
| | - Nathan P Manes
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892-1892, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892-1892, USA.
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33
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Höpfner D, Cichy A, Pogenberg V, Krisp C, Mezouar S, Bach NC, Grotheer J, Zarza SM, Martinez E, Bonazzi M, Feige MJ, Sieber SA, Schlüter H, Itzen A. The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3. Commun Biol 2023; 6:1124. [PMID: 37932372 PMCID: PMC10628234 DOI: 10.1038/s42003-023-05494-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
The intracellular bacterial pathogen Coxiella burnetii evades the host response by secreting effector proteins that aid in establishing a replication-friendly niche. Bacterial filamentation induced by cyclic AMP (Fic) enzymes can act as effectors by covalently modifying target proteins with the posttranslational AMPylation by transferring adenosine monophosphate (AMP) from adenosine triphosphate (ATP) to a hydroxyl-containing side chain. Here we identify the gene product of C. burnetii CBU_0822, termed C. burnetii Fic 2 (CbFic2), to AMPylate host cell histone H3 at serine 10 and serine 28. We show that CbFic2 acts as a bifunctional enzyme, both capable of AMPylation as well as deAMPylation, and is regulated by the binding of DNA via a C-terminal helix-turn-helix domain. We propose that CbFic2 performs AMPylation in its monomeric state, switching to a deAMPylating dimer upon DNA binding. This study unveils reversible histone modification by a specific enzyme of a pathogenic bacterium.
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Affiliation(s)
- Dorothea Höpfner
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Adam Cichy
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Group of Proteinchemistry, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Vivian Pogenberg
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Christoph Krisp
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Soraya Mezouar
- Aix-Marseille University, Institut de Recherche pour la Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Boulevard Jean Moulin, 13005, Marseille, France
| | - Nina C Bach
- Technical University of Munich (TUM), TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Jan Grotheer
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Sandra Madariaga Zarza
- Aix-Marseille University, Institut de Recherche pour la Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Boulevard Jean Moulin, 13005, Marseille, France
| | - Eric Martinez
- Cellular and Molecular Biology of Bacterial Infections, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, UMR 9004 - Centre national de la recherche scientifique (CNRS), 1919 Route de Mende, 34293, Montpellier, France
| | - Matteo Bonazzi
- Cellular and Molecular Biology of Bacterial Infections, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, UMR 9004 - Centre national de la recherche scientifique (CNRS), 1919 Route de Mende, 34293, Montpellier, France
| | - Matthias J Feige
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Stephan A Sieber
- Technical University of Munich (TUM), TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Aymelt Itzen
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.
- Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.
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McIlvenna LC, Whitham M. Exercise, healthy ageing, and the potential role of small extracellular vesicles. J Physiol 2023; 601:4937-4951. [PMID: 35388915 PMCID: PMC10952297 DOI: 10.1113/jp282468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/29/2022] [Indexed: 11/08/2022] Open
Abstract
Extracellular vesicles (EVs) can be released from most cells in the body and act as intercellular messengers transferring information in their cargo to affect cellular function. A growing body of evidence suggests that a subset of EVs, referred to here as 'small extracellular vesicles' (sEVs), can accelerate or slow the processes of ageing and age-related diseases dependent on their molecular cargo and cellular origin. Continued exploration of the vast complexity of the sEV cargo aims to further characterise these systemic vehicles that may be targeted to ameliorate age-related pathologies. Marked progress in the development of mass spectrometry-based technologies means that it is now possible to characterise a significant proportion of the proteome of sEVs (surface and cargo) via unbiased proteomics. This information is vital for identifying biomarkers and the development of sEV-based therapeutics in the context of ageing. Although exercise and physical activity are prominent features in maintaining health in advancing years, the mechanisms responsible are unclear. A potential mechanism by which plasma sEVs released during exercise could influence ageing and senescence is via the increased delivery of cargo proteins that function as antioxidant enzymes or inhibitors of senescence. These have been observed to increase in sEVs following acute and chronic exercise, as identified via independent interrogation of high coverage, publicly available proteomic datasets. Establishing tropism and exchange of functionally active proteins by these processes represents a promising line of enquiry in implicating sEVs as biologically relevant mediators of the ageing process.
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Affiliation(s)
- Luke C. McIlvenna
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
| | - Martin Whitham
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
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Koc MA, Wiles TA, Weinhold DC, Rightmyer S, Weaver AL, McDowell CT, Roder J, Asmellash S, Pestano GA, Roder H, Georgantas III RW. Molecular and translational biology of the blood-based VeriStrat® proteomic test used in cancer immunotherapy treatment guidance. J Mass Spectrom Adv Clin Lab 2023; 30:51-60. [PMID: 38074293 PMCID: PMC10709509 DOI: 10.1016/j.jmsacl.2023.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 10/16/2023] [Accepted: 11/08/2023] [Indexed: 03/09/2024] Open
Abstract
INTRODUCTION The VeriStrat® test (VS) is a blood-based assay that predicts a patient's response to therapy by analyzing eight features in a spectrum obtained from matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis of human serum and plasma. In a recent analysis of the INSIGHT clinical trial (NCT03289780), it was found that the VS labels, VS Good and VS Poor, can effectively predict the responsiveness of non-small cell lung cancer (NSCLC) patients to immune checkpoint inhibitor (ICI) therapy. However, while VS measures the intensities of spectral features using MALDI-TOF analysis, the specific proteoforms underlying these features have not been comprehensively identified. OBJECTIVES The objective of this study was to identify the proteoforms that are measured by VS. METHODS To resolve the features obtained from the low-resolution MALDI-TOF procedure used to acquire mass spectra for VS DeepMALDI® analysis of serum was employed. This technique allowed for the identification of finer peaks within these features. Additionally, a combination of reversed-phase fractionation and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was then used to identify the proteoforms associated with these peaks. RESULTS The analysis revealed that the primary constituents of the spectrum measured by VS are serum amyloid A1, serum amyloid A2, serum amyloid A4, C-reactive protein, and beta-2 microglobulin. CONCLUSION Proteoforms involved in host immunity were identified as significant components of these features. This newly acquired information improves our understanding of how VS can accurately predict patient response to therapy. It opens up additional studies that can expand our understanding even further.
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Affiliation(s)
| | | | - Daniel C. Weinhold
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Steven Rightmyer
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Amanda L. Weaver
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Colin T. McDowell
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Joanna Roder
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Senait Asmellash
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Gary A. Pestano
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Heinrich Roder
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
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Will A, Oliinyk D, Bleiholder C, Meier F. Peptide collision cross sections of 22 post-translational modifications. Anal Bioanal Chem 2023; 415:6633-6645. [PMID: 37758903 PMCID: PMC10598134 DOI: 10.1007/s00216-023-04957-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 07/13/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023]
Abstract
Recent advances have rekindled the interest in ion mobility as an additional dimension of separation in mass spectrometry (MS)-based proteomics. Ion mobility separates ions according to their size and shape in the gas phase. Here, we set out to investigate the effect of 22 different post-translational modifications (PTMs) on the collision cross section (CCS) of peptides. In total, we analyzed ~4300 pairs of matching modified and unmodified peptide ion species by trapped ion mobility spectrometry (TIMS). Linear alignment based on spike-in reference peptides resulted in highly reproducible CCS values with a median coefficient of variation of 0.26%. On a global level, we observed a redistribution in the m/z vs. ion mobility space for modified peptides upon changes in their charge state. Pairwise comparison between modified and unmodified peptides of the same charge state revealed median shifts in CCS between -1.4% (arginine citrullination) and +4.5% (O-GlcNAcylation). In general, increasing modified peptide masses were correlated with higher CCS values, in particular within homologous PTM series. However, investigating the ion populations in more detail, we found that the change in CCS can vary substantially for a given PTM and is partially correlated with the gas phase structure of its unmodified counterpart. In conclusion, our study shows PTM- and sequence-specific effects on the cross section of peptides, which could be further leveraged for proteome-wide PTM analysis.
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Affiliation(s)
- Andreas Will
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Denys Oliinyk
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32304, USA
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.
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Huttenhower C, Finn RD, McHardy AC. Challenges and opportunities in sharing microbiome data and analyses. Nat Microbiol 2023; 8:1960-1970. [PMID: 37783751 DOI: 10.1038/s41564-023-01484-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 08/28/2023] [Indexed: 10/04/2023]
Abstract
Microbiome data, metadata and analytical workflows have become 'big' in terms of volume and complexity. Although the infrastructure and technologies to share data have been established, the interdisciplinary and multi-omic nature of the field can make resources difficult to identify and use. Following best practices for data deposition requires substantial effort, with sometimes little obvious reward. Gaps remain where microbiome-specific resources for data sharing or reproducibility do not yet exist. We outline available best practices, challenges to their adoption and opportunities in data sharing in microbiome research. We showcase examples of best practices and advocate for their enforcement and incentivization for data sharing. This includes recognition of data curation and sharing endeavours by individuals, institutions, journals and funders. Opportunities for progress include enabling microbiome-specific databases to incorporate future methods for data analysis, integration and reuse.
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Affiliation(s)
- Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Departments of Biostatistics and Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alice Carolyn McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.
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Mundt F, Albrechtsen NJW, Mann SP, Treit P, Ghodgaonkar-Steger M, O’Flaherty M, Raijmakers R, Vizcaíno JA, Heck AJ, Mann M. Foresight in clinical proteomics: current status, ethical considerations, and future perspectives. OPEN RESEARCH EUROPE 2023; 3:59. [PMID: 37645494 PMCID: PMC10446044 DOI: 10.12688/openreseurope.15810.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/26/2023] [Indexed: 08/31/2023]
Abstract
With the advent of robust and high-throughput mass spectrometric technologies and bioinformatics tools to analyze large data sets, proteomics has penetrated broadly into basic and translational life sciences research. More than 95% of FDA-approved drugs currently target proteins, and most diagnostic tests are protein-based. The introduction of proteomics to the clinic, for instance to guide patient stratification and treatment, is already ongoing. Importantly, ethical challenges come with this success, which must also be adequately addressed by the proteomics and medical communities. Consortium members of the H2020 European Union-funded proteomics initiative: European Proteomics Infrastructure Consortium-providing access (EPIC-XS) met at the Core Technologies for Life Sciences (CTLS) conference to discuss the emerging role and implementation of proteomics in the clinic. The discussion, involving leaders in the field, focused on the current status, related challenges, and future efforts required to make proteomics a more mainstream technology for translational and clinical research. Here we report on that discussion and provide an expert update concerning the feasibility of clinical proteomics, the ethical implications of generating and analyzing large-scale proteomics clinical data, and recommendations to ensure both ethical and effective implementation in real-world applications.
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Affiliation(s)
- Filip Mundt
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicolai J. Wewer Albrechtsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, University Hospital, Bispebjerg Hospital, Bispebjerg, Denmark
| | | | - Peter Treit
- Max Planck Institute of Biochemistry, Proteomics and Signal Transduction, Martinsried, Germany
| | | | - Martina O’Flaherty
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Reinout Raijmakers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Max Planck Institute of Biochemistry, Proteomics and Signal Transduction, Martinsried, Germany
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Gerber M, Suppanz I, Oeljeklaus S, Niemann M, Käser S, Warscheid B, Schneider A, Dewar CE. A Msp1-containing complex removes orphaned proteins in the mitochondrial outer membrane of T. brucei. Life Sci Alliance 2023; 6:e202302004. [PMID: 37586887 PMCID: PMC10432679 DOI: 10.26508/lsa.202302004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
The AAA-ATPase Msp1 extracts mislocalised outer membrane proteins and thus contributes to mitochondrial proteostasis. Using pulldown experiments, we show that trypanosomal Msp1 localises to both glycosomes and the mitochondrial outer membrane, where it forms a complex with four outer membrane proteins. The trypanosome-specific pATOM36 mediates complex assembly of α-helically anchored mitochondrial outer membrane proteins such as protein translocase subunits. Inhibition of their assembly triggers a pathway that results in the proteasomal digestion of unassembled substrates. Using inducible single, double, and triple RNAi cell lines combined with proteomic analyses, we demonstrate that not only Msp1 but also the trypanosomal homolog of the AAA-ATPase VCP are implicated in this quality control pathway. Moreover, in the absence of VCP three out of the four Msp1-interacting mitochondrial proteins are required for efficient proteasomal digestion of pATOM36 substrates, suggesting they act in concert with Msp1. pATOM36 is a functional analog of the yeast mitochondrial import complex complex and possibly of human mitochondrial animal-specific carrier homolog 2, suggesting that similar mitochondrial quality control pathways linked to Msp1 might also exist in yeast and humans.
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Affiliation(s)
- Markus Gerber
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Ida Suppanz
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Silke Oeljeklaus
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Moritz Niemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Sandro Käser
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Warscheid
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
- Institute for Advanced Study (Wissenschaftskolleg) Berlin, Berlin, Germany
| | - Caroline E Dewar
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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Casini I, McCubbin T, Esquivel-Elizondo S, Luque GG, Evseeva D, Fink C, Beblawy S, Youngblut ND, Aristilde L, Huson DH, Dräger A, Ley RE, Marcellin E, Angenent LT, Molitor B. An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter. iScience 2023; 26:108016. [PMID: 37854702 PMCID: PMC10579436 DOI: 10.1016/j.isci.2023.108016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/29/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023] Open
Abstract
Methanogenesis allows methanogenic archaea to generate cellular energy for their growth while producing methane. Thermophilic hydrogenotrophic species of the genus Methanothermobacter have been recognized as robust biocatalysts for a circular carbon economy and are already applied in power-to-gas technology with biomethanation, which is a platform to store renewable energy and utilize captured carbon dioxide. Here, we generated curated genome-scale metabolic reconstructions for three Methanothermobacter strains and investigated differences in the growth performance of these same strains in chemostat bioreactor experiments with hydrogen and carbon dioxide or formate as substrates. Using an integrated systems biology approach, we identified differences in formate anabolism between the strains and revealed that formate anabolism influences the diversion of carbon between biomass and methane. This finding, together with the omics datasets and the metabolic models we generated, can be implemented for biotechnological applications of Methanothermobacter in power-to-gas technology, and as a perspective, for value-added chemical production.
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Affiliation(s)
- Isabella Casini
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sofia Esquivel-Elizondo
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Guillermo G. Luque
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Daria Evseeva
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Christian Fink
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Sebastian Beblawy
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Daniel H. Huson
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Andreas Dräger
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Largus T. Angenent
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- AG Angenent, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10D, 8000 Aarhus C, Denmark
- The Novo Nordisk Foundation CO2 Research Center (CORC), Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Bastian Molitor
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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Biswas D, Halder A, Barpanda A, Ghosh S, Chauhan A, Bhat L, Epari S, Shetty P, Moiyadi A, Ball GR, Srivastava S. Integrated Meta-Omics Analysis Unveils the Pathways Modulating Tumorigenesis and Proliferation in High-Grade Meningioma. Cells 2023; 12:2483. [PMID: 37887327 PMCID: PMC10604908 DOI: 10.3390/cells12202483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Meningioma, a primary brain tumor, is commonly encountered and accounts for 39% of overall CNS tumors. Despite significant progress in clinical research, conventional surgical and clinical interventions remain the primary treatment options for meningioma. Several proteomics and transcriptomics studies have identified potential markers and altered biological pathways; however, comprehensive exploration and data integration can help to achieve an in-depth understanding of the altered pathobiology. This study applied integrated meta-analysis strategies to proteomic and transcriptomic datasets comprising 48 tissue samples, identifying around 1832 common genes/proteins to explore the underlying mechanism in high-grade meningioma tumorigenesis. The in silico pathway analysis indicated the roles of extracellular matrix organization (EMO) and integrin binding cascades in regulating the apoptosis, angiogenesis, and proliferation responsible for the pathobiology. Subsequently, the expression of pathway components was validated in an independent cohort of 32 fresh frozen tissue samples using multiple reaction monitoring (MRM), confirming their expression in high-grade meningioma. Furthermore, proteome-level changes in EMO and integrin cell surface interactions were investigated in a high-grade meningioma (IOMM-Lee) cell line by inhibiting integrin-linked kinase (ILK). Inhibition of ILK by administrating Cpd22 demonstrated an anti-proliferative effect, inducing apoptosis and downregulating proteins associated with proliferation and metastasis, which provides mechanistic insight into the disease pathophysiology.
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Affiliation(s)
- Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| | - Susmita Ghosh
- Leibniz-Institut für Analytische Wissenschaften—ISAS, 44227 Dortmund, Germany;
| | - Aparna Chauhan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| | - Lipika Bhat
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed-to-be University, Mumbai 400056, India;
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre, Mumbai 400012, India;
| | - Prakash Shetty
- Department of Neurosurgery, Tata Memorial Centre, Mumbai 400012, India; (P.S.); (A.M.)
| | - Aliasgar Moiyadi
- Department of Neurosurgery, Tata Memorial Centre, Mumbai 400012, India; (P.S.); (A.M.)
| | - Graham Roy Ball
- Medical Technology Research Centre, Anglia Ruskin University, East Rd., Cambridge CB1 1PT, UK;
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
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Pandi B, Brenman S, Black A, Ng DCM, Lau E, Lam MPY. Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561375. [PMID: 37873130 PMCID: PMC10592692 DOI: 10.1101/2023.10.08.561375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A computational analysis of mass spectrometry data was performed to uncover alternative splicing derived protein variants across chambers of the human heart. Evidence for 216 non-canonical isoforms was apparent in the atrium and the ventricle, including 52 isoforms not documented on SwissProt and recovered using an RNA sequencing derived database. Among non-canonical isoforms, 29 show signs of regulation based on statistically significant preferences in tissue usage, including a ventricular enriched protein isoform of tensin-1 (TNS1) and an atrium-enriched PDZ and LIM Domain 3 (PDLIM3) isoform 2 (PDLIM3-2/ALP-H). Examined variant regions that differ between alternative and canonical isoforms are highly enriched in intrinsically disordered regions, and over two-thirds of such regions are predicted to function in protein binding and/or RNA binding. The analysis here lends further credence to the notion that alternative splicing diversifies the proteome by rewiring intrinsically disordered regions, which are increasingly recognized to play important roles in the generation of biological function from protein sequences.
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Affiliation(s)
- Boomathi Pandi
- Department of Medicine/Division of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Stella Brenman
- Department of Medicine/Division of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Alexander Black
- Department of Medicine/Division of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Dominic C. M. Ng
- Department of Medicine/Division of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Edward Lau
- Department of Medicine/Division of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Consortium for Fibrosis Research and Translation (CFReT), University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Maggie P. Y. Lam
- Department of Medicine/Division of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Consortium for Fibrosis Research and Translation (CFReT), University of Colorado School of Medicine, Aurora, CO 80045, USA
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43
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Wu L, Hoque A, Lam H. Spectroscape enables real-time query and visualization of a spectral archive in proteomics. Nat Commun 2023; 14:6267. [PMID: 37805652 PMCID: PMC10560257 DOI: 10.1038/s41467-023-42006-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/26/2023] [Indexed: 10/09/2023] Open
Abstract
In proteomics, spectral archives organize the enormous amounts of publicly available peptide tandem mass spectra by similarity, offering opportunities for error correction and novel discoveries. Here we adapt an indexing algorithm developed by Facebook for organizing online multimedia resources to tandem mass spectra and achieve practically instantaneous retrieval and clustering of approximate nearest neighbors in a large spectral archive. An interactive web-based graphical user interface enables the user to view a query spectrum in its clustered neighborhood, which facilitates contextual validation of peptide identifications and exploration of the dark proteome.
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Affiliation(s)
- Long Wu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
- Department of Electrical and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Ayman Hoque
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
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44
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Hou JY, Li N, Wang J, Gao LJ, Chang JS, Cao JM. Histone crotonylation of peripheral blood mononuclear cells is a potential biomarker for diagnosis of colorectal cancer. Epigenetics Chromatin 2023; 16:35. [PMID: 37749610 PMCID: PMC10521402 DOI: 10.1186/s13072-023-00509-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/17/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Blood-based tests have public appeal in screening cancers due to their minimally invasive nature, ability to integrate with other routine blood tests, and high compliance. This study aimed to investigate whether certain epigenetic modulation of peripheral blood mononuclear cells (PBMCs) could be a biomarker of colorectal cancer (CRC). RESULTS Western blotting of histones in the PBMCs from 40 colorectal cancer patients and 40 healthy controls was performed to identify the crotonylation sites of proteins. The correlation of crotonylation with tumor staging and diagnostic efficacy were analyzed. Crotonylation of H2BK12 (H2BK12cr) was identified significantly upregulated in the PBMCs of CRC patients compared to healthy controls, and were closely related to distant metastasis (P = 0.0478) and late TNM stage (P = 0.0201). Receiver operator characteristic curve (ROC) analysis demonstrated that the area under curve (AUC) of H2BK12cr was 0.8488, the sensitivity was 70%, and the specificity was 92.5%. The H2BK12cr parameter significantly increased the diagnostic effectiveness of CRC compared with the commercial carcinoembryonic antigen assays. CONCLUSIONS The H2BK12cr level in PBMCs of CRC patients has a potential to be a biomarker for distinguishing CRC patients from healthy controls with the advantages of easy operation and high diagnostic efficacy.
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Affiliation(s)
- Jia-Yi Hou
- Department of Clinical Laboratory, Shanxi Provincial Academy of Traditional Chinese Medicine, Taiyuan, China
| | - Ning Li
- Department of Gastrointestinal and Pancreatic Surgery and Hernia and Abdominal Surgery, Shanxi Provincial People's Hospital, Taiyuan, China
| | - Jie Wang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Li-Juan Gao
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Jia-Song Chang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Ji-Min Cao
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China.
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45
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Martucci LF, Eichler RA, Silva RN, Costa TJ, Tostes RC, Busatto GF, Seelaender MC, Duarte AJ, Souza HP, Ferro ES. Intracellular peptides in SARS-CoV-2-infected patients. iScience 2023; 26:107542. [PMID: 37636076 PMCID: PMC10448160 DOI: 10.1016/j.isci.2023.107542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/29/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023] Open
Abstract
Intracellular peptides (InPeps) generated by the orchestrated action of the proteasome and intracellular peptidases have biological and pharmacological significance. Here, human plasma relative concentration of specific InPeps was compared between 175 patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and 45 SARS-CoV-2 non-infected patients; 2,466 unique peptides were identified, of which 67% were InPeps. The results revealed differences of a specific group of peptides in human plasma comparing non-infected individuals to patients infected by SARS-CoV-2, following the results of the semi-quantitative analyses by isotope-labeled electrospray mass spectrometry. The protein-protein interactions networks enriched pathways, drawn by genes encoding the proteins from which the peptides originated, revealed the presence of the coronavirus disease/COVID-19 network solely in the group of patients fatally infected by SARS-CoV-2. Thus, modulation of the relative plasma levels of specific InPeps could be employed as a predictive tool for disease outcome.
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Affiliation(s)
- Luiz Felipe Martucci
- Department of Pharmacology, Biomedical Sciences Institute, São Paulo 05508-000, Brazil
| | | | - Renée N.O. Silva
- Department of Pharmacology, Biomedical Sciences Institute, São Paulo 05508-000, Brazil
| | - Tiago J. Costa
- Department of Pharmacology, Ribeirao Preto Medical School, Ribeirão Preto 14049-900, Brazil
| | - Rita C. Tostes
- Department of Pharmacology, Ribeirao Preto Medical School, Ribeirão Preto 14049-900, Brazil
| | - Geraldo F. Busatto
- Department of Psichiatry, Medical School and Hospital das Clínicas, University of São Paulo, 01246-903 SP, Brazil
| | - Marilia C.L. Seelaender
- Department of Surgery, Medical School and Hospital das Clínicas, University of São Paulo, 01246-903 SP, Brazil
| | - Alberto J.S. Duarte
- Department of Patology, Medical School and Hospital das Clínicas, University of São Paulo, 01246-903 SP, Brazil
| | - Heraldo P. Souza
- Department of Internal Medicine, Medical School and Hospital das Clínicas, University of São Paulo, 01246-903 SP, Brazil
| | - Emer S. Ferro
- Department of Pharmacology, Biomedical Sciences Institute, São Paulo 05508-000, Brazil
- Department of Patology, Medical School and Hospital das Clínicas, University of São Paulo, 01246-903 SP, Brazil
- Department of Internal Medicine, Medical School and Hospital das Clínicas, University of São Paulo, 01246-903 SP, Brazil
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46
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Fitzsimons S, Muñoz-San Martín M, Nally F, Dillon E, Fashina IA, Strowitzki MJ, Ramió-Torrentà L, Dowling JK, De Santi C, McCoy CE. Inhibition of pro-inflammatory signaling in human primary macrophages by enhancing arginase-2 via target site blockers. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:941-959. [PMID: 37701067 PMCID: PMC10494319 DOI: 10.1016/j.omtn.2023.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 08/17/2023] [Indexed: 09/14/2023]
Abstract
The modulation of macrophage phenotype from a pro-inflammatory to an anti-inflammatory state holds therapeutic potential in the treatment of inflammatory disease. We have previously shown that arginase-2 (Arg2), a mitochondrial enzyme, is a key regulator of the macrophage anti-inflammatory response. Here, we investigate the therapeutic potential of Arg2 enhancement via target site blockers (TSBs) in human macrophages. TSBs are locked nucleic acid antisense oligonucleotides that were specifically designed to protect specific microRNA recognition elements (MREs) in human ARG2 3' UTR mRNA. TSBs targeting miR-155 (TSB-155) and miR-3202 (TSB-3202) MREs increased ARG2 expression in human monocyte-derived macrophages. This resulted in decreased gene expression and cytokine production of TNF-α and CCL2 and, for TSB-3202, in an increase in the anti-inflammatory macrophage marker, CD206. Proteomic analysis demonstrated that a network of pro-inflammatory responsive proteins was modulated by TSBs. In silico bioinformatic analysis predicted that TSB-3202 suppressed upstream pro-inflammatory regulators including STAT-1 while enhancing anti-inflammatory associated proteins. Proteomic data were validated by confirming increased levels of sequestosome-1 and decreased levels of phosphorylated STAT-1 and STAT-1 upon TSB treatment. In conclusion, upregulation of Arg2 by TSBs inhibits pro-inflammatory signaling and is a promising novel therapeutic strategy to modulate inflammatory signaling in human macrophages.
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Affiliation(s)
- Stephen Fitzsimons
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green, Dublin 2, Ireland
| | - María Muñoz-San Martín
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Frances Nally
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Eugene Dillon
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ifeolutembi A. Fashina
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Moritz J. Strowitzki
- Department of General, Visceral & Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Lluís Ramió-Torrentà
- Neuroinflammation and Neurodegeneration Group, Girona Biomedical Research Institute (IDIBGI), CERCA Programme/Generalitat de Catalunya, Salt, Girona, Spain
| | - Jennifer K. Dowling
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green, Dublin 2, Ireland
| | - Chiara De Santi
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Claire E. McCoy
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green, Dublin 2, Ireland
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47
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Rochman M, Rochman Y, Caldwell JM, Mack LE, Besse JA, Manes NP, Yoon SH, Shoda T, Nita-Lazar A, Rothenberg ME. The minichromosome maintenance complex drives esophageal basal zone hyperplasia. JCI Insight 2023; 8:e172143. [PMID: 37490338 PMCID: PMC10544209 DOI: 10.1172/jci.insight.172143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023] Open
Abstract
Eosinophilic esophagitis (EoE) is a chronic gastrointestinal disorder characterized by food antigen-driven eosinophilic inflammation and hyperproliferation of esophageal mucosa. By utilizing a large-scale, proteomic screen of esophageal biopsies, we aimed to uncover molecular drivers of the disease. Proteomic analysis by liquid chromatography-tandem mass spectrometry identified 402 differentially expressed proteins (DEPs) that correlated with the EoE transcriptome. Immune cell-related proteins were among the most highly upregulated DEPs in EoE compared with controls, whereas proteins linked to epithelial differentiation were primarily downregulated. Notably, in the inflamed esophageal tissue, all 6 subunits of the minichromosome maintenance (MCM) complex, a DNA helicase essential for genomic DNA replication, were significantly upregulated at the gene and protein levels. Furthermore, treating esophageal epithelial cells with a known inhibitor of the MCM complex (ciprofloxacin) blocked esophageal epithelial proliferation. In a murine model of EoE driven by overexpression of IL-13, ciprofloxacin treatment decreased basal zone thickness and reduced dilated intercellular spaces by blocking the transition of epithelial cells through the S-phase of the cell cycle. Collectively, a broad-spectrum proteomic screen has identified the involvement of the MCM complex in EoE and has highlighted MCM inhibitors as potential therapeutic agents for the disease.
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Affiliation(s)
- Mark Rochman
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yrina Rochman
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Julie M. Caldwell
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Lydia E. Mack
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - John A. Besse
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Nathan P. Manes
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Sung Hwan Yoon
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Tetsuo Shoda
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Marc E. Rothenberg
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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48
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Lu M, Tong J, Fang W, Wang J, An S, Wang R, Jiang H, Yu C. Column storage enables edge computation of biological big data on 5G networks. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:17197-17219. [PMID: 37920052 DOI: 10.3934/mbe.2023766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
With the continuous improvement of biological detection technology, the scale of biological data is also increasing, which overloads the central-computing server. The use of edge computing in 5G networks can provide higher processing performance for large biological data analysis, reduce bandwidth consumption and improve data security. Appropriate data compression and reading strategy becomes the key technology to implement edge computing. We introduce the column storage strategy into mass spectrum data so that part of the analysis scenario can be completed by edge computing. Data produced by mass spectrometry is a typical biological big data based. A blood sample analysed by mass spectrometry can produce a 10 gigabytes digital file. By introducing the column storage strategy and combining the related prior knowledge of mass spectrometry, the structure of the mass spectrum data is reorganized, and the result file is effectively compressed. Data can be processed immediately near the scientific instrument, reducing the bandwidth requirements and the pressure of the central server. Here, we present Aird-Slice, a mass spectrum data format using the column storage strategy. Aird-Slice reduces volume by 48% compared to vendor files and speeds up the critical computational step of ion chromatography extraction by an average of 116 times over the test dataset. Aird-Slice provides the ability to analyze biological data using an edge computing architecture on 5G networks.
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Affiliation(s)
- Miaoshan Lu
- Zhejiang University, Hangzhou 310009, Zhejiang Province, China
- School of Engineering, Westlake University, Hangzhou, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Junjie Tong
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Weidong Fang
- Guangxi Key Laboratory of Wireless Wideband Communication and Signal Processing, Guilin University of Electronic Technology, Guilin 541004, China
| | - Jinyin Wang
- Zhejiang University, Hangzhou 310009, Zhejiang Province, China
| | | | | | - Hengxuan Jiang
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Changbin Yu
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
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49
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Seo YR, Lee J, Ryu HS, Kim EG, Kim SH, Jeong J, Jung H, Jung Y, Kim HB, Jo YH, Kim YD, Jin MS, Lee YY, Kim KM, Yi EC. Lateral interactions between CD276 and CD147 are essential for stemness in breast cancer: a novel insight from proximal proteome analysis. Sci Rep 2023; 13:14242. [PMID: 37648771 PMCID: PMC10469185 DOI: 10.1038/s41598-023-41416-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023] Open
Abstract
Oncogenic cell-surface membrane proteins contribute to the phenotypic and functional characteristics of cancer stem cells (CSCs). We employed a proximity-labeling proteomic approach to quantitatively analyze the cell-surface membrane proteins in close proximity to CD147 in CSCs. Furthermore, we compared CSCs to non-CSCs to identify CSC-specific cell-surface membrane proteins that are closely interact with CD147 and revealed that lateral interaction between CD147 and CD276 concealed within the lipid raft microdomain in CSCs, confers resistance to docetaxel, a commonly used chemotherapy agent for various cancer types, including metastatic breast cancer. Moreover, we investigated the clinical relevance of CD147 and CD276 co-expression in HER2+ breast cancer (BC) and triple-negative breast cancer patients who underwent chemotherapy. We observed poor disease-free survival and Overall survival rates in patients of CD147 and CD276 (p = 0.04 and 0.08, respectively). Subsequent immunohistochemical analysis in independent cohorts of HER2+ BC support for the association between co-expression of CD147 and CD276 and a poor response to chemotherapy. Collectively, our study suggests that the lateral interaction between CD147 and its proximal partners, such as CD276, may serve as a poor prognostic factor in BC and a predictive marker for the critical phenotypic determinant of BC stemness.
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Affiliation(s)
- Yu Ri Seo
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Junghyeon Lee
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, Republic of Korea
- Department of Systems Immunology, Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - EunHee G Kim
- Department of Systems Immunology, Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - So Hyun Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Jieun Jeong
- Department of Systems Immunology, Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Hyeryeon Jung
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - YeoJin Jung
- Department of Systems Immunology, Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Han Byeol Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Yeon Hui Jo
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Yeong Dong Kim
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Min-Sun Jin
- Department of Pathology, Bucheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Yong Yook Lee
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Kristine M Kim
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, Republic of Korea.
- Department of Systems Immunology, Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea.
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea.
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50
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Claushuis B, Cordfunke RA, de Ru AH, Otte A, van Leeuwen HC, Klychnikov OI, van Veelen PA, Corver J, Drijfhout JW, Hensbergen PJ. In-Depth Specificity Profiling of Endopeptidases Using Dedicated Mix-and-Split Synthetic Peptide Libraries and Mass Spectrometry. Anal Chem 2023; 95:11621-11631. [PMID: 37495545 PMCID: PMC10413326 DOI: 10.1021/acs.analchem.3c01215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023]
Abstract
Proteases comprise the class of enzymes that catalyzes the hydrolysis of peptide bonds, thereby playing a pivotal role in many aspects of life. The amino acids surrounding the scissile bond determine the susceptibility toward protease-mediated hydrolysis. A detailed understanding of the cleavage specificity of a protease can lead to the identification of its endogenous substrates, while it is also essential for the design of inhibitors. Although many methods for protease activity and specificity profiling exist, none of these combine the advantages of combinatorial synthetic libraries, i.e., high diversity, equimolar concentration, custom design regarding peptide length, and randomization, with the sensitivity and detection power of mass spectrometry. Here, we developed such a method and applied it to study a group of bacterial metalloproteases that have the unique specificity to cleave between two prolines, i.e., Pro-Pro endopeptidases (PPEPs). We not only confirmed the prime-side specificity of PPEP-1 and PPEP-2, but also revealed some new unexpected peptide substrates. Moreover, we have characterized a new PPEP (PPEP-3) that has a prime-side specificity that is very different from that of the other two PPEPs. Importantly, the approach that we present in this study is generic and can be extended to investigate the specificity of other proteases.
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Affiliation(s)
- Bart Claushuis
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Robert A. Cordfunke
- Department
of Immunology, Leiden University Medical
Center, Leiden, 2333 ZA, The Netherlands
| | - Arnoud H. de Ru
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Annemarie Otte
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Hans C. van Leeuwen
- Department
of CBRN Protection, Netherlands Organization
for Applied Scientific Research TNO, Rijswijk, 2280 AA, The Netherlands
| | - Oleg I. Klychnikov
- Department
of Biochemistry, Moscow State University, Moscow 119991, Russian Federation
| | - Peter A. van Veelen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Jeroen Corver
- Department
of Medical Microbiology, Leiden University
Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Jan W. Drijfhout
- Department
of Immunology, Leiden University Medical
Center, Leiden, 2333 ZA, The Netherlands
| | - Paul J. Hensbergen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden, 2333 ZA, The Netherlands
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