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Nourisa J, Passemiers A, Shakeri F, Omidi M, Helmholz H, Raimondi D, Moreau Y, Tomforde S, Schlüter H, Luthringer-Feyerabend B, Cyron CJ, Aydin RC, Willumeit-Römer R, Zeller-Plumhoff B. Gene regulatory network analysis identifies MYL1, MDH2, GLS, and TRIM28 as the principal proteins in the response of mesenchymal stem cells to Mg 2+ ions. Comput Struct Biotechnol J 2024; 23:1773-1785. [PMID: 38689715 PMCID: PMC11058716 DOI: 10.1016/j.csbj.2024.04.033] [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: 12/15/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
Magnesium (Mg)-based implants have emerged as a promising alternative for orthopedic applications, owing to their bioactive properties and biodegradability. As the implants degrade, Mg2+ ions are released, influencing all surrounding cell types, especially mesenchymal stem cells (MSCs). MSCs are vital for bone tissue regeneration, therefore, it is essential to understand their molecular response to Mg2+ ions in order to maximize the potential of Mg-based biomaterials. In this study, we conducted a gene regulatory network (GRN) analysis to examine the molecular responses of MSCs to Mg2+ ions. We used time-series proteomics data collected at 11 time points across a 21-day period for the GRN construction. We studied the impact of Mg2+ ions on the resulting networks and identified the key proteins and protein interactions affected by the application of Mg2+ ions. Our analysis highlights MYL1, MDH2, GLS, and TRIM28 as the primary targets of Mg2+ ions in the response of MSCs during 1-21 days phase. Our results also identify MDH2-MYL1, MDH2-RPS26, TRIM28-AK1, TRIM28-SOD2, and GLS-AK1 as the critical protein relationships affected by Mg2+ ions. By offering a comprehensive understanding of the regulatory role of Mg2+ ions on MSCs, our study contributes valuable insights into the molecular response of MSCs to Mg-based materials, thereby facilitating the development of innovative therapeutic strategies for orthopedic applications.
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Affiliation(s)
- Jalil Nourisa
- Institute of Material Systems Modeling, Helmholtz Zentrum Hereon, Geesthacht, Germany
| | | | - Farhad Shakeri
- Institute of Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Maryam Omidi
- Institute of Clinical Chemistry/Central Laboratories, University Medical Center Hamburg, Hamburg, Germany
| | - Heike Helmholz
- Institute of Metallic Biomaterials, Helmholtz Zentrum Hereon, Geesthacht, Germany
| | | | | | - Sven Tomforde
- Department of Computer Science, Intelligent Systems, University of Kiel, Kiel, Germany
| | - Hartmuth Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine Diagnostic Center, University of Hamburg, Hamburg, Germany
| | | | - Christian J. Cyron
- Institute of Material Systems Modeling, Helmholtz Zentrum Hereon, Geesthacht, Germany
- Institute for Continuum and Material Mechanics, Hamburg University of Technology, Hamburg, Germany
| | - Roland C. Aydin
- Institute of Material Systems Modeling, Helmholtz Zentrum Hereon, Geesthacht, Germany
- Institute for Continuum and Material Mechanics, Hamburg University of Technology, Hamburg, Germany
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2
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Hamza H, Ghosh M, Löffler MW, Rammensee HG, Planz O. Identification and relative abundance of naturally presented and cross-reactive influenza A virus MHC class I-restricted T cell epitopes. Emerg Microbes Infect 2024; 13:2306959. [PMID: 38240239 PMCID: PMC10854457 DOI: 10.1080/22221751.2024.2306959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/14/2024] [Indexed: 02/10/2024]
Abstract
Cytotoxic T lymphocytes are key for controlling viral infection. Unravelling CD8+ T cell-mediated immunity to distinct influenza virus strains and subtypes across prominent HLA types is relevant for combating seasonal infections and emerging new variants. Using an immunopeptidomics approach, naturally presented influenza A virus-derived ligands restricted to HLA-A*24:02, HLA-A*68:01, HLA-B*07:02, and HLA-B*51:01 molecules were identified. Functional characterization revealed multifunctional memory CD8+ T cell responses for nine out of sixteen peptides. Peptide presentation kinetics was optimal around 12 h post infection and presentation of immunodominant epitopes shortly after infection was not always persistent. Assessment of immunogenic epitopes revealed that they are highly conserved across the major zoonotic reservoirs and may contain a single substitution in the vicinity of the anchor residues. These findings demonstrate how the identified epitopes promote T cell pools, possibly cross-protective in individuals and can be potential targets for vaccination.
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Affiliation(s)
- Hazem Hamza
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Virology Laboratory, Environmental Research Division, National Research Centre, Giza, Egypt
| | - Michael Ghosh
- Institute for Immunology, University of Tübingen, Tübingen, Germany
| | - Markus W Löffler
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Institute for Clinical and Experimental Transfusion Medicine, Medical Faculty of Tübingen, Tübingen, Germany
- Centre for Clinical Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence CMFI (EXC2124) "Controlling Microbes to Fight Infections", University of Tübingen, Tübingen, Germany
| | - Oliver Planz
- Institute for Immunology, University of Tübingen, Tübingen, Germany
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An DW, Yu YL, Martens DS, Latosinska A, Zhang ZY, Mischak H, Nawrot TS, Staessen JA. Statistical approaches applicable in managing OMICS data: Urinary proteomics as exemplary case. MASS SPECTROMETRY REVIEWS 2024; 43:1237-1254. [PMID: 37143314 DOI: 10.1002/mas.21849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/04/2023] [Accepted: 03/20/2023] [Indexed: 05/06/2023]
Abstract
With urinary proteomics profiling (UPP) as exemplary omics technology, this review describes a workflow for the analysis of omics data in large study populations. The proposed workflow includes: (i) planning omics studies and sample size considerations; (ii) preparing the data for analysis; (iii) preprocessing the UPP data; (iv) the basic statistical steps required for data curation; (v) the selection of covariables; (vi) relating continuously distributed or categorical outcomes to a series of single markers (e.g., sequenced urinary peptide fragments identifying the parental proteins); (vii) showing the added diagnostic or prognostic value of the UPP markers over and beyond classical risk factors, and (viii) pathway analysis to identify targets for personalized intervention in disease prevention or treatment. Additionally, two short sections respectively address multiomics studies and machine learning. In conclusion, the analysis of adverse health outcomes in relation to omics biomarkers rests on the same statistical principle as any other data collected in large population or patient cohorts. The large number of biomarkers, which have to be considered simultaneously requires planning ahead how the study database will be structured and curated, imported in statistical software packages, analysis results will be triaged for clinical relevance, and presented.
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Affiliation(s)
- De-Wei An
- Non-Profit Research Association Alliance for the Promotion of Preventive Medicine, Mechelen, Belgium
- Research Unit Environment and Health, KU Leuven Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Yu-Ling Yu
- Non-Profit Research Association Alliance for the Promotion of Preventive Medicine, Mechelen, Belgium
- Research Unit Environment and Health, KU Leuven Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | | | - Zhen-Yu Zhang
- Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | | | - Tim S Nawrot
- Research Unit Environment and Health, KU Leuven Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Jan A Staessen
- Non-Profit Research Association Alliance for the Promotion of Preventive Medicine, Mechelen, Belgium
- Biomedical Research Group, Faculty of Medicine, University of Leuven, Leuven, Belgium
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4
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Cheung ST, Kim Y, Cho JH, Brandvold KR, Ghosh B, Del Rosario AM, Bell-Temin H. End-to-End Throughput Chemical Proteomics for Photoaffinity Labeling Target Engagement and Deconvolution. J Proteome Res 2024. [PMID: 39374182 DOI: 10.1021/acs.jproteome.4c00442] [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: 10/09/2024]
Abstract
Photoaffinity labeling (PAL) methodologies have proven to be instrumental for the unbiased deconvolution of protein-ligand binding events in physiologically relevant systems. However, like other chemical proteomic workflows, they are limited in many ways by time-intensive sample manipulations and data acquisition techniques. Here, we describe an approach to address this challenge through the innovation of a carboxylate bead-based protein cleanup procedure to remove excess small-molecule contaminants and couple it to plate-based, proteomic sample processing as a semiautomated solution. The analysis of samples via label-free, data-independent acquisition (DIA) techniques led to significant improvements on a workflow time per sample basis over current standard practices. Experiments utilizing three established PAL ligands with known targets, (+)-JQ-1, lenalidomide, and dasatinib, demonstrated the utility of having the flexibility to design experiments with a myriad of variables. Data revealed that this workflow can enable the confident identification and rank ordering of known and putative targets with outstanding protein signal-to-background enrichment sensitivity. This unified end-to-end throughput strategy for processing and analyzing these complex samples could greatly facilitate efficient drug discovery efforts and open up new opportunities in the chemical proteomics field.
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Affiliation(s)
- Sheldon T Cheung
- Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Yongkang Kim
- Janssen Research & Development, LLC, 301 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ji-Hoon Cho
- Janssen Research & Development, LLC, 301 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Kristoffer R Brandvold
- Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Brahma Ghosh
- Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Amanda M Del Rosario
- Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Harris Bell-Temin
- Janssen Research & Development, LLC, 301 Binney Street, Cambridge, Massachusetts 02142, United States
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Edelbroek B, Westholm JO, Bergquist J, Söderbom F. Multi-omics analysis of aggregative multicellularity. iScience 2024; 27:110659. [PMID: 39224513 PMCID: PMC11367525 DOI: 10.1016/j.isci.2024.110659] [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: 03/14/2024] [Revised: 06/14/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
All organisms have to carefully regulate their gene expression, not least during development. mRNA levels are often used as proxy for protein output; however, this approach ignores post-transcriptional effects. In particular, mRNA-protein correlation remains elusive for organisms that exhibit aggregative rather than clonal multicellularity. We addressed this issue by generating a paired transcriptomics and proteomics time series during the transition from uni-to multicellular stage in the social ameba Dictyostelium discoideum. Our data reveals that mRNA and protein levels correlate highly during unicellular growth, but decrease when multicellular development is initiated. This accentuates that transcripts alone cannot accurately predict protein levels. The dataset provides a useful resource to study gene expression during aggregative multicellular development. Additionally, our study provides an example of how to analyze and visualize mRNA and protein levels, which should be broadly applicable to other organisms and conditions.
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Affiliation(s)
- Bart Edelbroek
- Department of Cell and Molecular Biology, BMC, Uppsala University, 751 24 Uppsala, Sweden
| | - Jakub Orzechowski Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry and Neurochemistry, Uppsala University, Uppsala, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, BMC, Uppsala University, 751 24 Uppsala, Sweden
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Yu YL, Siwy J, An DW, González A, Hansen T, Latosinska A, Pellicori P, Ravassa S, Mariottoni B, Verdonschot JA, Ahmed F, Petutschnigg J, Rossignol P, Heymans S, Cuthbert JJ, Girerd N, Clark AL, Verhamme P, Nawrot TS, Janssens S, Cleland JG, Zannad F, Diez J, Mischak H, Ferreira JP, Staessen JA. Urinary proteomic signature of mineralocorticoid receptor antagonism by spironolactone: evidence from the HOMAGE trial. Heart 2024; 110:1180-1187. [PMID: 38729636 PMCID: PMC11420742 DOI: 10.1136/heartjnl-2023-323796] [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: 12/14/2023] [Accepted: 04/28/2024] [Indexed: 05/12/2024] Open
Abstract
OBJECTIVE Heart failure (HF) is characterised by collagen deposition. Urinary proteomic profiling (UPP) followed by peptide sequencing identifies parental proteins, for over 70% derived from collagens. This study aimed to refine understanding of the antifibrotic action of spironolactone. METHODS In this substudy (n=290) to the Heart 'Omics' in Ageing Study trial, patients were randomised to usual therapy combined or not with spironolactone 25-50 mg/day and followed for 9 months. The analysis included 1498 sequenced urinary peptides detectable in ≥30% of patients and carboxyterminal propeptide of procollagen I (PICP) and PICP/carboxyterminal telopeptide of collagen I (CITP) as serum biomarkers of COL1A1 synthesis. After rank normalisation of biomarker distributions, between-group differences in their changes were assessed by multivariable-adjusted mixed model analysis of variance. Correlations between the changes in urinary peptides and in serum PICP and PICP/CITP were compared between groups using Fisher's Z transform. RESULTS Multivariable-adjusted between-group differences in the urinary peptides with error 1 rate correction were limited to 27 collagen fragments, of which 16 were upregulated (7 COL1A1 fragments) on spironolactone and 11 downregulated (4 COL1A1 fragments). Over 9 months of follow-up, spironolactone decreased serum PICP from 81 (IQR 66-95) to 75 (61-90) µg/L and PICP/CITP from 22 (17-28) to 18 (13-26), whereas no changes occurred in the control group, resulting in a difference (spironolactone minus control) expressed in standardised units of -0.321 (95% CI 0.0007). Spironolactone did not affect the correlations between changes in urinary COL1A1 fragments and in PICP or the PICP/CITP ratio. CONCLUSIONS Spironolactone decreased serum markers of collagen synthesis and predominantly downregulated urinary collagen-derived peptides, but upregulated others. The interpretation of these opposite UPP trends might be due to shrinking the body-wide pool of collagens, explaining downregulation, while some degree of collagen synthesis must be maintained to sustain vital organ functions, explaining upregulation. Combining urinary and serum fibrosis markers opens new avenues for the understanding of the action of antifibrotic drugs. TRIAL REGISTRATION NUMBER NCT02556450.
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Affiliation(s)
- Yu-Ling Yu
- Research Unit Environment and Health, KU Leuven Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
- Non-Profit Research Association Alliance for the Promotion of Preventive Medicine (APPREMED), Mechelen, Belgium
| | | | - De-Wei An
- Research Unit Environment and Health, KU Leuven Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
- Non-Profit Research Association Alliance for the Promotion of Preventive Medicine (APPREMED), Mechelen, Belgium
- Department of Cardiovascular Medicine, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Arantxa González
- Program of Cardiovascular Diseases, CIMA, Universidad de Navarra and IdiSNA, Pamplona, Spain CIBERCV, Carlos III Institute of Health, Madrid, Spain
| | - Tine Hansen
- Non-Profit Research Association Alliance for the Promotion of Preventive Medicine (APPREMED), Mechelen, Belgium
- Steno Diabetes Center Copenhagen, the Capital Region of Denmark, Gentofte, Denmark
| | | | - Pierpaolo Pellicori
- Université de Lorraine, Inserm, Centre d'Investigation Clinique Plurithématique 1433, U1116, CHRU de Nancy, F-CRIN INI-CRCT, Nancy, France
| | - Susana Ravassa
- Program of Cardiovascular Diseases, CIMA, Universidad de Navarra and IdiSNA, Pamplona, Spain CIBERCV, Carlos III Institute of Health, Madrid, Spain
| | | | - Job Aj Verdonschot
- Department of Cardiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Fozia Ahmed
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Johannes Petutschnigg
- Department of Internal Medicine and Cardiology, Campus Virchow Klinikum, Charité University Medicine Berlin, Berlin Institute of Health and German Center for Cardiovascular Research, Partner Site Berlin, Germany
| | - Patrick Rossignol
- Université de Lorraine, Inserm, Centre d'Investigation Clinique Plurithématique 1433, U1116, CHRU de Nancy, F-CRIN INI-CRCT, Nancy, France
| | - Stephane Heymans
- Department of Cardiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Joe J Cuthbert
- Department of Cardiology, University of Hull, Castle Hill Hospital, Cottingham, East Riding of Yorkshire, UK
| | - Nicolas Girerd
- Université de Lorraine, Inserm, Centre d'Investigation Clinique Plurithématique 1433, U1116, CHRU de Nancy, F-CRIN INI-CRCT, Nancy, France
| | - Andrew L Clark
- Department of Cardiology, University of Hull, Castle Hill Hospital, Cottingham, East Riding of Yorkshire, UK
| | - Peter Verhamme
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Tim S Nawrot
- Research Unit Environment and Health, KU Leuven Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Stefan Janssens
- Research Unit Cardiology, Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - John G Cleland
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Faiez Zannad
- Université de Lorraine, Inserm, Centre d'Investigation Clinique Plurithématique 1433, U1116, CHRU de Nancy, F-CRIN INI-CRCT, Nancy, France
| | - Javier Diez
- Program of Cardiovascular Diseases, CIMA, Universidad de Navarra and IdiSNA, Pamplona, Spain CIBERCV, Carlos III Institute of Health, Madrid, Spain
| | | | - João Pedro Ferreira
- Université de Lorraine, Inserm, Centre d'Investigation Clinique Plurithématique 1433, U1116, CHRU de Nancy, F-CRIN INI-CRCT, Nancy, France
- Cardiovascular R&D Centre UniC@rRISE, Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto Portugal, Porto, Portugal
- Portugal % Heart Failure Clinics, Department of Internal Medicine, Centro Hospitalar de Vila Nova de Gaia/Espinho, Vila Nova de Gaia/Espinho, Portugal
| | - Jan A Staessen
- Non-Profit Research Association Alliance for the Promotion of Preventive Medicine (APPREMED), Mechelen, Belgium
- Department of Cardiovascular Medicine, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Biomedical Science Group, University of Leuven, Leuven, Belgium
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7
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Yan Y, Sankar BS, Mirza B, Ng DCM, Pelletier AR, Huang SD, Wang W, Watson K, Wang D, Ping P. Missing Values in Longitudinal Proteome Dynamics Studies: Making a Case for Data Multiple Imputation. J Proteome Res 2024; 23:4151-4162. [PMID: 39189460 PMCID: PMC11385379 DOI: 10.1021/acs.jproteome.4c00263] [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: 08/28/2024]
Abstract
Temporal proteomics data sets are often confounded by the challenges of missing values. These missing data points, in a time-series context, can lead to fluctuations in measurements or the omission of critical events, thus hindering the ability to fully comprehend the underlying biomedical processes. We introduce a Data Multiple Imputation (DMI) pipeline designed to address this challenge in temporal data set turnover rate quantifications, enabling robust downstream analysis to gain novel discoveries. To demonstrate its utility and generalizability, we applied this pipeline to two use cases: a murine cardiac temporal proteomics data set and a human plasma temporal proteomics data set, both aimed at examining protein turnover rates. This DMI pipeline significantly enhanced the detection of protein turnover rate in both data sets, and furthermore, the imputed data sets captured new representation of proteins, leading to an augmented view of biological pathways, protein complex dynamics, as well as biomarker-disease associations. Importantly, DMI exhibited superior performance in benchmark data sets compared to single imputation methods (DSI). In summary, we have demonstrated that this DMI pipeline is effective at overcoming challenges introduced by missing values in temporal proteome dynamics studies.
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Affiliation(s)
- Yu Yan
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
- NIH BRIDGE2AI Center & NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Baradwaj Simha Sankar
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NIH BRIDGE2AI Center & NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Bilal Mirza
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
| | - Dominic C M Ng
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
- NIH BRIDGE2AI Center & NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Alexander R Pelletier
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
- Department of Computer Science and Scalable Analytics Institute, UCLA School of Engineering, Los Angeles, California 90095, United States
| | - Sarah D Huang
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
| | - Wei Wang
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
- Department of Computer Science and Scalable Analytics Institute, UCLA School of Engineering, Los Angeles, California 90095, United States
| | - Karol Watson
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NIH BRIDGE2AI Center & NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Ding Wang
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
- NIH BRIDGE2AI Center & NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Peipei Ping
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
- NIH BRIDGE2AI Center & NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Drive South, Los Angeles, California 90095, United States
- Department of Computer Science and Scalable Analytics Institute, UCLA School of Engineering, Los Angeles, California 90095, United States
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8
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Reisman EG, Botella J, Huang C, Schittenhelm RB, Stroud DA, Granata C, Chandrasiri OS, Ramm G, Oorschot V, Caruana NJ, Bishop DJ. Fibre-specific mitochondrial protein abundance is linked to resting and post-training mitochondrial content in the muscle of men. Nat Commun 2024; 15:7677. [PMID: 39227581 PMCID: PMC11371815 DOI: 10.1038/s41467-024-50632-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 07/16/2024] [Indexed: 09/05/2024] Open
Abstract
Analyses of mitochondrial adaptations in human skeletal muscle have mostly used whole-muscle samples, where results may be confounded by the presence of a mixture of type I and II muscle fibres. Using our adapted mass spectrometry-based proteomics workflow, we provide insights into fibre-specific mitochondrial differences in the human skeletal muscle of men before and after training. Our findings challenge previous conclusions regarding the extent of fibre-type-specific remodelling of the mitochondrial proteome and suggest that most baseline differences in mitochondrial protein abundances between fibre types reported by us, and others, might be due to differences in total mitochondrial content or a consequence of adaptations to habitual physical activity (or inactivity). Most training-induced changes in different mitochondrial functional groups, in both fibre types, were no longer significant in our study when normalised to changes in markers of mitochondrial content.
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Affiliation(s)
- Elizabeth G Reisman
- Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, Australia
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, Australia
| | - Javier Botella
- Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, Australia
- Metabolic Research Unit, School of Medicine and Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Waurn Ponds, VIC, Australia
| | - Cheng Huang
- Monash Proteomics & Metabolomics Facility, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - David A Stroud
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Parkville, VIC, Australia
| | - Cesare Granata
- Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Institute for Clinical Diabetology, German, Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine-University, Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| | - Owala S Chandrasiri
- Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, Australia
| | - Georg Ramm
- Ramaciotti Centre for Cryo EM, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Viola Oorschot
- Ramaciotti Centre for Cryo EM, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nikeisha J Caruana
- Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, Australia.
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
| | - David J Bishop
- Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, Australia.
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9
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Pietz T, Gupta S, Schlaffner CN, Ahmed S, Steen H, Renard BY, Baum K. PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks. Bioinformatics 2024; 40:ii70-ii78. [PMID: 39230699 PMCID: PMC11373339 DOI: 10.1093/bioinformatics/btae389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024] Open
Abstract
MOTIVATION Accurate quantitative information about protein abundance is crucial for understanding a biological system and its dynamics. Protein abundance is commonly estimated using label-free, bottom-up mass spectrometry (MS) protocols. Here, proteins are digested into peptides before quantification via MS. However, missing peptide abundance values, which can make up more than 50% of all abundance values, are a common issue. They result in missing protein abundance values, which then hinder accurate and reliable downstream analyses. RESULTS To impute missing abundance values, we propose PEPerMINT, a graph neural network model working directly on the peptide level that flexibly takes both peptide-to-protein relationships in a graph format as well as amino acid sequence information into account. We benchmark our method against 11 common imputation methods on 6 diverse datasets, including cell lines, tissue, and plasma samples. We observe that PEPerMINT consistently outperforms other imputation methods. Its prediction performance remains high for varying degrees of missingness, different evaluation approaches, and differential expression prediction. As an additional novel feature, PEPerMINT provides meaningful uncertainty estimates and allows for tailoring imputation to the user's needs based on the reliability of imputed values. AVAILABILITY AND IMPLEMENTATION The code is available at https://github.com/DILiS-lab/pepermint.
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Affiliation(s)
- Tobias Pietz
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, 14482, Germany
| | - Sukrit Gupta
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, 14482, Germany
- Department of Computer Science and Engineering, Indian Institute of Technology, Ropar, Rupnagar, 140001, India
| | - Christoph N Schlaffner
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, 14482, Germany
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, United States
| | - Saima Ahmed
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, United States
| | - Hanno Steen
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, United States
| | - Bernhard Y Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, 14482, Germany
- Windreich Department for Artificial Intelligence and Human Health and Hasso Plattner Institute at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, United States
| | - Katharina Baum
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, 14482, Germany
- Windreich Department for Artificial Intelligence and Human Health and Hasso Plattner Institute at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, United States
- Department of Mathematics and Computer Science, Free University Berlin, Berlin, 14195, Germany
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10
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Chakraborty A, Wang C, Hodgson-Garms M, Broughton BRS, Frith JE, Kelly K, Samuel CS. Induced pluripotent stem cell-derived mesenchymal stem cells reverse bleomycin-induced pulmonary fibrosis and related lung stiffness. Biomed Pharmacother 2024; 178:117259. [PMID: 39116786 DOI: 10.1016/j.biopha.2024.117259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/23/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterised by lung scarring and stiffening, for which there is no effective cure. Based on the immunomodulatory and anti-fibrotic effects of induced pluripotent stem cell (iPSC) and mesenchymoangioblast-derived mesenchymal stem cells (iPSCs-MSCs), this study evaluated the therapeutic effects of iPSCs-MSCs in a bleomycin (BLM)-induced model of pulmonary fibrosis. Adult male C57BL/6 mice received a double administration of BLM (0.15 mg/day) 7-days apart and were then maintained for a further 28-days (until day-35), whilst control mice were administered saline 7-days apart and maintained for the same time-period. Sub-groups of BLM-injured mice were intravenously-injected with 1×106 iPSC-MSCs on day-21 alone or on day-21 and day-28 and left until day-35 post-injury. Measures of lung inflammation, fibrosis and compliance were then evaluated. BLM-injured mice presented with lung inflammation characterised by increased immune cell infiltration and increased pro-inflammatory cytokine expression, epithelial damage, lung transforming growth factor (TGF)-β1 activity, myofibroblast differentiation, interstitial collagen fibre deposition and topology (fibrosis), in conjunction with reduced matrix metalloproteinase (MMP)-to-tissue inhibitor of metalloproteinase (TIMP) ratios and dynamic lung compliance. All these measures were ameliorated by a single or once-weekly intravenous-administration of iPSC-MSCs, with the latter reducing dendritic cell infiltration and lung epithelial damage, whilst promoting anti-inflammatory interleukin (IL)-10 levels to a greater extent. Proteomic profiling of the conditioned media of cultured iPSC-MSCs that were stimulated with TNF-α and IFN-γ, revealed that these stem cells secreted protein levels of immunosuppressive factors that contributed to the anti-fibrotic and therapeutic potential of iPSCs-MSCs as a novel treatment option for IPF.
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Affiliation(s)
- Amlan Chakraborty
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute (BDI) and Department of Pharmacology, Monash University, Clayton, Victoria, Australia; Division of Immunology, Immunity to Infection and Respiratory Medicine, The University of Manchester, Manchester, England, UK
| | - Chao Wang
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute (BDI) and Department of Pharmacology, Monash University, Clayton, Victoria, Australia
| | - Margeaux Hodgson-Garms
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria, Australia
| | - Brad R S Broughton
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute (BDI) and Department of Pharmacology, Monash University, Clayton, Victoria, Australia
| | - Jessica E Frith
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria, Australia
| | - Kilian Kelly
- Cynata Therapeutics Ltd, Cremorne, Victoria, Australia
| | - Chrishan S Samuel
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute (BDI) and Department of Pharmacology, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria, Australia.
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11
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Laitila J, Seaborne RAE, Ranu N, Kolb JS, Wallgren-Pettersson C, Witting N, Vissing J, Vilchez JJ, Zanoteli E, Palmio J, Huovinen S, Granzier H, Ochala J. Myosin ATPase inhibition fails to rescue the metabolically dysregulated proteome of nebulin-deficient muscle. J Physiol 2024. [PMID: 39216086 DOI: 10.1113/jp286870] [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: 05/13/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
Nemaline myopathy (NM) is a genetic muscle disease, primarily caused by mutations in the NEB gene (NEB-NM) and with muscle myosin dysfunction as a major molecular pathogenic mechanism. Recently, we have observed that the myosin biochemical super-relaxed state was significantly impaired in NEB-NM, inducing an aberrant increase in ATP consumption and remodelling of the energy proteome in diseased muscle fibres. Because the small-molecule Mavacamten is known to promote the myosin super-relaxed state and reduce the ATP demand, we tested its potency in the context of NEB-NM. We first conducted in vitro experiments in isolated single myofibres from patients and found that Mavacamten successfully reversed the myosin ATP overconsumption. Following this, we assessed its short-term in vivo effects using the conditional nebulin knockout (cNeb KO) mouse model and subsequently performing global proteomics profiling in dissected soleus myofibres. After a 4 week treatment period, we observed a remodelling of a large number of proteins in both cNeb KO mice and their wild-type siblings. Nevertheless, these changes were not related to the energy proteome, indicating that short-term Mavacamten treatment is not sufficient to properly counterbalance the metabolically dysregulated proteome of cNeb KO mice. Taken together, our findings emphasize Mavacamten potency in vitro but challenge its short-term efficacy in vivo. KEY POINTS: No cure exists for nemaline myopathy, a type of genetic skeletal muscle disease mainly derived from mutations in genes encoding myofilament proteins. Applying Mavacamten, a small molecule directly targeting the myofilaments, to isolated membrane-permeabilized muscle fibres from human patients restored myosin energetic disturbances. Treating a mouse model of nemaline myopathy in vivo with Mavacamten for 4 weeks, remodelled the skeletal muscle fibre proteome without any noticeable effects on energetic proteins. Short-term Mavacamten treatment may not be sufficient to reverse the muscle phenotype in nemaline myopathy.
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Affiliation(s)
- Jenni Laitila
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Robert A E Seaborne
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Centre of Human and Applied Physiological Sciences, School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Natasha Ranu
- Centre of Human and Applied Physiological Sciences, School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Justin S Kolb
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, MO, USA
| | - Carina Wallgren-Pettersson
- The Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland and Department of Medical and Clinical Genetics, Medicum, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Nanna Witting
- Copenhagen Neuromuscular Center, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - John Vissing
- Copenhagen Neuromuscular Center, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Juan Jesus Vilchez
- Neuromuscular and Ataxias Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Spain, Valencia, Spain
| | - Edmar Zanoteli
- Department of Neurology, Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, Brazil
| | - Johanna Palmio
- Neuromuscular Research Center, Department of Neurology, Tampere University and University Hospital, Tampere, Finland
| | - Sanna Huovinen
- Department of Pathology, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Henk Granzier
- The Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland and Department of Medical and Clinical Genetics, Medicum, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Julien Ochala
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
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12
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Barbehenn A, Zhao SD. Nonparametric empirical Bayes biomarker imputation and estimation. Stat Med 2024; 43:3742-3758. [PMID: 38897921 DOI: 10.1002/sim.10150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 03/31/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024]
Abstract
Biomarkers are often measured in bulk to diagnose patients, monitor patient conditions, and research novel drug pathways. The measurement of these biomarkers often suffers from detection limits that result in missing and untrustworthy measurements. Frequently, missing biomarkers are imputed so that down-stream analysis can be conducted with modern statistical methods that cannot normally handle data subject to informative censoring. This work develops an empirical Bayesg $$ g $$ -modeling method for imputing and denoising biomarker measurements. We establish superior estimation properties compared to popular methods in simulations and with real data, providing the useful biomarker measurement estimations for down-stream analysis.
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Affiliation(s)
- Alton Barbehenn
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, USA
- Department of Statistics, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Sihai Dave Zhao
- Department of Statistics, University of Illinois, Urbana-Champaign, Illinois, USA
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13
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Ho WHJ, Marinova MB, Listijono DR, Bertoldo MJ, Richani D, Kim LJ, Brown A, Riepsamen AH, Cabot S, Frost ER, Bustamante S, Zhong L, Selesniemi K, Wong D, Madawala R, Marchante M, Goss DM, Li C, Araki T, Livingston DJ, Turner N, Sinclair DA, Walters KA, Homer HA, Gilchrist RB, Wu LE. Fertility protection during chemotherapy treatment by boosting the NAD(P) + metabolome. EMBO Mol Med 2024:10.1038/s44321-024-00119-w. [PMID: 39169162 DOI: 10.1038/s44321-024-00119-w] [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: 04/17/2024] [Revised: 07/24/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Chemotherapy induced ovarian failure and infertility is an important concern in female cancer patients of reproductive age or younger, and non-invasive, pharmacological approaches to maintain ovarian function are urgently needed. Given the role of reduced nicotinamide adenine dinucleotide phosphate (NADPH) as an essential cofactor for drug detoxification, we sought to test whether boosting the NAD(P)+ metabolome could protect ovarian function. We show that pharmacological or transgenic strategies to replenish the NAD+ metabolome ameliorates chemotherapy induced female infertility in mice, as measured by oocyte yield, follicle health, and functional breeding trials. Importantly, treatment of a triple-negative breast cancer mouse model with the NAD+ precursor nicotinamide mononucleotide (NMN) reduced tumour growth and did not impair the efficacy of chemotherapy drugs in vivo or in diverse cancer cell lines. Overall, these findings raise the possibility that NAD+ precursors could be a non-invasive strategy for maintaining ovarian function in cancer patients, with potential benefits in cancer therapy.
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Affiliation(s)
- Wing-Hong Jonathan Ho
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia
- The Kinghorn Cancer Centre, St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Maria B Marinova
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Dave R Listijono
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Michael J Bertoldo
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Dulama Richani
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Lynn-Jee Kim
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Amelia Brown
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia
| | | | - Safaa Cabot
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Emily R Frost
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Sonia Bustamante
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Kaisa Selesniemi
- Paul F Glenn Laboratories for the Biological Mechanisms of Aging, Harvard Medical School, Boston, MA, USA
| | - Derek Wong
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Romanthi Madawala
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Maria Marchante
- IVI Foundation, Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynaecology, Faculty of Medicine, University of Valencia, Valencia, Spain
| | - Dale M Goss
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Catherine Li
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Toshiyuki Araki
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-higashi, Kodaira, Tokyo, 187-8502, Japan
| | | | - Nigel Turner
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - David A Sinclair
- Paul F Glenn Laboratories for the Biological Mechanisms of Aging, Harvard Medical School, Boston, MA, USA
| | - Kirsty A Walters
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Hayden A Homer
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia
- Christopher Chen Oocyte Biology Laboratory, University of Queensland Centre for Clinical Research, Royal Brisbane & Women's Hospital, Herston, QLD, 4029, Australia
| | - Robert B Gilchrist
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Lindsay E Wu
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia.
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14
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Muneer G, Chen CS, Lee TT, Chen BY, Chen YJ. A Rapid One-Pot Workflow for Sensitive Microscale Phosphoproteomics. J Proteome Res 2024; 23:3294-3309. [PMID: 39038167 DOI: 10.1021/acs.jproteome.3c00862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Compared to advancements in single-cell proteomics, phosphoproteomics sensitivity has lagged behind due to low abundance, complex sample preparation, and substantial sample input requirements. We present a simple and rapid one-pot phosphoproteomics workflow (SOP-Phos) integrated with data-independent acquisition mass spectrometry (DIA-MS) for microscale phosphoproteomic analysis. SOP-Phos adapts sodium deoxycholate based one-step lysis, reduction/alkylation, direct trypsinization, and phosphopeptide enrichment by TiO2 beads in a single-tube format. By reducing surface adsorptive losses via utilizing n-dodecyl β-d-maltoside precoated tubes and shortening the digestion time, SOP-Phos is completed within 3-4 h with a 1.4-fold higher identification coverage. SOP-Phos coupled with DIA demonstrated >90% specificity, enhanced sensitivity, lower missing values (<1%), and improved reproducibility (8%-10% CV). With a sample size-comparable spectral library, SOP-Phos-DIA identified 33,787 ± 670 to 22,070 ± 861 phosphopeptides from 5 to 0.5 μg cell lysate and 30,433 ± 284 to 6,548 ± 21 phosphopeptides from 50,000 to 2,500 cells. Such sensitivity enabled mapping key lung cancer signaling sites, such as EGFR autophosphorylation sites Y1197/Y1172 and drug targets. The feasibility of SOP-Phos-DIA was demonstrated on EGFR-TKI sensitive and resistant cells, revealing the interplay of multipathway Hippo-EGFR-ERBB signaling cascades underlying the mechanistic insight into EGFR-TKI resistance. Overall, SOP-Phos-DIA is an efficient and robust protocol that can be easily adapted in the community for microscale phosphoproteomic analysis.
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Affiliation(s)
- Gul Muneer
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
| | - Ciao-Syuan Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Tzu-Tsung Lee
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Bo-Yu Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
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15
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Trinh MDL, Visintainer D, Günther J, Østerberg JT, da Fonseca RR, Fondevilla S, Moog MW, Luo G, Nørrevang AF, Crocoll C, Nielsen PV, Jacobsen S, Wendt T, Bak S, López‐Marqués RL, Palmgren M. Site-directed genotype screening for elimination of antinutritional saponins in quinoa seeds identifies TSARL1 as a master controller of saponin biosynthesis selectively in seeds. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2216-2234. [PMID: 38572508 PMCID: PMC11258981 DOI: 10.1111/pbi.14340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 04/05/2024]
Abstract
Climate change may result in a drier climate and increased salinization, threatening agricultural productivity worldwide. Quinoa (Chenopodium quinoa) produces highly nutritious seeds and tolerates abiotic stresses such as drought and high salinity, making it a promising future food source. However, the presence of antinutritional saponins in their seeds is an undesirable trait. We mapped genes controlling seed saponin content to a genomic region that includes TSARL1. We isolated desired genetic variation in this gene by producing a large mutant library of a commercial quinoa cultivar and screening the library for specific nucleotide substitutions using droplet digital PCR. We were able to rapidly isolate two independent tsarl1 mutants, which retained saponins in the leaves and roots for defence, but saponins were undetectable in the seed coat. We further could show that TSARL1 specifically controls seed saponin biosynthesis in the committed step after 2,3-oxidosqualene. Our work provides new important knowledge on the function of TSARL1 and represents a breakthrough for quinoa breeding.
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Affiliation(s)
- Mai Duy Luu Trinh
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Davide Visintainer
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Jan Günther
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | | | - Rute R. da Fonseca
- Section for BiodiversityGlobe Institute, University of CopenhagenKøbenhavn ØDenmark
| | | | - Max William Moog
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Guangbin Luo
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Anton F. Nørrevang
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Christoph Crocoll
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Philip V. Nielsen
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | | | | | - Søren Bak
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | | | - Michael Palmgren
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
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16
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Marino F, Wang D, Merrihew GE, MacCoss MJ, Dubal DB. A second X chromosome improves cognition in aging male and female mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605328. [PMID: 39091744 PMCID: PMC11291180 DOI: 10.1101/2024.07.26.605328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Women show resilience to cognitive aging, in the absence of dementia, in many populations. To dissect sex differences, we utilized the FCG and XY* mouse models. Female gonads and sex chromosomes improved cognition in aging mice of both sexes. Further, presence of a second X in male and female mice conferred cognitive resilience while its absence in females blocked it. In the hippocampal proteome of aging female mice, the second X increased proteins involved in synaptogenesis signaling - a potential pathway to improved cognition.
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Affiliation(s)
- Francesca Marino
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Neurosciences Graduate Program, University of California, San Francisco, CA, US
| | - Dan Wang
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Dena B. Dubal
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Neurosciences Graduate Program, University of California, San Francisco, CA, US
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17
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Li Y, Minic Z, Hüttmann N, Khraibah A, Storey KB, Berezovski MV. Proteomic analysis of Rana sylvatica reveals differentially expressed proteins in liver in response to anoxia, dehydration or freezing stress. Sci Rep 2024; 14:15388. [PMID: 38965296 PMCID: PMC11224343 DOI: 10.1038/s41598-024-65417-2] [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: 03/26/2024] [Accepted: 06/20/2024] [Indexed: 07/06/2024] Open
Abstract
Ectothermic animals that live in seasonally cold regions must adapt to seasonal variation and specific environmental conditions. During the winter, some amphibians hibernate on land and encounter limited environmental water, deficient oxygen, and extremely low temperatures that can cause the whole body freezing. These stresses trigger physiological and biochemical adaptations in amphibians that allow them to survive. Rana sylvatica, commonly known as the wood frog, shows excellent freeze tolerance. They can slow their metabolic activity to a near halt and endure freezing of 65-70% of their total body water as extracellular ice during hibernation, returning to normal when the temperatures rise again. To investigate the molecular adaptations of freeze-tolerant wood frogs, a comprehensive proteomic analysis was performed on frog liver tissue after anoxia, dehydration, or freezing exposures using a label-free LC-MS/MS proteomic approach. Quantitative proteomic analysis revealed that 87, 118, and 86 proteins were significantly upregulated in dehydrated, anoxic, and frozen groups, suggesting potential protective functions. The presence of three upregulated enzymes, glutathione S-transferase (GST), aldolase (ALDOA), and sorbitol dehydrogenase (SORD), was also validated. For all enzymes, the specific enzymatic activity was significantly higher in the livers of frozen and anoxic groups than in the controls. This study reveals that GST, ALDOA, and SORD might participate in the freeze tolerance mechanism by contributing to regulating cellular detoxification and energy metabolism.
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Affiliation(s)
- Yingxi Li
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Nico Hüttmann
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Abdullah Khraibah
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Kenneth B Storey
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
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18
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Strongin Z, Raymond Marchand L, Deleage C, Pampena MB, Cardenas MA, Beusch CM, Hoang TN, Urban EA, Gourves M, Nguyen K, Tharp GK, Lapp S, Rahmberg AR, Harper J, Del Rio Estrada PM, Gonzalez-Navarro M, Torres-Ruiz F, Luna-Villalobos YA, Avila-Rios S, Reyes-Teran G, Sekaly R, Silvestri G, Kulpa DA, Saez-Cirion A, Brenchley JM, Bosinger SE, Gordon DE, Betts MR, Kissick HT, Paiardini M. Distinct SIV-specific CD8 + T cells in the lymph node exhibit simultaneous effector and stem-like profiles and are associated with limited SIV persistence. Nat Immunol 2024; 25:1245-1256. [PMID: 38886592 DOI: 10.1038/s41590-024-01875-0] [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: 06/16/2023] [Accepted: 05/14/2024] [Indexed: 06/20/2024]
Abstract
Human immunodeficiency virus (HIV) cure efforts are increasingly focused on harnessing CD8+ T cell functions, which requires a deeper understanding of CD8+ T cells promoting HIV control. Here we identifiy an antigen-responsive TOXhiTCF1+CD39+CD8+ T cell population with high expression of inhibitory receptors and low expression of canonical cytolytic molecules. Transcriptional analysis of simian immunodeficiency virus (SIV)-specific CD8+ T cells and proteomic analysis of purified CD8+ T cell subsets identified TOXhiTCF1+CD39+CD8+ T cells as intermediate effectors that retained stem-like features with a lineage relationship with terminal effector T cells. TOXhiTCF1+CD39+CD8+ T cells were found at higher frequency than TCF1-CD39+CD8+ T cells in follicular microenvironments and were preferentially located in proximity of SIV-RNA+ cells. Their frequency was associated with reduced plasma viremia and lower SIV reservoir size. Highly similar TOXhiTCF1+CD39+CD8+ T cells were detected in lymph nodes from antiretroviral therapy-naive and antiretroviral therapy-suppressed people living with HIV, suggesting this population of CD8+ T cells contributes to limiting SIV and HIV persistence.
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Affiliation(s)
- Zachary Strongin
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Laurence Raymond Marchand
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - M Betina Pampena
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Christian Michel Beusch
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Timothy N Hoang
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Elizabeth A Urban
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Mael Gourves
- Institut Pasteur, Université Paris Cité, Viral Reservoirs and Immune Control Unit, Paris, France
- Institut Pasteur, Université Paris Cité, HIV Inflammation and Persistence Unit, Paris, France
| | - Kevin Nguyen
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gregory K Tharp
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Stacey Lapp
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Andrew R Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAIDNIH, Bethesda, MD, USA
| | - Justin Harper
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Perla M Del Rio Estrada
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Mauricio Gonzalez-Navarro
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Fernanda Torres-Ruiz
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Yara Andrea Luna-Villalobos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Santiago Avila-Rios
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Comision Coordinadora de los Institutos Nacionales de Salud y Hospitales de Alta Especialidad, Mexico City, Mexico
| | - Rafick Sekaly
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Deanna A Kulpa
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Asier Saez-Cirion
- Institut Pasteur, Université Paris Cité, Viral Reservoirs and Immune Control Unit, Paris, France
- Institut Pasteur, Université Paris Cité, HIV Inflammation and Persistence Unit, Paris, France
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAIDNIH, Bethesda, MD, USA
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - David Ezra Gordon
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haydn T Kissick
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Vaccine Center, Emory University, Atlanta, GA, USA.
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19
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Webel H, Niu L, Nielsen AB, Locard-Paulet M, Mann M, Jensen LJ, Rasmussen S. Imputation of label-free quantitative mass spectrometry-based proteomics data using self-supervised deep learning. Nat Commun 2024; 15:5405. [PMID: 38926340 PMCID: PMC11208500 DOI: 10.1038/s41467-024-48711-5] [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: 02/01/2023] [Accepted: 05/13/2024] [Indexed: 06/28/2024] Open
Abstract
Imputation techniques provide means to replace missing measurements with a value and are used in almost all downstream analysis of mass spectrometry (MS) based proteomics data using label-free quantification (LFQ). Here we demonstrate how collaborative filtering, denoising autoencoders, and variational autoencoders can impute missing values in the context of LFQ at different levels. We applied our method, proteomics imputation modeling mass spectrometry (PIMMS), to an alcohol-related liver disease (ALD) cohort with blood plasma proteomics data available for 358 individuals. Removing 20 percent of the intensities we were able to recover 15 out of 17 significant abundant protein groups using PIMMS-VAE imputations. When analyzing the full dataset we identified 30 additional proteins (+13.2%) that were significantly differentially abundant across disease stages compared to no imputation and found that some of these were predictive of ALD progression in machine learning models. We, therefore, suggest the use of deep learning approaches for imputing missing values in MS-based proteomics on larger datasets and provide workflows for these.
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Affiliation(s)
- Henry Webel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Lili Niu
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Annelaura Bach Nielsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Marie Locard-Paulet
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark.
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark.
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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20
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Lewis JM, Jebeli L, Coulon PML, Lay CE, Scott NE. Glycoproteomic and proteomic analysis of Burkholderia cenocepacia reveals glycosylation events within FliF and MotB are dispensable for motility. Microbiol Spectr 2024; 12:e0034624. [PMID: 38709084 PMCID: PMC11237607 DOI: 10.1128/spectrum.00346-24] [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: 02/10/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
Across the Burkholderia genus O-linked protein glycosylation is highly conserved. While the inhibition of glycosylation has been shown to be detrimental for virulence in Burkholderia cepacia complex species, such as Burkholderia cenocepacia, little is known about how specific glycosylation sites impact protein functionality. Within this study, we sought to improve our understanding of the breadth, dynamics, and requirement for glycosylation across the B. cenocepacia O-glycoproteome. Assessing the B. cenocepacia glycoproteome across different culture media using complementary glycoproteomic approaches, we increase the known glycoproteome to 141 glycoproteins. Leveraging this repertoire of glycoproteins, we quantitively assessed the glycoproteome of B. cenocepacia using Data-Independent Acquisition (DIA) revealing the B. cenocepacia glycoproteome is largely stable across conditions with most glycoproteins constitutively expressed. Examination of how the absence of glycosylation impacts the glycoproteome reveals that the protein abundance of only five glycoproteins (BCAL1086, BCAL2974, BCAL0525, BCAM0505, and BCAL0127) are altered by the loss of glycosylation. Assessing ΔfliF (ΔBCAL0525), ΔmotB (ΔBCAL0127), and ΔBCAM0505 strains, we demonstrate the loss of FliF, and to a lesser extent MotB, mirror the proteomic effects observed in the absence of glycosylation in ΔpglL. While both MotB and FliF are essential for motility, we find loss of glycosylation sites in MotB or FliF does not impact motility supporting these sites are dispensable for function. Combined this work broadens our understanding of the B. cenocepacia glycoproteome supporting that the loss of glycoproteins in the absence of glycosylation is not an indicator of the requirement for glycosylation for protein function. IMPORTANCE Burkholderia cenocepacia is an opportunistic pathogen of concern within the Cystic Fibrosis community. Despite a greater appreciation of the unique physiology of B. cenocepacia gained over the last 20 years a complete understanding of the proteome and especially the O-glycoproteome, is lacking. In this study, we utilize systems biology approaches to expand the known B. cenocepacia glycoproteome as well as track the dynamics of glycoproteins across growth phases, culturing media and in response to the loss of glycosylation. We show that the glycoproteome of B. cenocepacia is largely stable across conditions and that the loss of glycosylation only impacts five glycoproteins including the motility associated proteins FliF and MotB. Examination of MotB and FliF shows, while these proteins are essential for motility, glycosylation is dispensable. Combined this work supports that B. cenocepacia glycosylation can be dispensable for protein function and may influence protein properties beyond stability.
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Affiliation(s)
- Jessica M Lewis
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Leila Jebeli
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Pauline M L Coulon
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Catrina E Lay
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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21
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Zhu Q, Geng D, Li J, Zhang J, Sun H, Fan Z, He J, Hao N, Tian Y, Wen L, Li T, Qin W, Chu X, Wang Y, Yi W. A Computational and Chemical Design Strategy for Manipulating Glycan-Protein Recognition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308522. [PMID: 38582526 PMCID: PMC11199974 DOI: 10.1002/advs.202308522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/23/2024] [Indexed: 04/08/2024]
Abstract
Glycans are complex biomolecules that encode rich information and regulate various biological processes, such as fertilization, host-pathogen binding, and immune recognition, through interactions with glycan-binding proteins. A key driving force for glycan-protein recognition is the interaction between the π electron density of aromatic amino acid side chains and polarized C─H groups of the pyranose (termed the CH-π interaction). However, the relatively weak binding affinity between glycans and proteins has hindered the application of glycan detection and imaging. Here, computational modeling and molecular dynamics simulations are employed to design a chemical strategy that enhances the CH-π interaction between glycans and proteins by genetically incorporating electron-rich tryptophan derivatives into a lectin PhoSL, which specifically recognizes core fucosylated N-linked glycans. This significantly enhances the binding affinity of PhoSL with the core fucose ligand and enables sensitive detection and imaging of core fucosylated glycans in vitro and in xenograft tumors in mice. Further, the study showed that this strategy is applicable to improve the binding affinity of GafD lectin for N-acetylglucosamine-containing glycans. The approach thus provides a general and effective way to manipulate glycan-protein recognition for glycoscience applications.
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Affiliation(s)
- Qiang Zhu
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Didi Geng
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Jingchao Li
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Jinqiu Zhang
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Haofan Sun
- National Center for Protein Sciences BeijingState Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of LifeomicsBeijing100026China
| | - Zhiya Fan
- National Center for Protein Sciences BeijingState Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of LifeomicsBeijing100026China
| | - Jiahui He
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Ninghui Hao
- The Provincial International Science and Technology Cooperation Base on Engineering BiologyShanghai Institute for Advanced StudyInstitute of Quantitative BiologyInternational Campus of Zhejiang UniversityHaining314499China
| | - Yinping Tian
- Carbohydrate‐Based Drug Research CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Liuqing Wen
- Carbohydrate‐Based Drug Research CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Tiehai Li
- Carbohydrate‐Based Drug Research CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Weijie Qin
- National Center for Protein Sciences BeijingState Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of LifeomicsBeijing100026China
| | - Xiakun Chu
- Advanced Materials ThrustFunction HubThe Hong Kong University of Science and TechnologyGuangzhou511400China
| | - Yong Wang
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
- The Provincial International Science and Technology Cooperation Base on Engineering BiologyShanghai Institute for Advanced StudyInstitute of Quantitative BiologyInternational Campus of Zhejiang UniversityHaining314499China
| | - Wen Yi
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
- Cancer CentreZhejiang UniversityHangzhou310012China
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22
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Hunt AL, Khan I, Wu AML, Makohon-Moore SC, Hood BL, Conrads KA, Abulez T, Ogata J, Mitchell D, Gist G, Oliver J, Wei D, Chung MA, Rahman S, Bateman NW, Zhang W, Conrads TP, Steeg PS. The murine metastatic microenvironment of experimental brain metastases of breast cancer differs by host age in vivo: a proteomic study. Clin Exp Metastasis 2024; 41:229-249. [PMID: 37917186 DOI: 10.1007/s10585-023-10233-7] [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: 05/25/2023] [Accepted: 09/07/2023] [Indexed: 11/04/2023]
Abstract
Breast cancer in young patients is known to exhibit more aggressive biological behavior and is associated with a less favorable prognosis than the same disease in older patients, owing in part to an increased incidence of brain metastases. The mechanistic explanations behind these findings remain poorly understood. We recently reported that young mice, in comparison to older mice, developed significantly greater brain metastases in four mouse models of triple-negative and luminal B breast cancer. Here we have performed a quantitative mass spectrometry-based proteomic analysis to identify proteins potentially contributing to age-related disparities in the development of breast cancer brain metastases. Using a mouse hematogenous model of brain-tropic triple-negative breast cancer (MDA-MB-231BR), we harvested subpopulations of tumor metastases, the tumor-adjacent metastatic microenvironment, and uninvolved brain tissues via laser microdissection followed by quantitative proteomic analysis using high resolution mass spectrometry to characterize differentially abundant proteins potentially contributing to age-dependent rates of brain metastasis. Pathway analysis revealed significant alterations in signaling pathways, particularly in the metastatic microenvironment, modulating tumorigenesis, metabolic processes, inflammation, and neuronal signaling. Tenascin C (TNC) was significantly elevated in all laser microdissection (LMD) enriched compartments harvested from young mice relative to older hosts, which was validated and confirmed by immunoblot analysis of whole brain lysates. Additional in vitro studies including migration and wound-healing assays demonstrated TNC as a positive regulator of tumor cell migration. These results provide important new insights regarding microenvironmental factors, including TNC, as mechanisms contributing to the increased brain cancer metastatic phenotype observed in young breast cancer patients.
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Affiliation(s)
- Allison L Hunt
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA, 22042, USA
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Imran Khan
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA
| | - Alex M L Wu
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA
- Zymeworks Inc, Vancouver, BC, V5T 1G4, Canada
| | - Sasha C Makohon-Moore
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Jonathan Ogata
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Debbie Wei
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA
| | - Monika A Chung
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA
- Rutgers New Jersey Medical School, 185 S Orange Ave, Newark, NJ, 07103, USA
| | - Samiur Rahman
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Wei Zhang
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA, 22042, USA.
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.
| | - Patricia S Steeg
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA.
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23
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Du D, Bhardwaj S, Lu Y, Wang Y, Parker SJ, Zhang Z, Van Eyk JE, Yu G, Clarke R, Herrington DM, Wang Y. ABDS: a bioinformatics tool suite for analyzing biologically diverse samples. RESEARCH SQUARE 2024:rs.3.rs-4419408. [PMID: 38853832 PMCID: PMC11160903 DOI: 10.21203/rs.3.rs-4419408/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Bioinformatics software tools are essential to identify informative molecular features that define different phenotypic sample groups. Among the most fundamental and interrelated tasks are missing value imputation, signature gene detection, and differential pattern visualization. However, many commonly used analytics tools can be problematic when handling biologically diverse samples if either informative missingness possess high missing rates with mixed missing mechanisms, or multiple sample groups are compared and visualized in parallel. We developed the ABDS tool suite specifically for analyzing biologically diverse samples. Collectively, a mechanism-integrated group-wise pre-imputation scheme is proposed to retain informative missingness associated with signature genes, a cosine-based one-sample test is extended to detect group-silenced signature genes, and a unified heatmap is designed to display multiple sample groups. We describe the methodological principles and demonstrate the effectiveness of three analytics tools under targeted scenarios, supported by comparative evaluations and biomedical showcases. As an open-source R package, ABDS tool suite complements rather than replaces existing tools and will allow biologists to more accurately detect interpretable molecular signals among phenotypically diverse sample groups.
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Affiliation(s)
- Dongping Du
- Department of Electrical & Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Saurabh Bhardwaj
- Department of Electrical & Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
- Department of Electrical and Instrumentation Engineering, Thapar Institute of Engineering and Technology, Patiala, Punjab 147004, India
| | - Yingzhou Lu
- Department of Electrical & Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Yizhi Wang
- Department of Electrical & Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Sarah J. Parker
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Zhen Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Guoqiang Yu
- Department of Automation, Tsinghua University, Beijing 100084, P. R. China
| | - Robert Clarke
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - David M. Herrington
- Department of Internal Medicine, Wake Forest University, Winston-Salem, NC 27157, USA
| | - Yue Wang
- Department of Electrical & Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
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24
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Peng H, Wang H, Kong W, Li J, Goh WWB. Optimizing differential expression analysis for proteomics data via high-performing rules and ensemble inference. Nat Commun 2024; 15:3922. [PMID: 38724498 PMCID: PMC11082229 DOI: 10.1038/s41467-024-47899-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: 06/19/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Identification of differentially expressed proteins in a proteomics workflow typically encompasses five key steps: raw data quantification, expression matrix construction, matrix normalization, missing value imputation (MVI), and differential expression analysis. The plethora of options in each step makes it challenging to identify optimal workflows that maximize the identification of differentially expressed proteins. To identify optimal workflows and their common properties, we conduct an extensive study involving 34,576 combinatoric experiments on 24 gold standard spike-in datasets. Applying frequent pattern mining techniques to top-ranked workflows, we uncover high-performing rules that demonstrate optimality has conserved properties. Via machine learning, we confirm optimal workflows are indeed predictable, with average cross-validation F1 scores and Matthew's correlation coefficients surpassing 0.84. We introduce an ensemble inference to integrate results from individual top-performing workflows for expanding differential proteome coverage and resolve inconsistencies. Ensemble inference provides gains in pAUC (up to 4.61%) and G-mean (up to 11.14%) and facilitates effective aggregation of information across varied quantification approaches such as topN, directLFQ, MaxLFQ intensities, and spectral counts. However, further development and evaluation are needed to establish acceptable frameworks for conducting ensemble inference on multiple proteomics workflows.
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Affiliation(s)
- Hui Peng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - He Wang
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Weijia Kong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jinyan Li
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Wilson Wen Bin Goh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Center for Biomedical Informatics, Nanyang Technological University, Singapore, Singapore.
- Center of AI in Medicine, Nanyang Technological University, Singapore, Singapore.
- Division of Neurology, Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, UK.
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25
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Sun J, Xia Y. Pretreating and normalizing metabolomics data for statistical analysis. Genes Dis 2024; 11:100979. [PMID: 38299197 PMCID: PMC10827599 DOI: 10.1016/j.gendis.2023.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 04/09/2023] [Indexed: 02/02/2024] Open
Abstract
Metabolomics as a research field and a set of techniques is to study the entire small molecules in biological samples. Metabolomics is emerging as a powerful tool generally for precision medicine. Particularly, integration of microbiome and metabolome has revealed the mechanism and functionality of microbiome in human health and disease. However, metabolomics data are very complicated. Preprocessing/pretreating and normalizing procedures on metabolomics data are usually required before statistical analysis. In this review article, we comprehensively review various methods that are used to preprocess and pretreat metabolomics data, including MS-based data and NMR -based data preprocessing, dealing with zero and/or missing values and detecting outliers, data normalization, data centering and scaling, data transformation. We discuss the advantages and limitations of each method. The choice for a suitable preprocessing method is determined by the biological hypothesis, the characteristics of the data set, and the selected statistical data analysis method. We then provide the perspective of their applications in the microbiome and metabolome research.
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Affiliation(s)
- Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, Department of Microbiology/Immunology, UIC Cancer Center, University of Illinois Chicago, Jesse Brown VA Medical Center Chicago (537), Chicago, IL 60612, USA
| | - Yinglin Xia
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA
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26
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Nurmi K, Silventoinen K, Keskitalo S, Rajamäki K, Kouri VP, Kinnunen M, Jalil S, Maldonado R, Wartiovaara K, Nievas EI, Denita-Juárez SP, Duncan CJA, Kuismin O, Saarela J, Romo I, Martelius T, Parantainen J, Beklen A, Bilicka M, Matikainen S, Nordström DC, Kaustio M, Wartiovaara-Kautto U, Kilpivaara O, Klein C, Hauck F, Jahkola T, Hautala T, Varjosalo M, Barreto G, Seppänen MRJ, Eklund KK. Truncating NFKB1 variants cause combined NLRP3 inflammasome activation and type I interferon signaling and predispose to necrotizing fasciitis. Cell Rep Med 2024; 5:101503. [PMID: 38593810 PMCID: PMC11031424 DOI: 10.1016/j.xcrm.2024.101503] [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: 12/14/2022] [Revised: 01/04/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
In monogenic autoinflammatory diseases, mutations in genes regulating innate immune responses often lead to uncontrolled activation of inflammasome pathways or the type I interferon (IFN-I) response. We describe a mechanism of autoinflammation potentially predisposing patients to life-threatening necrotizing soft tissue inflammation. Six unrelated families are identified in which affected members present with necrotizing fasciitis or severe soft tissue inflammations. Exome sequencing reveals truncating monoallelic loss-of-function variants of nuclear factor κ light-chain enhancer of activated B cells (NFKB1) in affected patients. In patients' macrophages and in NFKB1-variant-bearing THP-1 cells, activation increases both interleukin (IL)-1β secretion and IFN-I signaling. Truncation of NF-κB1 impairs autophagy, accompanied by the accumulation of reactive oxygen species and reduced degradation of inflammasome receptor nucleotide-binding oligomerization domain, leucine-rich repeat-containing protein 3 (NLRP3), and Toll/IL-1 receptor domain-containing adaptor protein inducing IFN-β (TRIF), thus leading to combined excessive inflammasome and IFN-I activity. Many of the patients respond to anti-inflammatory treatment, and targeting IL-1β and/or IFN-I signaling could represent a therapeutic approach for these patients.
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Affiliation(s)
- Katariina Nurmi
- Faculty of Medicine, Clinicum, Translational Immunology Research Program, Research Program Unit (RPU), University of Helsinki (UH), 00014 Helsinki, Finland
| | - Kristiina Silventoinen
- Faculty of Medicine, Clinicum, Translational Immunology Research Program, Research Program Unit (RPU), University of Helsinki (UH), 00014 Helsinki, Finland
| | - Salla Keskitalo
- Systems Biology/Pathology Research Group, iCAN Digital Precision Cancer Medicine Flagship, Institute of Biotechnology, HiLIFE, UH, 00014 Helsinki, Finland
| | - Kristiina Rajamäki
- Faculty of Medicine, Clinicum, Translational Immunology Research Program, Research Program Unit (RPU), University of Helsinki (UH), 00014 Helsinki, Finland; Department of Medical and Clinical Genetics, Applied Tumor Genomics Research Program, RPU, UH, 00014 Helsinki, Finland
| | - Vesa-Petteri Kouri
- Faculty of Medicine, Clinicum, Translational Immunology Research Program, Research Program Unit (RPU), University of Helsinki (UH), 00014 Helsinki, Finland
| | - Matias Kinnunen
- Systems Biology/Pathology Research Group, iCAN Digital Precision Cancer Medicine Flagship, Institute of Biotechnology, HiLIFE, UH, 00014 Helsinki, Finland
| | - Sami Jalil
- Clinical Genetics UH and Helsinki University Hospital (HUH), 00014 Helsinki, Finland
| | - Rocio Maldonado
- Clinical Genetics UH and Helsinki University Hospital (HUH), 00014 Helsinki, Finland
| | - Kirmo Wartiovaara
- Clinical Genetics UH and Helsinki University Hospital (HUH), 00014 Helsinki, Finland
| | | | | | - Christopher J A Duncan
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 4HH, UK
| | - Outi Kuismin
- Department of Clinical Genetics, Oulu University Hospital (OUH), 90014 Oulu, Finland; PEDEGO Research Unit and Medical Research Center Oulu, OUH and University of Oulu (OU), 90014 Oulu, Finland
| | - Janna Saarela
- Institute for Molecular Medicine Finland, HiLIFE, UH, 00014 Helsinki, Finland; Centre for Molecular Medicine Norway, University of Oslo, 0313 Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, 0450 Oslo, Norway
| | - Inka Romo
- Inflammation Center, Department of Infectious Disease, HUH, 00029 Helsinki, Finland
| | - Timi Martelius
- Inflammation Center, Department of Infectious Disease, HUH, 00029 Helsinki, Finland
| | - Jukka Parantainen
- Faculty of Medicine, Clinicum, Translational Immunology Research Program, Research Program Unit (RPU), University of Helsinki (UH), 00014 Helsinki, Finland
| | - Arzu Beklen
- Faculty of Medicine, Clinicum, Translational Immunology Research Program, Research Program Unit (RPU), University of Helsinki (UH), 00014 Helsinki, Finland
| | - Marcelina Bilicka
- Faculty of Medicine, Clinicum, Translational Immunology Research Program, Research Program Unit (RPU), University of Helsinki (UH), 00014 Helsinki, Finland
| | - Sampsa Matikainen
- Faculty of Medicine, Clinicum, Translational Immunology Research Program, Research Program Unit (RPU), University of Helsinki (UH), 00014 Helsinki, Finland
| | - Dan C Nordström
- Faculty of Medicine, Clinicum, Translational Immunology Research Program, Research Program Unit (RPU), University of Helsinki (UH), 00014 Helsinki, Finland; Department of Internal Medicine and Rehabilitation, HUH and UH, 00029 Helsinki, Finland
| | - Meri Kaustio
- Institute for Molecular Medicine Finland, HiLIFE, UH, 00014 Helsinki, Finland
| | - Ulla Wartiovaara-Kautto
- Department of Hematology, HUH, Comprehensive Cancer Center, UH, 00029 Helsinki, Finland; Applied Tumor Genomics Research Program, RPU, Faculty of Medicine, UH, 00014 Helsinki, Finland
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, RPU, Faculty of Medicine, UH, 00014 Helsinki, Finland; Department of Medical and Clinical Genetics/Medicum, Faculty of Medicine, UH, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, UH, 00014 Helsinki, Finland; HUS Diagnostic Center, HUSLAB Laboratory of Genetics, HUH, 00029 Helsinki, Finland
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Fabian Hauck
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Tiina Jahkola
- Department of Plastic Surgery, HUH, 00029 Helsinki, Finland
| | - Timo Hautala
- Research Unit of Internal Medicine and Biomedicine, OU, and Infectious Diseases Clinic, OUH, 90014 Oulu, Finland
| | - Markku Varjosalo
- Systems Biology/Pathology Research Group, iCAN Digital Precision Cancer Medicine Flagship, Institute of Biotechnology, HiLIFE, UH, 00014 Helsinki, Finland
| | - Goncalo Barreto
- Faculty of Medicine, Clinicum, Translational Immunology Research Program, Research Program Unit (RPU), University of Helsinki (UH), 00014 Helsinki, Finland
| | - Mikko R J Seppänen
- Adult Immunodeficiency Unit, Infectious Diseases, Inflammation Center, HUH and UH, 00029 Helsinki, Finland; Rare Disease Center, Children and Adolescents, HUH and UH, 00029 Helsinki, Finland.
| | - Kari K Eklund
- Faculty of Medicine, Clinicum, Translational Immunology Research Program, Research Program Unit (RPU), University of Helsinki (UH), 00014 Helsinki, Finland; Department of Rheumatology, HUH and UH, 00029 Helsinki, Finland; Orton Orthopaedic Hospital, 00280 Helsinki, Finland.
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27
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Burns AR, Wiedrick J, Feryn A, Maes M, Midha MK, Baxter DH, Morrone SR, Prokop TJ, Kapil C, Hoopmann MR, Kusebauch U, Deutsch EW, Rappaport N, Watanabe K, Moritz RL, Miller RA, Lapidus JA, Orwoll ES. Proteomic changes induced by longevity-promoting interventions in mice. GeroScience 2024; 46:1543-1560. [PMID: 37653270 PMCID: PMC10828338 DOI: 10.1007/s11357-023-00917-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/20/2023] [Indexed: 09/02/2023] Open
Abstract
Using mouse models and high-throughput proteomics, we conducted an in-depth analysis of the proteome changes induced in response to seven interventions known to increase mouse lifespan. This included two genetic mutations, a growth hormone receptor knockout (GHRKO mice) and a mutation in the Pit-1 locus (Snell dwarf mice), four drug treatments (rapamycin, acarbose, canagliflozin, and 17α-estradiol), and caloric restriction. Each of the interventions studied induced variable changes in the concentrations of proteins across liver, kidney, and gastrocnemius muscle tissue samples, with the strongest responses in the liver and limited concordance in protein responses across tissues. To the extent that these interventions promote longevity through common biological mechanisms, we anticipated that proteins associated with longevity could be identified by characterizing shared responses across all or multiple interventions. Many of the proteome alterations induced by each intervention were distinct, potentially implicating a variety of biological pathways as being related to lifespan extension. While we found no protein that was affected similarly by every intervention, we identified a set of proteins that responded to multiple interventions. These proteins were functionally diverse but tended to be involved in peroxisomal oxidation and metabolism of fatty acids. These results provide candidate proteins and biological mechanisms related to enhancing longevity that can inform research on therapeutic approaches to promote healthy aging.
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Affiliation(s)
- Adam R Burns
- Biostatistics & Design Program, Oregon Health & Science University, Portland, OR, USA.
| | - Jack Wiedrick
- Biostatistics & Design Program, Oregon Health & Science University, Portland, OR, USA
| | - Alicia Feryn
- Biostatistics & Design Program, Oregon Health & Science University, Portland, OR, USA
| | - Michal Maes
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | | | - Charu Kapil
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | | | | | | | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Jodi A Lapidus
- School of Public Health, Oregon Health & Science University-Portland State University, Portland, OR, USA
| | - Eric S Orwoll
- Department of Endocrinology, Oregon Health & Science University, Portland, OR, USA
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28
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Luige J, Armaos A, Tartaglia GG, Ørom UAV. Predicting nuclear G-quadruplex RNA-binding proteins with roles in transcription and phase separation. Nat Commun 2024; 15:2585. [PMID: 38519458 PMCID: PMC10959947 DOI: 10.1038/s41467-024-46731-9] [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: 04/06/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
RNA-binding proteins are central for many biological processes and their characterization has demonstrated a broad range of functions as well as a wide spectrum of target structures. RNA G-quadruplexes are important regulatory elements occurring in both coding and non-coding transcripts, yet our knowledge of their structure-based interactions is at present limited. Here, using theoretical predictions and experimental approaches, we show that many chromatin-binding proteins bind to RNA G-quadruplexes, and we classify them based on their RNA G-quadruplex-binding potential. Combining experimental identification of nuclear RNA G-quadruplex-binding proteins with computational approaches, we build a prediction tool that assigns probability score for a nuclear protein to bind RNA G-quadruplexes. We show that predicted G-quadruplex RNA-binding proteins exhibit a high degree of protein disorder and hydrophilicity and suggest involvement in both transcription and phase-separation into membrane-less organelles. Finally, we present the G4-Folded/UNfolded Nuclear Interaction Explorer System (G4-FUNNIES) for estimating RNA G4-binding propensities at http://service.tartaglialab.com/new_submission/G4FUNNIES .
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Affiliation(s)
- Johanna Luige
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alexandros Armaos
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy.
- Catalan Institution for Research and Advanced Studies ICREA Passeig Lluis Companys, 23 08010, Barcelona, Spain.
| | - Ulf Andersson Vang Ørom
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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29
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Matzinger M, Schmücker A, Yelagandula R, Stejskal K, Krššáková G, Berger F, Mechtler K, Mayer RL. Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications. Nat Commun 2024; 15:1019. [PMID: 38310095 PMCID: PMC10838342 DOI: 10.1038/s41467-024-45391-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 01/19/2024] [Indexed: 02/05/2024] Open
Abstract
Comprehensive proteomic analysis is essential to elucidate molecular pathways and protein functions. Despite tremendous progress in proteomics, current studies still suffer from limited proteomic coverage and dynamic range. Here, we utilize micropillar array columns (µPACs) together with wide-window acquisition and the AI-based CHIMERYS search engine to achieve excellent proteomic comprehensiveness for bulk proteomics, affinity purification mass spectrometry and single cell proteomics. Our data show that µPACs identify ≤50% more peptides and ≤24% more proteins, while offering improved throughput, which is critical for large (clinical) proteomics studies. Combining wide precursor isolation widths of m/z 4-12 with the CHIMERYS search engine identified +51-74% and +59-150% more proteins and peptides, respectively, for single cell, co-immunoprecipitation, and multi-species samples over a conventional workflow at well-controlled false discovery rates. The workflow further offers excellent precision, with CVs <7% for low input bulk samples, and accuracy, with deviations <10% from expected fold changes for regular abundance two-proteome mixes. Compared to a conventional workflow, our entire optimized platform discovered 92% more potential interactors in a protein-protein interaction study on the chromatin remodeler Smarca5/Snf2h. These include previously described Smarca5 binding partners and undescribed ones including Arid1a, another chromatin remodeler with key roles in neurodevelopmental and malignant disorders.
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Affiliation(s)
- Manuel Matzinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
| | - Anna Schmücker
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Ramesh Yelagandula
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Laboratory of Epigenetics, Cell Fate & Disease, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Karel Stejskal
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Gabriela Krššáková
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
| | - Rupert L Mayer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
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30
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O'Brien JJ, Raj A, Gaun A, Waite A, Li W, Hendrickson DG, Olsson N, McAllister FE. A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments. Nat Methods 2024; 21:290-300. [PMID: 38110636 DOI: 10.1038/s41592-023-02120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/31/2023] [Indexed: 12/20/2023]
Abstract
We present a framework for the analysis of multiplexed mass spectrometry proteomics data that reduces estimation error when combining multiple isobaric batches. Variations in the number and quality of observations have long complicated the analysis of isobaric proteomics data. Here we show that the power to detect statistical associations is substantially improved by utilizing models that directly account for known sources of variation in the number and quality of observations that occur across batches.In a multibatch benchmarking experiment, our open-source software (msTrawler) increases the power to detect changes, especially in the range of less than twofold changes, while simultaneously increasing quantitative proteome coverage by utilizing more low-signal observations. Further analyses of previously published multiplexed datasets of 4 and 23 batches highlight both increased power and the ability to navigate complex missing data patterns without relying on unverifiable imputations or discarding reliable measurements.
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Affiliation(s)
| | - Anil Raj
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | - Adam Waite
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Wenzhou Li
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | - Niclas Olsson
- Calico Life Sciences LLC, South San Francisco, CA, USA
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31
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Sun H, Fu B, Qian X, Xu P, Qin W. Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction. Nat Commun 2024; 15:852. [PMID: 38286993 PMCID: PMC10825125 DOI: 10.1038/s41467-024-44987-9] [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: 06/21/2022] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221 nuclear RBPs and 1333 cytoplasmic RBPs were enriched and identified using nuclear/cytoplasm targeting enrichment probes, representing an increase of 54.4% and 85.7% compared with previous reports. The probes were further applied in the omics-level investigation of subcellular-specific RBP-RNA interactions upon ferroptosis induction. Interestingly, large-scale RBPs display enhanced interaction with RNAs in nucleus but reduced association with RNAs in cytoplasm during ferroptosis process. Furthermore, we discovered dozens of nucleoplasmic translocation candidate RBPs upon ferroptosis induction and validated representative ones by immunofluorescence imaging. The enrichment of Tricarboxylic acid cycle in the translocation candidate RBPs may provide insights for investigating their possible roles in ferroptosis induced metabolism dysregulation.
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Affiliation(s)
- Haofan Sun
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Bin Fu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Ping Xu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Weijie Qin
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
- College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China.
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32
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Hüttmann N, Li Y, Poolsup S, Zaripov E, D’Mello R, Susevski V, Minic Z, Berezovski MV. Surface Proteome of Extracellular Vesicles and Correlation Analysis Reveal Breast Cancer Biomarkers. Cancers (Basel) 2024; 16:520. [PMID: 38339272 PMCID: PMC10854524 DOI: 10.3390/cancers16030520] [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: 12/23/2023] [Revised: 01/13/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Breast cancer (BC) is the second most frequently diagnosed cancer and accounts for approximately 25% of new cancer cases in Canadian women. Using biomarkers as a less-invasive BC diagnostic method is currently under investigation but is not ready for practical application in clinical settings. During the last decade, extracellular vesicles (EVs) have emerged as a promising source of biomarkers because they contain cancer-derived proteins, RNAs, and metabolites. In this study, EV proteins from small EVs (sEVs) and medium EVs (mEVs) were isolated from BC MDA-MB-231 and MCF7 and non-cancerous breast epithelial MCF10A cell lines and then analyzed by two approaches: global proteomic analysis and enrichment of EV surface proteins by Sulfo-NHS-SS-Biotin labeling. From the first approach, proteomic profiling identified 2459 proteins, which were subjected to comparative analysis and correlation network analysis. Twelve potential biomarker proteins were identified based on cell line-specific expression and filtered by their predicted co-localization with known EV marker proteins, CD63, CD9, and CD81. This approach resulted in the identification of 11 proteins, four of which were further investigated by Western blot analysis. The presence of transmembrane serine protease matriptase (ST14), claudin-3 (CLDN3), and integrin alpha-7 (ITGA7) in each cell line was validated by Western blot, revealing that ST14 and CLDN3 may be further explored as potential EV biomarkers for BC. The surface labeling approach enriched proteins that were not identified using the first approach. Ten potential BC biomarkers (Glutathione S-transferase P1 (GSTP1), Elongation factor 2 (EEF2), DEAD/H box RNA helicase (DDX10), progesterone receptor (PGR), Ras-related C3 botulinum toxin substrate 2 (RAC2), Disintegrin and metalloproteinase domain-containing protein 10 (ADAM10), Aconitase 2 (ACO2), UTP20 small subunit processome component (UTP20), NEDD4 binding protein 2 (N4BP2), Programmed cell death 6 (PDCD6)) were selected from surface proteins commonly identified from MDA-MB-231 and MCF7, but not identified in MCF10A EVs. In total, 846 surface proteins were identified from the second approach, of which 11 were already known as BC markers. This study supports the proposition that Evs are a rich source of known and novel biomarkers that may be used for non-invasive detection of BC. Furthermore, the presented datasets could be further explored for the identification of potential biomarkers in BC.
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Affiliation(s)
- Nico Hüttmann
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
| | - Yingxi Li
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
| | - Suttinee Poolsup
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
| | - Emil Zaripov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
| | - Rochelle D’Mello
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
| | - Vanessa Susevski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
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33
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Afonin AM, Piironen AK, de Sousa Maciel I, Ivanova M, Alatalo A, Whipp AM, Pulkkinen L, Rose RJ, van Kamp I, Kaprio J, Kanninen KM. Proteomic insights into mental health status: plasma markers in young adults. Transl Psychiatry 2024; 14:55. [PMID: 38267423 PMCID: PMC10808121 DOI: 10.1038/s41398-024-02751-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
Global emphasis on enhancing prevention and treatment strategies necessitates an increased understanding of the biological mechanisms of psychopathology. Plasma proteomics is a powerful tool that has been applied in the context of specific mental disorders for biomarker identification. The p-factor, also known as the "general psychopathology factor", is a concept in psychopathology suggesting that there is a common underlying factor that contributes to the development of various forms of mental disorders. It has been proposed that the p-factor can be used to understand the overall mental health status of an individual. Here, we aimed to discover plasma proteins associated with the p-factor in 775 young adults in the FinnTwin12 cohort. Using liquid chromatography-tandem mass spectrometry, 13 proteins with a significant connection with the p-factor were identified, 8 of which were linked to epidermal growth factor receptor (EGFR) signaling. This exploratory study provides new insight into biological alterations associated with mental health status in young adults.
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Affiliation(s)
- Alexey M Afonin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Aino-Kaisa Piironen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Izaque de Sousa Maciel
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mariia Ivanova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Arto Alatalo
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Alyce M Whipp
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Lea Pulkkinen
- Department of Psychology, University of Jyvaskyla, Jyvaskyla, Finland
| | - Richard J Rose
- Department of Psychological & Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Irene van Kamp
- Centre for Sustainability, Environment and Health, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
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34
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Hunt AL, Bateman NW, Barakat W, Makohon-Moore SC, Abulez T, Driscoll JA, Schaaf JP, Hood BL, Conrads KA, Zhou M, Calvert V, Pierobon M, Loffredo J, Wilson KN, Litzi TJ, Teng PN, Oliver J, Mitchell D, Gist G, Rojas C, Blanton B, Darcy KM, Rao UNM, Petricoin EF, Phippen NT, Maxwell GL, Conrads TP. Mapping three-dimensional intratumor proteomic heterogeneity in uterine serous carcinoma by multiregion microsampling. Clin Proteomics 2024; 21:4. [PMID: 38254014 PMCID: PMC10804562 DOI: 10.1186/s12014-024-09451-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Although uterine serous carcinoma (USC) represents a small proportion of all uterine cancer cases, patients with this aggressive subtype typically have high rates of chemotherapy resistance and disease recurrence that collectively result in a disproportionately high death rate. The goal of this study was to provide a deeper view of the tumor microenvironment of this poorly characterized uterine cancer variant through multi-region microsampling and quantitative proteomics. METHODS Tumor epithelium, tumor-involved stroma, and whole "bulk" tissue were harvested by laser microdissection (LMD) from spatially resolved levels from nine USC patient tumor specimens and underwent proteomic analysis by mass spectrometry and reverse phase protein arrays, as well as transcriptomic analysis by RNA-sequencing for one patient's tumor. RESULTS LMD enriched cell subpopulations demonstrated varying degrees of relatedness, indicating substantial intratumor heterogeneity emphasizing the necessity for enrichment of cellular subpopulations prior to molecular analysis. Known prognostic biomarkers were quantified with stable levels in both LMD enriched tumor and stroma, which were shown to be highly variable in bulk tissue. These USC data were further used in a comparative analysis with a data generated from another serous gynecologic malignancy, high grade serous ovarian carcinoma, and have been added to our publicly available data analysis tool, the Heterogeneity Analysis Portal ( https://lmdomics.org/ ). CONCLUSIONS Here we identified extensive three-dimensional heterogeneity within the USC tumor microenvironment, with disease-relevant biomarkers present in both the tumor and the stroma. These data underscore the critical need for upfront enrichment of cellular subpopulations from tissue specimens for spatial proteogenomic analysis.
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Grants
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
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Affiliation(s)
- Allison L Hunt
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Suite 375, Annandale, VA, 22042, USA
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Waleed Barakat
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Sasha C Makohon-Moore
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Jordan A Driscoll
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Joshua P Schaaf
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Ming Zhou
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Suite 375, Annandale, VA, 22042, USA
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Valerie Calvert
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Jeremy Loffredo
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Katlin N Wilson
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Tracy J Litzi
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Christine Rojas
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Brian Blanton
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Uma N M Rao
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - G Larry Maxwell
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Suite 375, Annandale, VA, 22042, USA
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Suite 375, Annandale, VA, 22042, USA.
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.
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35
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Cherkaoui S, Yang L, McBride M, Turn CS, Lu W, Eigenmann C, Allen GE, Panasenko OO, Zhang L, Vu A, Liu K, Li Y, Gandhi OH, Surrey L, Wierer M, White E, Rabinowitz JD, Hogarty MD, Morscher RJ. Reprogramming neuroblastoma by diet-enhanced polyamine depletion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.573662. [PMID: 38260457 PMCID: PMC10802427 DOI: 10.1101/2024.01.07.573662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Neuroblastoma is a highly lethal childhood tumor derived from differentiation-arrested neural crest cells1,2. Like all cancers, its growth is fueled by metabolites obtained from either circulation or local biosynthesis3,4. Neuroblastomas depend on local polyamine biosynthesis, with the inhibitor difluoromethylornithine showing clinical activity5. Here we show that such inhibition can be augmented by dietary restriction of upstream amino acid substrates, leading to disruption of oncogenic protein translation, tumor differentiation, and profound survival gains in the TH-MYCN mouse model. Specifically, an arginine/proline-free diet decreases the polyamine precursor ornithine and augments tumor polyamine depletion by difluoromethylornithine. This polyamine depletion causes ribosome stalling, unexpectedly specifically at adenosine-ending codons. Such codons are selectively enriched in cell cycle genes and low in neuronal differentiation genes. Thus, impaired translation of these codons, induced by the diet-drug combination, favors a pro-differentiation proteome. These results suggest that the genes of specific cellular programs have evolved hallmark codon usage preferences that enable coherent translational rewiring in response to metabolic stresses, and that this process can be targeted to activate differentiation of pediatric cancers.
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Affiliation(s)
- Sarah Cherkaoui
- Pediatric Cancer Metabolism Laboratory, Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
- Division of Oncology, University Children’s Hospital Zurich and Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
| | - Lifeng Yang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
| | - Matthew McBride
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
| | - Christina S. Turn
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenyun Lu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
| | - Caroline Eigenmann
- Pediatric Cancer Metabolism Laboratory, Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
- Division of Oncology, University Children’s Hospital Zurich and Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
| | - George E. Allen
- Bioinformatics Support Platform, Faculty of Medicine, University of Geneva 1211, Switzerland
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Olesya O. Panasenko
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
- BioCode: RNA to proteins (R2P) Platform, University of Geneva, 1211 Geneva, Switzerland
| | - Lu Zhang
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08901, USA
- Department of Molecular Biology and Biochemistry, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Annette Vu
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kangning Liu
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yimei Li
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Om H. Gandhi
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lea Surrey
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael Wierer
- Proteomics Research Infrastructure, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Eileen White
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08901, USA
- Department of Molecular Biology and Biochemistry, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
| | - Michael D. Hogarty
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raphael J. Morscher
- Pediatric Cancer Metabolism Laboratory, Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
- Division of Oncology, University Children’s Hospital Zurich and Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
- Division of Human Genetics, Medical University Innsbruck, Peter-Mayr-Str. 1, 6020 Innsbruck, Austria
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36
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Grégoire S, Vanderaa C, Dit Ruys SP, Kune C, Mazzucchelli G, Vertommen D, Gatto L. Standardized Workflow for Mass-Spectrometry-Based Single-Cell Proteomics Data Processing and Analysis Using the scp Package. Methods Mol Biol 2024; 2817:177-220. [PMID: 38907155 DOI: 10.1007/978-1-0716-3934-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Abstract
Mass-spectrometry (MS)-based single-cell proteomics (SCP) explores cellular heterogeneity by focusing on the functional effectors of the cells-proteins. However, extracting meaningful biological information from MS data is far from trivial, especially with single cells. Currently, data analysis workflows are substantially different from one research team to another. Moreover, it is difficult to evaluate pipelines as ground truths are missing. Our team has developed the R/Bioconductor package called scp to provide a standardized framework for SCP data analysis. It relies on the widely used QFeatures and SingleCellExperiment data structures. In addition, we used a design containing cell lines mixed in known proportions to generate controlled variability for data analysis benchmarking. In this chapter, we provide a flexible data analysis protocol for SCP data using the scp package together with comprehensive explanations at each step of the processing. Our main steps are quality control on the feature and cell level, aggregation of the raw data into peptides and proteins, normalization, and batch correction. We validate our workflow using our ground truth data set. We illustrate how to use this modular, standardized framework and highlight some crucial steps.
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Affiliation(s)
- Samuel Grégoire
- Computational Biology and Bioinformatics Unit, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Christophe Vanderaa
- Computational Biology and Bioinformatics Unit, de Duve Institute, UCLouvain, Brussels, Belgium
| | | | - Christopher Kune
- Laboratory of Mass Spectrometry, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- Laboratory of Mass Spectrometry, MolSys Research Unit, University of Liège, Liège, Belgium
- GIGA Proteomics Facility, University of Liège, Liège, Belgium
| | - Didier Vertommen
- Protein Phosphorylation Unit, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Laurent Gatto
- Computational Biology and Bioinformatics Unit, de Duve Institute, UCLouvain, Brussels, Belgium.
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Abid MSR, Qiu H, Checco JW. Label-Free Quantitation of Endogenous Peptides. Methods Mol Biol 2024; 2758:125-150. [PMID: 38549012 PMCID: PMC11027169 DOI: 10.1007/978-1-0716-3646-6_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] [Indexed: 04/02/2024]
Abstract
Liquid chromatography-mass spectrometry (LC-MS)-based peptidomics methods allow for the detection and identification of many peptides in a complex biological mixture in an untargeted manner. Quantitative peptidomics approaches allow for comparisons of peptide abundance between different samples, allowing one to draw conclusions about peptide differences as a function of experimental treatment or physiology. While stable isotope labeling is a powerful approach for quantitative proteomics and peptidomics, advances in mass spectrometry instrumentation and analysis tools have allowed label-free methods to gain popularity in recent years. In a general label-free quantitative peptidomics experiment, peak intensity information for each peptide is compared across multiple LC-MS runs. Here, we outline a general approach for label-free quantitative peptidomics experiments, including steps for sample preparation, LC-MS data acquisition, data processing, and statistical analysis. Special attention is paid to address run-to-run variability, which can lead to several major problems in label-free experiments. Overall, our method provides researchers with a framework for the development of their own quantitative peptidomics workflows applicable to quantitation of peptides from a wide variety of different biological sources.
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Affiliation(s)
| | - Haowen Qiu
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA.
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Li Z, Weller CA, Shah S, Johnson N, Hao Y, Roberts J, Bereda C, Klaisner S, Machado P, Fratta P, Petrucelli L, Prudencio M, Oskarsson B, Staff NP, Dickson DW, Cookson MR, Ward ME, Singleton AB, Nalls MA, Qi YA. ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571327. [PMID: 38168437 PMCID: PMC10760195 DOI: 10.1101/2023.12.12.571327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Mass spectrometry (MS) is a technique widely employed for the identification and characterization of proteins, personalized medicine, systems biology and biomedical applications. By combining MS with different proteomics approaches such as immunopurification MS, immunopeptidomics, and total protein proteomics, researchers can gain insights into protein-protein interactions, immune responses, cellular processes, and disease mechanisms. The application of MS-based proteomics in these areas continues to advance our understanding of protein function, cellular signaling, and complex biological systems. Data analysis for mass spectrometry is a critical process that includes identifying and quantifying proteins and peptides and exploring biological functions for these proteins in downstream analysis. To address the complexities associated with MS data analysis, we developed ProtPipe to streamline and automate the processing and analysis of high-throughput proteomics and peptidomics datasets. The pipeline facilitates data quality control, sample filtering, and normalization, ensuring robust and reliable downstream analysis. ProtPipe provides downstream analysis including identifying differential abundance proteins and peptides, pathway enrichment analysis, protein-protein interaction analysis, and MHC1-peptide binding affinity. ProtPipe generates annotated tables and diagnostic visualizations from statistical postprocessing and computation of fold-changes across pairwise conditions, predefined in an experimental design. ProtPipe is well-documented open-source software and is available at https://github.com/NIH-CARD/ProtPipe , accompanied by a web interface.
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Vicente-Santos A, Lock LR, Allira M, Dyer KE, Dunsmore A, Tu W, Volokhov DV, Herrera C, Lei GS, Relich RF, Janech MG, Bland AM, Simmons NB, Becker DJ. Serum proteomics reveals a tolerant immune phenotype across multiple pathogen taxa in wild vampire bats. Front Immunol 2023; 14:1281732. [PMID: 38193073 PMCID: PMC10773587 DOI: 10.3389/fimmu.2023.1281732] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/24/2023] [Indexed: 01/10/2024] Open
Abstract
Bats carry many zoonotic pathogens without showing pronounced pathology, with a few exceptions. The underlying immune tolerance mechanisms in bats remain poorly understood, although information-rich omics tools hold promise for identifying a wide range of immune markers and their relationship with infection. To evaluate the generality of immune responses to infection, we assessed the differences and similarities in serum proteomes of wild vampire bats (Desmodus rotundus) across infection status with five taxonomically distinct pathogens: bacteria (Bartonella spp., hemoplasmas), protozoa (Trypanosoma cruzi), and DNA (herpesviruses) and RNA (alphacoronaviruses) viruses. From 19 bats sampled in 2019 in Belize, we evaluated the up- and downregulated immune responses of infected versus uninfected individuals for each pathogen. Using a high-quality genome annotation for vampire bats, we identified 586 serum proteins but found no evidence for differential abundance nor differences in composition between infected and uninfected bats. However, using receiver operating characteristic curves, we identified four to 48 candidate biomarkers of infection depending on the pathogen, including seven overlapping biomarkers (DSG2, PCBP1, MGAM, APOA4, DPEP1, GOT1, and IGFALS). Enrichment analysis of these proteins revealed that our viral pathogens, but not the bacteria or protozoa studied, were associated with upregulation of extracellular and cytoplasmatic secretory vesicles (indicative of viral replication) and downregulation of complement activation and coagulation cascades. Additionally, herpesvirus infection elicited a downregulation of leukocyte-mediated immunity and defense response but an upregulation of an inflammatory and humoral immune response. In contrast to our two viral infections, we found downregulation of lipid and cholesterol homeostasis and metabolism with Bartonella spp. infection, of platelet-dense and secretory granules with hemoplasma infection, and of blood coagulation pathways with T. cruzi infection. Despite the small sample size, our results suggest that vampire bats have a similar suite of immune mechanisms for viruses distinct from responses to the other pathogen taxa, and we identify potential biomarkers that can expand our understanding of pathogenesis of these infections in bats. By applying a proteomic approach to a multi-pathogen system in wild animals, our study provides a distinct framework that could be expanded across bat species to increase our understanding of how bats tolerate pathogens.
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Affiliation(s)
| | - Lauren R. Lock
- School of Biological Sciences, University of Oklahoma, Norman, OK, United States
| | - Meagan Allira
- School of Biological Sciences, University of Oklahoma, Norman, OK, United States
| | - Kristin E. Dyer
- School of Biological Sciences, University of Oklahoma, Norman, OK, United States
| | - Annalise Dunsmore
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
- Vector-Borne and Infectious Disease Research Center, Tulane University, New Orleans, LA, United States
| | - Weihong Tu
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
- Vector-Borne and Infectious Disease Research Center, Tulane University, New Orleans, LA, United States
| | - Dmitriy V. Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Claudia Herrera
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
- Vector-Borne and Infectious Disease Research Center, Tulane University, New Orleans, LA, United States
| | - Guang-Sheng Lei
- Department of Pathology and Laboratory Medicine, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Ryan F. Relich
- Department of Pathology and Laboratory Medicine, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Michael G. Janech
- Hollings Marine Laboratory, Charleston, SC, United States
- Department of Biology, College of Charleston, Charleston, SC, United States
| | - Alison M. Bland
- Hollings Marine Laboratory, Charleston, SC, United States
- Department of Biology, College of Charleston, Charleston, SC, United States
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, United States
| | - Daniel J. Becker
- School of Biological Sciences, University of Oklahoma, Norman, OK, United States
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Rifes P, Isaksson M, Rusimbi C, Ramón Santonja A, Nelander J, Laurell T, Kirkeby A. Identifying secreted biomarkers of dopaminergic ventral midbrain progenitor cells. Stem Cell Res Ther 2023; 14:354. [PMID: 38072935 PMCID: PMC10712201 DOI: 10.1186/s13287-023-03580-5] [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: 03/13/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Ventral midbrain (VM) dopaminergic progenitor cells derived from human pluripotent stem cells have the potential to replace endogenously lost dopamine neurons and are currently in preclinical and clinical development for treatment of Parkinson's Disease (PD). However, one main challenge in the quality control of the cells is that rostral and caudal VM progenitors are extremely similar transcriptionally though only the caudal VM cells give rise to dopaminergic (DA) neurons with functionality relevant for cell replacement in PD. Therefore, it is critical to develop assays which can rapidly and reliably discriminate rostral from caudal VM cells during clinical manufacturing. METHODS We performed shotgun proteomics on cell culture supernatants from rostral and caudal VM progenitor cells to search for novel secreted biomarkers specific to DA progenitors from the caudal VM. Key hits were validated by qRT-PCR and ELISA. RESULTS We identified and validated novel secreted markers enriched in caudal VM progenitor cultures (CPE, LGI1 and PDGFC), and found these markers to correlate strongly with the expression of EN1, which is a predictive marker for successful graft outcome in DA cell transplantation products. Other markers (CNTN2 and CORIN) were found to conversely be enriched in the non-dopaminergic rostral VM cultures. Key novel ELISA markers were further validated on supernatant samples from GMP-manufactured caudal VM batches. CONCLUSION As a non-invasive in-process quality control test for predicting correctly patterned batches of caudal VM DA cells during clinical manufacturing, we propose a dual ELISA panel measuring LGI1/CORIN ratios around day 16 of differentiation.
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Affiliation(s)
- Pedro Rifes
- Novo Nordisk Foundation Center for Stem Cell Medicine - reNEW, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Marc Isaksson
- Department of Biomedical Engineering, Lund University, Ole Römers Väg 3, 223 63, Lund, Sweden
- Department of Experimental Medical Science, Lund University, Sölvegatan 17, BMC-B11, 221 84, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Sölvegatan 17, BMC-B11, 221 84, Lund, Sweden
| | - Charlotte Rusimbi
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Adrián Ramón Santonja
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Jenny Nelander
- Department of Experimental Medical Science, Lund University, Sölvegatan 17, BMC-B11, 221 84, Lund, Sweden
| | - Thomas Laurell
- Department of Biomedical Engineering, Lund University, Ole Römers Väg 3, 223 63, Lund, Sweden
| | - Agnete Kirkeby
- Novo Nordisk Foundation Center for Stem Cell Medicine - reNEW, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
- Department of Experimental Medical Science, Lund University, Sölvegatan 17, BMC-B11, 221 84, Lund, Sweden.
- Wallenberg Center for Molecular Medicine, Lund University, Sölvegatan 17, BMC-B11, 221 84, Lund, Sweden.
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Snieckute G, Ryder L, Vind AC, Wu Z, Arendrup FS, Stoneley M, Chamois S, Martinez-Val A, Leleu M, Dreos R, Russell A, Gay DM, Genzor AV, Choi BSY, Basse AL, Sass F, Dall M, Dollet LCM, Blasius M, Willis AE, Lund AH, Treebak JT, Olsen JV, Poulsen SS, Pownall ME, Jensen BAH, Clemmensen C, Gerhart-Hines Z, Gatfield D, Bekker-Jensen S. ROS-induced ribosome impairment underlies ZAKα-mediated metabolic decline in obesity and aging. Science 2023; 382:eadf3208. [PMID: 38060659 DOI: 10.1126/science.adf3208] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
The ribotoxic stress response (RSR) is a signaling pathway in which the p38- and c-Jun N-terminal kinase (JNK)-activating mitogen-activated protein kinase kinase kinase (MAP3K) ZAKα senses stalling and/or collision of ribosomes. Here, we show that reactive oxygen species (ROS)-generating agents trigger ribosomal impairment and ZAKα activation. Conversely, zebrafish larvae deficient for ZAKα are protected from ROS-induced pathology. Livers of mice fed a ROS-generating diet exhibit ZAKα-activating changes in ribosomal elongation dynamics. Highlighting a role for the RSR in metabolic regulation, ZAK-knockout mice are protected from developing high-fat high-sugar (HFHS) diet-induced blood glucose intolerance and liver steatosis. Finally, ZAK ablation slows animals from developing the hallmarks of metabolic aging. Our work highlights ROS-induced ribosomal impairment as a physiological activation signal for ZAKα that underlies metabolic adaptation in obesity and aging.
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Affiliation(s)
- Goda Snieckute
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Laura Ryder
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Anna Constance Vind
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Zhenzhen Wu
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | | | - Mark Stoneley
- MRC Toxicology Unit, University of Cambridge, Cambridge CB2 1QR, UK
| | - Sébastien Chamois
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Ana Martinez-Val
- Mass Spectrometry for Quantitative Proteomics, Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Marion Leleu
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne and University of Lausanne, CH-1015 Lausanne, Switzerland
| | - René Dreos
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | | | - David Michael Gay
- Biotech Research and Innovation Center, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Aitana Victoria Genzor
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Beatrice So-Yun Choi
- Department of Biomedical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Astrid Linde Basse
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Frederike Sass
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Morten Dall
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Lucile Chantal Marie Dollet
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Melanie Blasius
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Cambridge CB2 1QR, UK
| | - Anders H Lund
- Biotech Research and Innovation Center, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jesper Velgaard Olsen
- Mass Spectrometry for Quantitative Proteomics, Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Steen Seier Poulsen
- Department of Biomedical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | | | | | - Christoffer Clemmensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Zach Gerhart-Hines
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Simon Bekker-Jensen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
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Wang H, Lim KP, Kong W, Gao H, Wong BJH, Phua SX, Guo T, Goh WWB. MultiPro: DDA-PASEF and diaPASEF acquired cell line proteomic datasets with deliberate batch effects. Sci Data 2023; 10:858. [PMID: 38042886 PMCID: PMC10693559 DOI: 10.1038/s41597-023-02779-8] [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: 04/11/2023] [Accepted: 11/23/2023] [Indexed: 12/04/2023] Open
Abstract
Mass spectrometry-based proteomics plays a critical role in current biological and clinical research. Technical issues like data integration, missing value imputation, batch effect correction and the exploration of inter-connections amongst these technical issues, can produce errors but are not well studied. Although proteomic technologies have improved significantly in recent years, this alone cannot resolve these issues. What is needed are better algorithms and data processing knowledge. But to obtain these, we need appropriate proteomics datasets for exploration, investigation, and benchmarking. To meet this need, we developed MultiPro (Multi-purpose Proteome Resource), a resource comprising four comprehensive large-scale proteomics datasets with deliberate batch effects using the latest parallel accumulation-serial fragmentation in both Data-Dependent Acquisition (DDA) and Data Independent Acquisition (DIA) modes. Each dataset contains a balanced two-class design based on well-characterized and widely studied cell lines (A549 vs K562 or HCC1806 vs HS578T) with 48 or 36 biological and technical replicates altogether, allowing for investigation of a multitude of technical issues. These datasets allow for investigation of inter-connections between class and batch factors, or to develop approaches to compare and integrate data from DDA and DIA platforms.
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Affiliation(s)
- He Wang
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Kai Peng Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Weijia Kong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Huanhuan Gao
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, 310030, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, 310030, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310030, China
| | - Bertrand Jern Han Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Ser Xian Phua
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, 310030, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, 310030, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310030, China
| | - Wilson Wen Bin Goh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
- Center for Biomedical Informatics, Nanyang Technological University, Singapore, 636921, Singapore.
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Harris L, Fondrie WE, Oh S, Noble WS. Evaluating Proteomics Imputation Methods with Improved Criteria. J Proteome Res 2023; 22:3427-3438. [PMID: 37861703 PMCID: PMC10949645 DOI: 10.1021/acs.jproteome.3c00205] [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: 10/21/2023]
Abstract
Quantitative measurements produced by tandem mass spectrometry proteomics experiments typically contain a large proportion of missing values. Missing values hinder reproducibility, reduce statistical power, and make it difficult to compare across samples or experiments. Although many methods exist for imputing missing values, in practice, the most commonly used methods are among the worst performing. Furthermore, previous benchmarking studies have focused on relatively simple measurements of error such as the mean-squared error between imputed and held-out values. Here we evaluate the performance of commonly used imputation methods using three practical, "downstream-centric" criteria. These criteria measure the ability to identify differentially expressed peptides, generate new quantitative peptides, and improve the peptide lower limit of quantification. Our evaluation comprises several experiment types and acquisition strategies, including data-dependent and data-independent acquisition. We find that imputation does not necessarily improve the ability to identify differentially expressed peptides but that it can identify new quantitative peptides and improve the peptide lower limit of quantification. We find that MissForest is generally the best performing method per our downstream-centric criteria. We also argue that existing imputation methods do not properly account for the variance of peptide quantifications and highlight the need for methods that do.
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Affiliation(s)
- Lincoln Harris
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | | | - Sewoong Oh
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
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Ewald J, Zhou G, Lu Y, Xia J. Using ExpressAnalyst for Comprehensive Gene Expression Analysis in Model and Non-Model Organisms. Curr Protoc 2023; 3:e922. [PMID: 37929753 DOI: 10.1002/cpz1.922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
ExpressAnalyst is a web-based platform that enables intuitive, end-to-end transcriptomics and proteomics data analysis. Users can start from FASTQ files, gene/protein abundance tables, or gene/protein lists. ExpressAnalyst will perform read quantification, gene expression table processing and normalization, differential expression analysis, or meta-analysis with complex study designs. The results are presented via various interactive visualizations such as volcano plots, heatmaps, networks, and ridgeline charts, with built-in functional enrichment analysis to allow flexible data exploration and understanding. ExpressAnalyst currently contains built-in support for 29 common organisms. For non-model organisms without good reference genomes, it can perform comprehensive transcriptome profiling directly from RNA-seq reads. These common tasks are covered in 11 Basic Protocols. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: RNA-seq count table uploading, processing, and normalization Basic Protocol 2: Differential expression analysis with linear models Basic Protocol 3: Functional analysis with volcano plot, enrichment network, and ridgeline visualization Basic Protocol 4: Hierarchical clustering analysis of transcriptomics data using interactive heatmaps Basic Protocol 5: Cross-species gene expression analysis based on ortholog mapping results Basic Protocol 6: Proteomics and microarray data processing and normalization Basic Protocol 7: Preparing multiple gene expression tables for meta-analysis Basic Protocol 8: Statistical and functional meta-analysis of gene expression data Basic Protocol 9: Functional analysis of transcriptomics signatures Basic Protocol 10: Dose-response and time-series data analysis Basic Protocol 11: RNA-seq reads processing and quantification with and without reference transcriptomes.
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Affiliation(s)
- Jessica Ewald
- Institute of Parasitology, McGill University, Montreal, Canada
| | - Guangyan Zhou
- Institute of Parasitology, McGill University, Montreal, Canada
| | - Yao Lu
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
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Hutchings C, Dawson CS, Krueger T, Lilley KS, Breckels LM. A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data. F1000Res 2023; 12:1402. [PMID: 38021401 PMCID: PMC10683783 DOI: 10.12688/f1000research.139116.1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/15/2023] [Indexed: 12/01/2023] Open
Abstract
Background: Expression proteomics involves the global evaluation of protein abundances within a system. In turn, differential expression analysis can be used to investigate changes in protein abundance upon perturbation to such a system. Methods: Here, we provide a workflow for the processing, analysis and interpretation of quantitative mass spectrometry-based expression proteomics data. This workflow utilizes open-source R software packages from the Bioconductor project and guides users end-to-end and step-by-step through every stage of the analyses. As a use-case we generated expression proteomics data from HEK293 cells with and without a treatment. Of note, the experiment included cellular proteins labelled using tandem mass tag (TMT) technology and secreted proteins quantified using label-free quantitation (LFQ). Results: The workflow explains the software infrastructure before focusing on data import, pre-processing and quality control. This is done individually for TMT and LFQ datasets. The application of statistical differential expression analysis is demonstrated, followed by interpretation via gene ontology enrichment analysis. Conclusions: A comprehensive workflow for the processing, analysis and interpretation of expression proteomics is presented. The workflow is a valuable resource for the proteomics community and specifically beginners who are at least familiar with R who wish to understand and make data-driven decisions with regards to their analyses.
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Affiliation(s)
- Charlotte Hutchings
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Charlotte S. Dawson
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Thomas Krueger
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Lisa M. Breckels
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QR, UK
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Huang L, Song M, Shen H, Hong H, Gong P, Deng HW, Zhang C. Deep Learning Methods for Omics Data Imputation. BIOLOGY 2023; 12:1313. [PMID: 37887023 PMCID: PMC10604785 DOI: 10.3390/biology12101313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
One common problem in omics data analysis is missing values, which can arise due to various reasons, such as poor tissue quality and insufficient sample volumes. Instead of discarding missing values and related data, imputation approaches offer an alternative means of handling missing data. However, the imputation of missing omics data is a non-trivial task. Difficulties mainly come from high dimensionality, non-linear or non-monotonic relationships within features, technical variations introduced by sampling methods, sample heterogeneity, and the non-random missingness mechanism. Several advanced imputation methods, including deep learning-based methods, have been proposed to address these challenges. Due to its capability of modeling complex patterns and relationships in large and high-dimensional datasets, many researchers have adopted deep learning models to impute missing omics data. This review provides a comprehensive overview of the currently available deep learning-based methods for omics imputation from the perspective of deep generative model architectures such as autoencoder, variational autoencoder, generative adversarial networks, and Transformer, with an emphasis on multi-omics data imputation. In addition, this review also discusses the opportunities that deep learning brings and the challenges that it might face in this field.
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Affiliation(s)
- Lei Huang
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Meng Song
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Hui Shen
- Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Ping Gong
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS 39180, USA
| | - Hong-Wen Deng
- Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Chaoyang Zhang
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, MS 39406, USA
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Sharifi MA, Wierer M, Dang TA, Milic J, Moggio A, Sachs N, von Scheidt M, Hinterdobler J, Müller P, Werner J, Stiller B, Aherrahrou Z, Erdmann J, Zaliani A, Graettinger M, Reinshagen J, Gul S, Gribbon P, Maegdefessel L, Bernhagen J, Sager HB, Mann M, Schunkert H, Kessler T. ADAMTS-7 Modulates Atherosclerotic Plaque Formation by Degradation of TIMP-1. Circ Res 2023; 133:674-686. [PMID: 37675562 PMCID: PMC7615141 DOI: 10.1161/circresaha.123.322737] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/23/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND The ADAMTS7 locus was genome-wide significantly associated with coronary artery disease. Lack of the ECM (extracellular matrix) protease ADAMTS-7 (A disintegrin and metalloproteinase-7) was shown to reduce atherosclerotic plaque formation. Here, we sought to identify molecular mechanisms and downstream targets of ADAMTS-7 mediating the risk of atherosclerosis. METHODS Targets of ADAMTS-7 were identified by high-resolution mass spectrometry of atherosclerotic plaques from Apoe-/- and Apoe-/-Adamts7-/- mice. ECM proteins were identified using solubility profiling. Putative targets were validated using immunofluorescence, in vitro degradation assays, coimmunoprecipitation, and Förster resonance energy transfer-based protein-protein interaction assays. ADAMTS7 expression was measured in fibrous caps of human carotid artery plaques. RESULTS In humans, ADAMTS7 expression was higher in caps of unstable as compared to stable carotid plaques. Compared to Apoe-/- mice, atherosclerotic aortas of Apoe-/- mice lacking Adamts-7 (Apoe-/-Adamts7-/-) contained higher protein levels of Timp-1 (tissue inhibitor of metalloprotease-1). In coimmunoprecipitation experiments, the catalytic domain of ADAMTS-7 bound to TIMP-1, which was degraded in the presence of ADAMTS-7 in vitro. ADAMTS-7 reduced the inhibitory capacity of TIMP-1 at its canonical target MMP-9 (matrix metalloprotease-9). As a downstream mechanism, we investigated collagen content in plaques of Apoe-/- and Apoe-/-Adamts7-/- mice after a Western diet. Picrosirius red staining of the aortic root revealed less collagen as a readout of higher MMP-9 activity in Apoe-/- as compared to Apoe-/- Adamts7-/- mice. To facilitate high-throughput screening for ADAMTS-7 inhibitors with the aim of decreasing TIMP-1 degradation, we designed a Förster resonance energy transfer-based assay targeting the ADAMTS-7 catalytic site. CONCLUSIONS ADAMTS-7, which is induced in unstable atherosclerotic plaques, decreases TIMP-1 stability reducing its inhibitory effect on MMP-9, which is known to promote collagen degradation and is likewise associated with coronary artery disease. Disrupting the interaction of ADAMTS-7 and TIMP-1 might be a strategy to increase collagen content and plaque stability for the reduction of atherosclerosis-related events.
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Affiliation(s)
- M. Amin Sharifi
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Tan An Dang
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Jelena Milic
- Division of Vascular Biology, Institute for Stroke and Dementia Research, Ludwig Maximilian University of Munich, Munich, Germany
| | - Aldo Moggio
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
| | - Nadja Sachs
- Vascular Biology and Experimental Vascular Medicine Unit, Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Moritz von Scheidt
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Julia Hinterdobler
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Philipp Müller
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Julia Werner
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Barbara Stiller
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
| | - Zouhair Aherrahrou
- Institute for Cardiogenetics and University Heart Centre Lübeck, University of Lübeck, Lübeck, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Hamburg/Kiel/Lübeck, Germany
| | - Jeanette Erdmann
- Institute for Cardiogenetics and University Heart Centre Lübeck, University of Lübeck, Lübeck, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Hamburg/Kiel/Lübeck, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Hamburg, Germany
| | - Mira Graettinger
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Hamburg, Germany
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Hamburg, Germany
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Hamburg, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Hamburg, Germany
| | - Lars Maegdefessel
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
- Vascular Biology and Experimental Vascular Medicine Unit, Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Jürgen Bernhagen
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
- Division of Vascular Biology, Institute for Stroke and Dementia Research, Ludwig Maximilian University of Munich, Munich, Germany
| | - Hendrik B. Sager
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Heribert Schunkert
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Thorsten Kessler
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
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Abstract
Missing values are a notable challenge when analyzing mass spectrometry-based proteomics data. While the field is still actively debating the best practices, the challenge increased with the emergence of mass spectrometry-based single-cell proteomics and the dramatic increase in missing values. A popular approach to deal with missing values is to perform imputation. Imputation has several drawbacks for which alternatives exist, but currently, imputation is still a practical solution widely adopted in single-cell proteomics data analysis. This perspective discusses the advantages and drawbacks of imputation. We also highlight 5 main challenges linked to missing value management in single-cell proteomics. Future developments should aim to solve these challenges, whether it is through imputation or data modeling. The perspective concludes with recommendations for reporting missing values, for reporting methods that deal with missing values, and for proper encoding of missing values.
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Affiliation(s)
- Christophe Vanderaa
- Computational Biology and Bioinformatics Unit (CBIO), de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Laurent Gatto
- Computational Biology and Bioinformatics Unit (CBIO), de Duve Institute, UCLouvain, 1200 Brussels, Belgium
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Teh WK, Ding Y, Gubellini F, Filloux A, Poyart C, Givskov M, Dramsi S. Characterization of TelE, a T7SS LXG Effector Exhibiting a Conserved C-Terminal Glycine Zipper Motif Required for Toxicity. Microbiol Spectr 2023; 11:e0148123. [PMID: 37432124 PMCID: PMC10434224 DOI: 10.1128/spectrum.01481-23] [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] [Received: 04/07/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023] Open
Abstract
Streptococcus gallolyticus subsp. gallolyticus (SGG) is an opportunistic bacterial pathogen strongly associated with colorectal cancer. Here, through comparative genomics analysis, we demonstrated that the genetic locus encoding the type VIIb secretion system (T7SSb) machinery is uniquely present in SGG in two different arrangements. SGG UCN34 carrying the most prevalent T7SSb genetic arrangement was chosen as the reference strain. To identify the effectors secreted by this secretion system, we inactivated the essC gene encoding the motor of this machinery. A comparison of the proteins secreted by UCN34 wild type and its isogenic ΔessC mutant revealed six T7SSb effector proteins, including the expected WXG effector EsxA and three LXG-containing proteins. In this work, we characterized an LXG-family toxin named herein TelE promoting the loss of membrane integrity. Seven homologs of TelE harboring a conserved glycine zipper motif at the C terminus were identified in different SGG isolates. Scanning mutagenesis of this motif showed that the glycine residue at position 470 was crucial for TelE membrane destabilization activity. TelE activity was antagonized by a small protein TipE belonging to the DUF5085 family. Overall, we report herein a unique SGG T7SSb effector exhibiting a toxic activity against nonimmune bacteria. IMPORTANCE In this study, 38 clinical isolates of Streptococcus gallolyticus subsp. gallolyticus (SGG) were sequenced and a genetic locus encoding the type VIIb secretion system (T7SSb) was found conserved and absent from 16 genomes of the closely related S. gallolyticus subsp. pasteurianus (SGP). The T7SSb is a bona fide pathogenicity island. Here, we report that the model organism SGG strain UCN34 secretes six T7SSb effectors. One of the six effectors named TelE displayed a strong toxicity when overexpressed in Escherichia coli. Our results indicate that TelE is probably a pore-forming toxin whose activity can be antagonized by a specific immunity protein named TipE. Overall, we report a unique toxin-immunity protein pair and our data expand the range of effectors secreted through T7SSb.
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Affiliation(s)
- Wooi Keong Teh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yichen Ding
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | | | - Alain Filloux
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Claire Poyart
- Université de Paris, Assistance Publique Hôpitaux de Paris, Service de Bactériologie, Centre National de Référence des Streptocoques, Groupe Hospitalier Paris Centre site Cochin, Paris, France
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Shaynoor Dramsi
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Biology of Gram-positive Pathogens Unit, Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2001, Paris, France
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50
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Cai D, Li QQ, Mohammed Z, Chou WC, Huang J, Kong M, Xie Y, Yu Y, Hu G, Qi J, Zhou Y, Tan W, Lin L, Qiu R, Dong G, Zeng XW. Fetal Glucocorticoid Mediates the Association between Prenatal Per- and Polyfluoroalkyl Substance Exposure and Neonatal Growth Index: Evidence from a Birth Cohort Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:11420-11429. [PMID: 37494580 DOI: 10.1021/acs.est.2c08831] [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: 07/28/2023]
Abstract
Glucocorticoid plays a key role in the growth and organ maturation of fetus. However, the effect of glucocorticoid on the association between per- and polyfluoroalkyl substance (PFAS) exposure and fetal growth is still unknown. We detected cord cortisol (active glucocorticoid in human) and 34 PFAS concentrations in the maternal serum samples, which were collected from 202 mother-fetus pairs in the Maoming Birth Cohort from 2015 to 2018. The mediation effect of cord cortisol on the association between maternal PFAS and the neonatal growth index (NGI) was estimated. We found that higher PFAS concentrations were associated with lower NGI in terms of ponderal index, birth weight (BW), head circumference (HC), and its z-scores (BWZ and HCZ) (P < 0.05). Fetal cortisol could mediate 12.6-27.3% of the associations between PFAS and NGI. Specifically, cord cortisol mediated the association between branched perfluorooctane sulfonate (branched PFOS) and HCZ by 20.4% and between perfluorooctanoate (PFOA) and HCZ by 27.3%. Our findings provide the first epidemiological data evincing that fetal cortisol could mediate the association between prenatal PFAS exposure and fetal growth. Further investigations are recommended to elucidate the interactions among cord cortisol, PFAS, and fetal growth.
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Affiliation(s)
- Dan Cai
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510655, China
| | - Qing-Qing Li
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Zeeshan Mohammed
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Wei-Chun Chou
- Center for Environmental and Human Toxicology, Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida 32611, United States
| | - Jinbo Huang
- Maoming Maternal and Child Health Hospital, Maoming 525000, China
| | - Minli Kong
- Maoming Maternal and Child Health Hospital, Maoming 525000, China
| | - Yanqi Xie
- Maoming Maternal and Child Health Hospital, Maoming 525000, China
| | - Yunjiang Yu
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510655, China
| | - Guocheng Hu
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510655, China
| | - Jianying Qi
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510655, China
| | - Yang Zhou
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510655, China
| | - Weihong Tan
- Department of Reproductive Medicine and Genetics Center, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning 530021, China
| | - Lizi Lin
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Rongliang Qiu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Guanghui Dong
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiao-Wen Zeng
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
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