1
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Wang S, Collins A, Prakash A, Fexova S, Papatheodorou I, Jones AR, Vizcaíno JA. Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues. J Proteome Res 2024; 23:1948-1959. [PMID: 38717300 DOI: 10.1021/acs.jproteome.3c00741] [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: 06/13/2024]
Abstract
The availability of an increasingly large amount of public proteomics data sets presents an opportunity for performing combined analyses to generate comprehensive organism-wide protein expression maps across different organisms and biological conditions. Sus scrofa, a domestic pig, is a model organism relevant for food production and for human biomedical research. Here, we reanalyzed 14 public proteomics data sets from the PRIDE database coming from pig tissues to assess baseline (without any biological perturbation) protein abundance in 14 organs, encompassing a total of 20 healthy tissues from 128 samples. The analysis involved the quantification of protein abundance in 599 mass spectrometry runs. We compared protein expression patterns among different pig organs and examined the distribution of proteins across these organs. Then, we studied how protein abundances were compared across different data sets and studied the tissue specificity of the detected proteins. Of particular interest, we conducted a comparative analysis of protein expression between pig and human tissues, revealing a high degree of correlation in protein expression among orthologs, particularly in brain, kidney, heart, and liver samples. We have integrated the protein expression results into the Expression Atlas resource for easy access and visualization of the protein expression data individually or alongside gene expression data.
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Affiliation(s)
- Shengbo Wang
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Andrew Collins
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Ananth Prakash
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Silvie Fexova
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Irene Papatheodorou
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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2
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Lobato S, Castillo-Granada AL, Bucio-Pacheco M, Salomón-Soto VM, Álvarez-Valenzuela R, Meza-Inostroza PM, Villegas-Vizcaíno R. PM 2.5, component cause of severe metabolically abnormal obesity: An in silico, observational and analytical study. Heliyon 2024; 10:e28936. [PMID: 38601536 PMCID: PMC11004224 DOI: 10.1016/j.heliyon.2024.e28936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
Obesity is currently one of the most alarming pathological conditions due to the progressive increase in its prevalence. In the last decade, it has been associated with fine particulate matter suspended in the air (PM2.5). The purpose of this study was to explore the mechanistic interaction of PM2.5 with a high-fat diet (HFD) through the differential regulation of transcriptional signatures, aiming to identify the association of these particles with metabolically abnormal obesity. The research design was observational, using bioinformatic methods and an explanatory approach based on Rothman's causal model. We propose three new transcriptional signatures in murine adipose tissue. The sum of transcriptional differences between the group exposed to an HFD and PM2.5, compared to the control group, were 0.851, 0.265, and -0.047 (p > 0.05). The HFD group increased body mass by 20% with two positive biomarkers of metabolic impact. The group exposed to PM2.5 maintained a similar weight to the control group but exhibited three positive biomarkers. Enriched biological pathways (p < 0.05) included PPAR signaling, small molecule transport, adipogenesis genes, cytokine-cytokine receptor interaction, and HIF-1 signaling. Transcriptional regulation predictions revealed CpG islands and common transcription factors. We propose three new transcriptional signatures: FAT-PM2.5-CEJUS, FAT-PM2.5-UP, and FAT-PM2.5-DN, whose transcriptional regulation profile in adipocytes was statistically similar by dietary intake and HFD and exposure to PM2.5 in mice; suggesting a mechanistic interaction between both factors. However, HFD-exposed murines developed moderate metabolically abnormal obesity, and PM2.5-exposed murines developed severe abnormal metabolism without obesity. Therefore, in Rothman's terms, it is concluded that HFD is a sufficient cause of the development of obesity, and PM2.5 is a component cause of severe abnormal metabolism of obesity. These signatures would be integrated into a systemic biological process that would induce transcriptional regulation in trans, activating obesogenic biological pathways, restricting lipid mobilization pathways, decreasing adaptive thermogenesis and angiogenesis, and altering vascular tone thus inducing a severe metabolically abnormal obesity.
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Affiliation(s)
- Sagrario Lobato
- Departamento de Investigación en Salud, Servicios de Salud del Estado de Puebla, 15 South Street 302, Puebla, Mexico
- Promoción y Educación para la Salud, Universidad Abierta y a Distancia de México. Universidad Avenue 1200, 1st Floor, quadrant 1-2, Xoco, Benito Juarez, 03330, Mexico City, Mexico
- Educación Superior, Centro de Estudios, “Justo Sierra”, Surutato, Badiraguato, Mexico
| | - A. Lourdes Castillo-Granada
- Educación Superior, Centro de Estudios, “Justo Sierra”, Surutato, Badiraguato, Mexico
- Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Guelatao Avenue 66, Ejército de Oriente Indeco II ISSSTE, Iztapalapa, 09230, Mexico City, Mexico
| | - Marcos Bucio-Pacheco
- Educación Superior, Centro de Estudios, “Justo Sierra”, Surutato, Badiraguato, Mexico
- Facultad de Biología, Universidad Autónoma de Sinaloa, Americas Avenue, Universitarios Blvd., University City, 80040, Culiacán Rosales, Mexico
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3
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Lin A, Torres CM, Hobbs EC, Bardhan J, Aley SB, Spencer CT, Taylor KL, Chiang T. Computational and Systems Biology Advances to Enable Bioagent Agnostic Signatures. Health Secur 2024; 22:130-139. [PMID: 38483337 PMCID: PMC11044874 DOI: 10.1089/hs.2023.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Affiliation(s)
- Andy Lin
- Andy Lin, PhD, is a Linus Pauling Distinguished Postdoctoral Fellow; in the National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA
| | - Cameron M. Torres
- Cameron M. Torres is a Graduate Research Assistant and Wieland Fellow, Department of Biological Sciences; at the University of Texas at El Paso, El Paso, TX
| | - Errett C. Hobbs
- Errett C. Hobbs, PhD, is a Data Scientist; in the National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA
| | - Jaydeep Bardhan
- Jaydeep Bardhan, PhD, is a Research Line Manager, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA
| | - Stephen B. Aley
- Stephen B. Aley, PhD, is a Professor, Biological Sciences, and an Associate Vice President for Research, Sponsored Projects; at the University of Texas at El Paso, El Paso, TX
| | - Charles T. Spencer
- Charles T. Spencer, PhD, is an Associate Professor, Biological Sciences, and Edward and Barbara Brown Egbert Endowed Chair of the Department of Biological Sciences; at the University of Texas at El Paso, El Paso, TX
| | - Karen L. Taylor
- Karen L. Taylor, MS, is a Research Line Manager; in the National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA
| | - Tony Chiang
- Tony Chiang, PhD, is a Data Scientist; in the National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA
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4
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Lin A, Torres C, Hobbs EC, Bardhan J, Aley S, Spencer CT, Taylor KL, Chiang T. Computational and Systems Biology Advances to Enable Bioagent Agnostic Signatures. ARXIV 2024:arXiv:2310.13898v3. [PMID: 37961741 PMCID: PMC10635321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Enumerated threat agent lists have long driven biodefense priorities. The global SARS-CoV-2 pandemic demonstrated the limitations of searching for known threat agents as compared to a more agnostic approach. Recent technological advances are enabling agent-agnostic biodefense, especially through the integration of multi-modal observations of host-pathogen interactions directed by a human immunological model. Although well-developed technical assays exist for many aspects of human-pathogen interaction, the analytic methods and pipelines to combine and holistically interpret the results of such assays are immature and require further investments to exploit new technologies. In this manuscript, we discuss potential immunologically based bioagent-agnostic approaches and the computational tool gaps the community should prioritize filling.
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Affiliation(s)
- Andy Lin
- National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA 98109, USA
| | - Cameron Torres
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas 79968 USA
| | - Errett C Hobbs
- National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA 98109, USA
| | - Jaydeep Bardhan
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Seattle, WA 98109, USA
| | - Stephen Aley
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas 79968 USA
| | - Charles T Spencer
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas 79968 USA
| | - Karen L Taylor
- National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA 98109, USA
| | - Tony Chiang
- National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA 98109, USA
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas 79968 USA
- Department of Mathematics, University of Washington, Seattle 98102 USA
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5
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Lou R, Shui W. Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023. Mol Cell Proteomics 2024; 23:100712. [PMID: 38182042 PMCID: PMC10847697 DOI: 10.1016/j.mcpro.2024.100712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024] Open
Abstract
Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful technology for high-throughput, accurate, and reproducible quantitative proteomics. This review provides a comprehensive overview of recent advances in both the experimental and computational methods for DIA proteomics, from data acquisition schemes to analysis strategies and software tools. DIA acquisition schemes are categorized based on the design of precursor isolation windows, highlighting wide-window, overlapping-window, narrow-window, scanning quadrupole-based, and parallel accumulation-serial fragmentation-enhanced DIA methods. For DIA data analysis, major strategies are classified into spectrum reconstruction, sequence-based search, library-based search, de novo sequencing, and sequencing-independent approaches. A wide array of software tools implementing these strategies are reviewed, with details on their overall workflows and scoring approaches at different steps. The generation and optimization of spectral libraries, which are critical resources for DIA analysis, are also discussed. Publicly available benchmark datasets covering global proteomics and phosphoproteomics are summarized to facilitate performance evaluation of various software tools and analysis workflows. Continued advances and synergistic developments of versatile components in DIA workflows are expected to further enhance the power of DIA-based proteomics.
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Affiliation(s)
- Ronghui Lou
- iHuman Institute, ShanghaiTech University, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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6
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Joshi SK, Piehowski P, Liu T, Gosline SJC, McDermott JE, Druker BJ, Traer E, Tyner JW, Agarwal A, Tognon CE, Rodland KD. Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine. Annu Rev Pharmacol Toxicol 2024; 64:455-479. [PMID: 37738504 PMCID: PMC10950354 DOI: 10.1146/annurev-pharmtox-022723-113921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools.
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Affiliation(s)
- Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Paul Piehowski
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sara J C Gosline
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jason E McDermott
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Karin D Rodland
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Pacific Northwest National Laboratory, Richland, Washington, USA
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7
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George N, Fexova S, Fuentes AM, Madrigal P, Bi Y, Iqbal H, Kumbham U, Nolte N, Zhao L, Thanki A, Yu I, Marugan Calles J, Erdos K, Vilmovsky L, Kurri S, Vathrakokoili-Pournara A, Osumi-Sutherland D, Prakash A, Wang S, Tello-Ruiz M, Kumari S, Ware D, Goutte-Gattat D, Hu Y, Brown N, Perrimon N, Vizcaíno JA, Burdett T, Teichmann S, Brazma A, Papatheodorou I. Expression Atlas update: insights from sequencing data at both bulk and single cell level. Nucleic Acids Res 2024; 52:D107-D114. [PMID: 37992296 PMCID: PMC10767917 DOI: 10.1093/nar/gkad1021] [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: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
Expression Atlas (www.ebi.ac.uk/gxa) and its newest counterpart the Single Cell Expression Atlas (www.ebi.ac.uk/gxa/sc) are EMBL-EBI's knowledgebases for gene and protein expression and localisation in bulk and at single cell level. These resources aim to allow users to investigate their expression in normal tissue (baseline) or in response to perturbations such as disease or changes to genotype (differential) across multiple species. Users are invited to search for genes or metadata terms across species or biological conditions in a standardised consistent interface. Alongside these data, new features in Single Cell Expression Atlas allow users to query metadata through our new cell type wheel search. At the experiment level data can be explored through two types of dimensionality reduction plots, t-distributed Stochastic Neighbor Embedding (tSNE) and Uniform Manifold Approximation and Projection (UMAP), overlaid with either clustering or metadata information to assist users' understanding. Data are also visualised as marker gene heatmaps identifying genes that help confer cluster identity. For some data, additional visualisations are available as interactive cell level anatomograms and cell type gene expression heatmaps.
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Affiliation(s)
- Nancy George
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Silvie Fexova
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Alfonso Munoz Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Pedro Madrigal
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Yalan Bi
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Haider Iqbal
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Upendra Kumbham
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Nadja Francesca Nolte
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Lingyun Zhao
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Anil S Thanki
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Iris D Yu
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Jose C Marugan Calles
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Karoly Erdos
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Liora Vilmovsky
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Sandeep R Kurri
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | | | - David Osumi-Sutherland
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Ananth Prakash
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Shengbo Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Marcela K Tello-Ruiz
- Cold Spring Harbour Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Sunita Kumari
- Cold Spring Harbour Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Doreen Ware
- Cold Spring Harbour Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
- USDA ARS NEA, Plant Soil & Nutrition Laboratory Research Unit, Ithaca, NY 14853, USA
| | - Damien Goutte-Gattat
- FlyBase-Cambridge, Department of Physiology, Development and Neuroscience, University of Cambridge Downing Street, Cambridge CB2 3DY, UK
| | - Yanhui Hu
- Perrimon Lab, Department of Genetics, Harvard Medical School, Boston MA 02115, USA
| | - Nick Brown
- FlyBase-Cambridge, Department of Physiology, Development and Neuroscience, University of Cambridge Downing Street, Cambridge CB2 3DY, UK
| | - Norbert Perrimon
- Perrimon Lab, Department of Genetics, Harvard Medical School, Boston MA 02115, USA
- FlyBase-Harvard Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Sarah Teichmann
- Wellcome Trust Sanger Institute. Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
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8
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Ferreira R, Amado F, Vitorino R. Empowering peptidomics: utilizing computational tools and approaches. Bioanalysis 2023; 15:1315-1325. [PMID: 37737150 DOI: 10.4155/bio-2023-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
Bioinformatics plays a critical role in the advancement of peptidomics by providing powerful tools for data analysis, interpretation and integration. Peptidomics is concerned with the study of peptides, short chains of amino acids with diverse biological functions. This area includes peptide identification and characterization, database construction, de novo sequencing, functional annotation, omics data integration and systems biology. Artificial intelligence techniques, such as machine learning and natural language processing, aid in the interpretation of peptide sequence data and the generation of biological insights. By using bioinformatics approaches, peptidomics researchers can accelerate peptide discovery, understand their functions and gain insights into complex molecular interactions.
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Affiliation(s)
- Rita Ferreira
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Francisco Amado
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui Vitorino
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
- Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Universidade do Porto, Porto, Portugal
- iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
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9
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Prakash A, García-Seisdedos D, Wang S, Kundu DJ, Collins A, George N, Moreno P, Papatheodorou I, Jones AR, Vizcaíno JA. Integrated View of Baseline Protein Expression in Human Tissues. J Proteome Res 2023; 22:729-742. [PMID: 36577097 PMCID: PMC9990129 DOI: 10.1021/acs.jproteome.2c00406] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The availability of proteomics datasets in the public domain, and in the PRIDE database, in particular, has increased dramatically in recent years. This unprecedented large-scale availability of data provides an opportunity for combined analyses of datasets to get organism-wide protein abundance data in a consistent manner. We have reanalyzed 24 public proteomics datasets from healthy human individuals to assess baseline protein abundance in 31 organs. We defined tissue as a distinct functional or structural region within an organ. Overall, the aggregated dataset contains 67 healthy tissues, corresponding to 3,119 mass spectrometry runs covering 498 samples from 489 individuals. We compared protein abundances between different organs and studied the distribution of proteins across these organs. We also compared the results with data generated in analogous studies. Additionally, we performed gene ontology and pathway-enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point, we have integrated the protein abundance results into the resource Expression Atlas, where they can be accessed and visualized either individually or together with gene expression data coming from transcriptomics datasets. We believe this is a good mechanism to make proteomics data more accessible for life scientists.
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Affiliation(s)
- Ananth Prakash
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CambridgeCB10 1SD, United Kingdom.,Open Targets, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SD, United Kingdom
| | - David García-Seisdedos
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CambridgeCB10 1SD, United Kingdom
| | - Shengbo Wang
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CambridgeCB10 1SD, United Kingdom
| | - Deepti Jaiswal Kundu
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CambridgeCB10 1SD, United Kingdom
| | - Andrew Collins
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, LiverpoolL69 7ZB, United Kingdom
| | - Nancy George
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CambridgeCB10 1SD, United Kingdom
| | - Pablo Moreno
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CambridgeCB10 1SD, United Kingdom
| | - Irene Papatheodorou
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CambridgeCB10 1SD, United Kingdom.,Open Targets, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SD, United Kingdom
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, LiverpoolL69 7ZB, United Kingdom
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CambridgeCB10 1SD, United Kingdom.,Open Targets, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SD, United Kingdom
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10
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Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver J, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman B, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, MacLean B, MacCoss M, Zhu Y, Ishihama Y, Vizcaíno J. The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res 2023; 51:D1539-D1548. [PMID: 36370099 PMCID: PMC9825490 DOI: 10.1093/nar/gkac1040] [Citation(s) in RCA: 141] [Impact Index Per Article: 141.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/20/2022] [Accepted: 10/23/2022] [Indexed: 11/13/2022] Open
Abstract
Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.
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Affiliation(s)
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Jeremy J Carver
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Luis Mendoza
- Institute for Systems Biology, Seattle WA 98109, USA
| | - Deepti J Kundu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Shengbo Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Chakradhar Bandla
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Selvakumar Kamatchinathan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Suresh Hewapathirana
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Benjamin S Pullman
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Julie Wertz
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Zhi Sun
- Institute for Systems Biology, Seattle WA 98109, USA
| | - Shin Kawano
- Faculty of Contemporary Society, Toyama University of International Studies, Toyama 930-1292, Japan
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Chiba 277-0871, Japan
- School of Frontier Engineering, Kitasato University, Sagamihara 252-0373, Japan
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Yu Watanabe
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | | | | | - Yunping Zhu
- Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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Vujić T, Schvartz D, Furlani IL, Meister I, González-Ruiz V, Rudaz S, Sanchez JC. Oxidative Stress and Extracellular Matrix Remodeling Are Signature Pathways of Extracellular Vesicles Released upon Morphine Exposure on Human Brain Microvascular Endothelial Cells. Cells 2022; 11:cells11233926. [PMID: 36497184 PMCID: PMC9741159 DOI: 10.3390/cells11233926] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/25/2022] [Accepted: 11/01/2022] [Indexed: 12/09/2022] Open
Abstract
Morphine, a commonly used antinociceptive drug in hospitals, is known to cross the blood-brain barrier (BBB) by first passing through brain endothelial cells. Despite its pain-relieving effect, morphine also has detrimental effects, such as the potential induction of redox imbalance in the brain. However, there is still insufficient evidence of these effects on the brain, particularly on the brain endothelial cells and the extracellular vesicles that they naturally release. Indeed, extracellular vesicles (EVs) are nanosized bioparticles produced by almost all cell types and are currently thought to reflect the physiological state of their parent cells. These vesicles have emerged as a promising source of biomarkers by indicating the functional or dysfunctional state of their parent cells and, thus, allowing a better understanding of the biological processes involved in an adverse state. However, there is very little information on the morphine effect on human brain microvascular endothelial cells (HBMECs), and even less on their released EVs. Therefore, the current study aimed at unraveling the detrimental mechanisms of morphine exposure (at 1, 10, 25, 50 and 100 µM) for 24 h on human brain microvascular endothelial cells as well as on their associated EVs. Isolation of EVs was carried out using an affinity-based method. Several orthogonal techniques (NTA, western blotting and proteomics analysis) were used to validate the EVs enrichment, quality and concentration. Data-independent mass spectrometry (DIA-MS)-based proteomics was applied in order to analyze the proteome modulations induced by morphine on HBMECs and EVs. We were able to quantify almost 5500 proteins in HBMECs and 1500 proteins in EVs, of which 256 and 148, respectively, were found to be differentially expressed in at least one condition. Pathway enrichment analysis revealed that the "cell adhesion and extracellular matrix remodeling" process and the "HIF1 pathway", a pathway related to oxidative stress responses, were significantly modulated upon morphine exposure in HBMECs and EVs. Altogether, the combination of proteomics and bioinformatics findings highlighted shared pathways between HBMECs exposed to morphine and their released EVs. These results put forward molecular signatures of morphine-induced toxicity in HBMECs that were also carried by EVs. Therefore, EVs could potentially be regarded as a useful tool to investigate brain endothelial cells dysfunction, and to a different extent, the BBB dysfunction in patient circulation using these "signature pathways".
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Affiliation(s)
- Tatjana Vujić
- Department of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | | | - Izadora Liranço Furlani
- School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
- Department of Chemistry, Federal University of São Carlos, São Carlos 13565-904, Brazil
| | - Isabel Meister
- School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
- Swiss Centre for Applied Human Toxicology, 4055 Basel, Switzerland
| | - Víctor González-Ruiz
- School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
- Swiss Centre for Applied Human Toxicology, 4055 Basel, Switzerland
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
- Swiss Centre for Applied Human Toxicology, 4055 Basel, Switzerland
| | - Jean-Charles Sanchez
- Department of Medicine, University of Geneva, 1211 Geneva, Switzerland
- Correspondence: ; Tel.: +41-22-379-54-86
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12
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Perez-Riverol Y. Proteomic repository data submission, dissemination, and reuse: key messages. Expert Rev Proteomics 2022; 19:297-310. [PMID: 36529941 PMCID: PMC7614296 DOI: 10.1080/14789450.2022.2160324] [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: 12/23/2022]
Abstract
INTRODUCTION The creation of ProteomeXchange data workflows in 2012 transformed the field of proteomics, consisting of the standardization of data submission and dissemination and enabling the widespread reanalysis of public MS proteomics data worldwide. ProteomeXchange has triggered a growing trend toward public dissemination of proteomics data, facilitating the assessment, reuse, comparative analyses, and extraction of new findings from public datasets. By 2022, the consortium is integrated by PRIDE, PeptideAtlas, MassIVE, jPOST, iProX, and Panorama Public. AREAS COVERED Here, we review and discuss the current ecosystem of resources, guidelines, and file formats for proteomics data dissemination and reanalysis. Special attention is drawn to new exciting quantitative and post-translational modification-oriented resources. The challenges and future directions on data depositions including the lack of metadata and cloud-based and high-performance software solutions for fast and reproducible reanalysis of the available data are discussed. EXPERT OPINION The success of ProteomeXchange and the amount of proteomics data available in the public domain have triggered the creation and/or growth of other protein knowledgebase resources. Data reuse is a leading, active, and evolving field; supporting the creation of new formats, tools, and workflows to rediscover and reshape the public proteomics data.
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Affiliation(s)
- Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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