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Raevskiy M, Sorokin M, Emelianova A, Zakharova G, Poddubskaya E, Zolotovskaia M, Buzdin A. Sample-Wise and Gene-Wise Comparisons Confirm a Greater Similarity of RNA and Protein Expression Data at the Level of Molecular Pathways and Suggest an Approach for the Data Quality Check in High-Throughput Expression Databases. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:737-746. [PMID: 38831509 DOI: 10.1134/s0006297924040126] [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: 10/31/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 06/05/2024]
Abstract
Identification of genes and molecular pathways with congruent profiles in the proteomic and transcriptomic datasets may result in the discovery of promising transcriptomic biomarkers that would be more relevant to phenotypic changes. In this study, we conducted comparative analysis of 943 paired RNA and proteomic profiles obtained for the same samples of seven human cancer types from The Cancer Genome Atlas (TCGA) and NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) [two major open human cancer proteomic and transcriptomic databases] that included 15,112 protein-coding genes and 1611 molecular pathways. Overall, our findings demonstrated statistically significant improvement of the congruence between RNA and proteomic profiles when performing analysis at the level of molecular pathways rather than at the level of individual gene products. Transition to the molecular pathway level of data analysis increased the correlation to 0.19-0.57 (Pearson) and 0.14-057 (Spearman), or 2-3-fold for some cancer types. Evaluating the gain of the correlation upon transition to the data analysis the pathway level can be used to refine the omics data by identifying outliers that can be excluded from the comparison of RNA and proteomic profiles. We suggest using sample- and gene-wise correlations for individual genes and molecular pathways as a measure of quality of RNA/protein paired molecular data. We also provide a database of human genes, molecular pathways, and samples related to the correlation between RNA and protein products to facilitate an exploration of new cancer transcriptomic biomarkers and molecular mechanisms at different levels of human gene expression.
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Affiliation(s)
- Mikhail Raevskiy
- Digital Biodesign and Personalized Healthcare Research Center, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Maxim Sorokin
- Omicsway Corp., Walnut, CA 91789, USA.
- Oncobox Ltd., Moscow, 121205, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Aleksandra Emelianova
- Digital Biodesign and Personalized Healthcare Research Center, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Galina Zakharova
- Digital Biodesign and Personalized Healthcare Research Center, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Elena Poddubskaya
- Digital Biodesign and Personalized Healthcare Research Center, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Marianna Zolotovskaia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Anton Buzdin
- Digital Biodesign and Personalized Healthcare Research Center, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
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Staniek J, Kalina T, Andrieux G, Boerries M, Janowska I, Fuentes M, Díez P, Bakardjieva M, Stancikova J, Raabe J, Neumann J, Schwenk S, Arpesella L, Stuchly J, Benes V, García Valiente R, Fernández García J, Carsetti R, Piano Mortari E, Catala A, de la Calle O, Sogkas G, Neven B, Rieux-Laucat F, Magerus A, Neth O, Olbrich P, Voll RE, Alsina L, Allende LM, Gonzalez-Granado LI, Böhler C, Thiel J, Venhoff N, Lorenzetti R, Warnatz K, Unger S, Seidl M, Mielenz D, Schneider P, Ehl S, Rensing-Ehl A, Smulski CR, Rizzi M. Non-apoptotic FAS signaling controls mTOR activation and extrafollicular maturation in human B cells. Sci Immunol 2024; 9:eadj5948. [PMID: 38215192 DOI: 10.1126/sciimmunol.adj5948] [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: 08/04/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024]
Abstract
Defective FAS (CD95/Apo-1/TNFRSF6) signaling causes autoimmune lymphoproliferative syndrome (ALPS). Hypergammaglobulinemia is a common feature in ALPS with FAS mutations (ALPS-FAS), but paradoxically, fewer conventional memory cells differentiate from FAS-expressing germinal center (GC) B cells. Resistance to FAS-induced apoptosis does not explain this phenotype. We tested the hypothesis that defective non-apoptotic FAS signaling may contribute to impaired B cell differentiation in ALPS. We analyzed secondary lymphoid organs of patients with ALPS-FAS and found low numbers of memory B cells, fewer GC B cells, and an expanded extrafollicular (EF) B cell response. Enhanced mTOR activity has been shown to favor EF versus GC fate decision, and we found enhanced PI3K/mTOR and BCR signaling in ALPS-FAS splenic B cells. Modeling initial T-dependent B cell activation with CD40L in vitro, we showed that FAS competent cells with transient FAS ligation showed specifically decreased mTOR axis activation without apoptosis. Mechanistically, transient FAS engagement with involvement of caspase-8 induced nuclear exclusion of PTEN, leading to mTOR inhibition. In addition, FASL-dependent PTEN nuclear exclusion and mTOR modulation were defective in patients with ALPS-FAS. In the early phase of activation, FAS stimulation promoted expression of genes related to GC initiation at the expense of processes related to the EF response. Hence, our data suggest that non-apoptotic FAS signaling acts as molecular switch between EF versus GC fate decisions via regulation of the mTOR axis and transcription. The defect of this modulatory circuit may explain the observed hypergammaglobulinemia and low memory B cell numbers in ALPS.
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Affiliation(s)
- Julian Staniek
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Tomas Kalina
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Iga Janowska
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC CB16/12/00400, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC CB16/12/00400, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Salamanca, Spain
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Marina Bakardjieva
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jitka Stancikova
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Raabe
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julika Neumann
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sabine Schwenk
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Leonardo Arpesella
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jan Stuchly
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rodrigo García Valiente
- Department of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC CB16/12/00400, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - Jonatan Fernández García
- Department of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC CB16/12/00400, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - Rita Carsetti
- B Cell Unit, Immunology Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Eva Piano Mortari
- B Cell Unit, Immunology Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Albert Catala
- Department of Hematology, Institut de Recerca Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Oscar de la Calle
- Immunology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Georgios Sogkas
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Bénédicte Neven
- Pediatric Hematology-Immunology and Rheumatology Department, University Hospital Necker-Enfants Malades, Paris, France
| | - Frédéric Rieux-Laucat
- Université de Paris, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Aude Magerus
- Université de Paris, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Olaf Neth
- Department of Paediatric Infectious Diseases, Rheumatology and Immunology, Hospital Universitario Virgen del Rocio (HUVR), Instituto de Biomedicina de Sevilla (IBIS), Universidad de Sevilla/CSIC, Red de Investigación Traslacional en Infectología Pediátrica RITIP, Sevilla, Spain
| | - Peter Olbrich
- Department of Paediatric Infectious Diseases, Rheumatology and Immunology, Hospital Universitario Virgen del Rocio (HUVR), Instituto de Biomedicina de Sevilla (IBIS), Universidad de Sevilla/CSIC, Red de Investigación Traslacional en Infectología Pediátrica RITIP, Sevilla, Spain
| | - Reinhard E Voll
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Laia Alsina
- Department of Hematology, Institut de Recerca Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
- Clinical Immunology and Primary Immunodeficiencies Unit, Department of Pediatric Allergy and Clinical Immunology, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Luis M Allende
- Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Luis I Gonzalez-Granado
- Primary Immunodeficiencies Unit, Department of Pediatrics, Research Institute Hospital 12 Octubre (i+12), Madrid, Spain
- School of Medicine, Complutense University, Madrid, Spain
| | - Chiara Böhler
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jens Thiel
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Division of Rheumatology and Clinical Immunology, Medical University Graz, Graz, Austria
| | - Nils Venhoff
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Raquel Lorenzetti
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Division of Rheumatology and Clinical Immunology, Medical University Graz, Graz, Austria
| | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Susanne Unger
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maximilian Seidl
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany
- Institute of Pathology, Heinrich-Heine University and University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus Fiebiger Zentrum, Friedrich Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Pascal Schneider
- Department of Immunobiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Stephan Ehl
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Pediatrics and Adolescent Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Anne Rensing-Ehl
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Cristian Roberto Smulski
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Medical Physics Department, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica (CNEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Carlos de Bariloche, Argentina
| | - Marta Rizzi
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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Psatha K, Kollipara L, Drakos E, Deligianni E, Brintakis K, Patsouris E, Sickmann A, Rassidakis GZ, Aivaliotis M. Interruption of p53-MDM2 Interaction by Nutlin-3a in Human Lymphoma Cell Models Initiates a Cell-Dependent Global Effect on Transcriptome and Proteome Level. Cancers (Basel) 2023; 15:3903. [PMID: 37568720 PMCID: PMC10417430 DOI: 10.3390/cancers15153903] [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: 05/10/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 08/13/2023] Open
Abstract
In most lymphomas, p53 signaling pathway is inactivated by various mechanisms independent to p53 gene mutations or deletions. In many cases, p53 function is largely regulated by alterations in the protein abundance levels by the action of E3 ubiquitin-protein ligase MDM2, targeting p53 to proteasome-mediated degradation. In the present study, an integrating transcriptomics and proteomics analysis was employed to investigate the effect of p53 activation by a small-molecule MDM2-antagonist, nutlin-3a, on three lymphoma cell models following p53 activation. Our analysis revealed a system-wide nutlin-3a-associated effect in all examined lymphoma types, identifying in total of 4037 differentially affected proteins involved in a plethora of pathways, with significant heterogeneity among lymphomas. Our findings include known p53-targets and novel p53 activation effects, involving transcription, translation, or degradation of protein components of pathways, such as a decrease in key members of PI3K/mTOR pathway, heat-shock response, and glycolysis, and an increase in key members of oxidative phoshosphorylation, autophagy and mitochondrial translation. Combined inhibition of HSP90 or PI3K/mTOR pathway with nutlin-3a-mediated p53-activation enhanced the apoptotic effects suggesting a promising strategy against human lymphomas. Integrated omic profiling after p53 activation offered novel insights on the regulatory role specific proteins and pathways may have in lymphomagenesis.
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Affiliation(s)
- Konstantina Psatha
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, 70013 Heraklion, Greece; (K.P.); (E.D.)
- Department of Pathology, Medical School, University of Crete, 70013 Heraklion, Greece;
- First Department of Pathology, National and Kapodistrian University of Athens, 15772 Athens, Greece;
- Functional Proteomics and Systems Biology (FunPATh), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), 54124 Thessaloniki, Greece
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften–ISAS–e.V., 44139 Dortmund, Germany; (L.K.); (A.S.)
| | - Elias Drakos
- Department of Pathology, Medical School, University of Crete, 70013 Heraklion, Greece;
| | - Elena Deligianni
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, 70013 Heraklion, Greece; (K.P.); (E.D.)
| | - Konstantinos Brintakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology—Hellas, 71110 Heraklion, Greece;
| | - Eustratios Patsouris
- First Department of Pathology, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften–ISAS–e.V., 44139 Dortmund, Germany; (L.K.); (A.S.)
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
- Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - George Z. Rassidakis
- Department of Oncology-Pathology, Karolinska Institute, 17164 Stockholm, Sweden;
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, 70013 Heraklion, Greece; (K.P.); (E.D.)
- Functional Proteomics and Systems Biology (FunPATh), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), 54124 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Laboratory of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Recurrent NOMO1 Gene Deletion Is a Potential Clinical Marker in Early-Onset Colorectal Cancer and Is Involved in the Regulation of Cell Migration. Cancers (Basel) 2022; 14:cancers14164029. [PMID: 36011023 PMCID: PMC9406593 DOI: 10.3390/cancers14164029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The incidence of EOCRC (age < 50 years at diagnosis) with unknown causes is rising worldwide, necessitating the mechanistical analysis of its molecular basis. The NOMO1 gene is deleted in a high number of EOCRC tumors compared to LOCRC. In this work, we aimed to test the NOMO1 gene mutational profile in EOCRC tumors and to characterize the effect of NOMO1 loss in different CRISPR/cas9-edited cell lines, as well as in murine models. Here, we show that the NOMO1 gene can be inactivated not only by deletion but also by pathogenic mutations in EOCRC. Our results indicate that NOMO1 loss could be a passenger mutation in the development of EOCRC, although it contributes significantly to colon cancer cell migration. Abstract The incidence of early-onset colorectal cancer (EOCRC; age younger than 50 years) has been progressively increasing over the last decades globally, with causes unexplained. A distinct molecular feature of EOCRC is that compared with cases of late-onset colorectal cancer, in EOCRC cases, there is a higher incidence of Nodal Modulator 1 (NOMO1) somatic deletions. However, the mechanisms of NOMO1 in early-onset colorectal carcinogenesis are currently unknown. In this study, we show that in 30% of EOCRCs with heterozygous deletion of NOMO1, there were pathogenic mutations in this gene, suggesting that NOMO1 can be inactivated by deletion or mutation in EOCRC. To study the role of NOMO1 in EOCRC, CRISPR/cas9 technology was employed to generate NOMO1 knockout HCT-116 (EOCRC) and HS-5 (bone marrow) cell lines. NOMO1 loss in these cell lines did not perturb Nodal pathway signaling nor cell proliferation. Expression microarrays, RNA sequencing, and protein expression analysis by LC–IMS/MS showed that NOMO1 inactivation deregulates other signaling pathways independent of the Nodal pathway, such as epithelial–mesenchymal transition and cell migration. Significantly, NOMO1 loss increased the migration capacity of CRC cells. Additionally, a gut-specific conditional NOMO1 KO mouse model revealed no subsequent tumor development in mice. Overall, these findings suggest that NOMO1 could play a secondary role in early-onset colorectal carcinogenesis because its loss increases the migration capacity of CRC cells. Therefore, further study is warranted to explore other signalling pathways deregulated by NOMO1 loss that may play a significant role in the pathogenesis of the disease.
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Landeira-Viñuela A, Díez P, Juanes-Velasco P, Lécrevisse Q, Orfao A, De Las Rivas J, Fuentes M. Deepening into Intracellular Signaling Landscape through Integrative Spatial Proteomics and Transcriptomics in a Lymphoma Model. Biomolecules 2021; 11:1776. [PMID: 34944421 PMCID: PMC8699084 DOI: 10.3390/biom11121776] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/23/2021] [Indexed: 12/12/2022] Open
Abstract
Human Proteome Project (HPP) presents a systematic characterization of the protein landscape under different conditions using several complementary-omic techniques (LC-MS/MS proteomics, affinity proteomics, transcriptomics, etc.). In the present study, using a B-cell lymphoma cell line as a model, comprehensive integration of RNA-Seq transcriptomics, MS/MS, and antibody-based affinity proteomics (combined with size-exclusion chromatography) (SEC-MAP) were performed to uncover correlations that could provide insights into protein dynamics at the intracellular level. Here, 5672 unique proteins were systematically identified by MS/MS analysis and subcellular protein extraction strategies (neXtProt release 2020-21, MS/MS data are available via ProteomeXchange with identifier PXD003939). Moreover, RNA deep sequencing analysis of this lymphoma B-cell line identified 19,518 expressed genes and 5707 protein coding genes (mapped to neXtProt). Among these data sets, 162 relevant proteins (targeted by 206 antibodies) were systematically analyzed by the SEC-MAP approach, providing information about PTMs, isoforms, protein complexes, and subcellular localization. Finally, a bioinformatic pipeline has been designed and developed for orthogonal integration of these high-content proteomics and transcriptomics datasets, which might be useful for comprehensive and global characterization of intracellular protein profiles.
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Affiliation(s)
- Alicia Landeira-Viñuela
- Department of Medicine and General Cytometry Service-Nucleus, USAL/IBSAL, 37000 Salamanca, Spain; (A.L.-V.); (P.D.); (P.J.-V.); (Q.L.); (A.O.)
| | - Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, USAL/IBSAL, 37000 Salamanca, Spain; (A.L.-V.); (P.D.); (P.J.-V.); (Q.L.); (A.O.)
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, USAL/IBSAL, 37000 Salamanca, Spain; (A.L.-V.); (P.D.); (P.J.-V.); (Q.L.); (A.O.)
| | - Quentin Lécrevisse
- Department of Medicine and General Cytometry Service-Nucleus, USAL/IBSAL, 37000 Salamanca, Spain; (A.L.-V.); (P.D.); (P.J.-V.); (Q.L.); (A.O.)
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, USAL/IBSAL, 37000 Salamanca, Spain; (A.L.-V.); (P.D.); (P.J.-V.); (Q.L.); (A.O.)
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain;
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, USAL/IBSAL, 37000 Salamanca, Spain; (A.L.-V.); (P.D.); (P.J.-V.); (Q.L.); (A.O.)
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
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6
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Díez P, Pérez-Andrés M, Bøgsted M, Azkargorta M, García-Valiente R, Dégano RM, Blanco E, Mateos-Gomez S, Bárcena P, Santa Cruz S, Góngora R, Elortza F, Landeira-Viñuela A, Juanes-Velasco P, Segura V, Manzano-Román R, Almeida J, Dybkaer K, Orfao A, Fuentes M. Dynamic Intracellular Metabolic Cell Signaling Profiles During Ag-Dependent B-Cell Differentiation. Front Immunol 2021; 12:637832. [PMID: 33859640 PMCID: PMC8043114 DOI: 10.3389/fimmu.2021.637832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/10/2021] [Indexed: 11/23/2022] Open
Abstract
Human B-cell differentiation has been extensively investigated on genomic and transcriptomic grounds; however, no studies have accomplished so far detailed analysis of antigen-dependent maturation-associated human B-cell populations from a proteomic perspective. Here, we investigate for the first time the quantitative proteomic profiles of B-cells undergoing antigen-dependent maturation using a label-free LC-MS/MS approach applied on 5 purified B-cell subpopulations (naive, centroblasts, centrocytes, memory and plasma B-cells) from human tonsils (data are available via ProteomeXchange with identifier PXD006191). Our results revealed that the actual differences among these B-cell subpopulations are a combination of expression of a few maturation stage-specific proteins within each B-cell subset and maturation-associated changes in relative protein expression levels, which are related with metabolic regulation. The considerable overlap of the proteome of the 5 studied B-cell subsets strengthens the key role of the regulation of the stoichiometry of molecules associated with metabolic regulation and programming, among other signaling cascades (such as antigen recognition and presentation and cell survival) crucial for the transition between each B-cell maturation stage.
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Affiliation(s)
- Paula Díez
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Martín Pérez-Andrés
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Martin Bøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Derio, Spain
| | | | - Rosa M Dégano
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Elena Blanco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Sheila Mateos-Gomez
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Paloma Bárcena
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Santiago Santa Cruz
- Service of Otolaryngology and Cervical Facial Pathology, University Hospital of Salamanca, Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Félix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Derio, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Pablo Juanes-Velasco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Victor Segura
- Division of Hepatology and Gene Therapy, Proteomics and BioInformatics Unit, Centre for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Raúl Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Julia Almeida
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Karen Dybkaer
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Alberto Orfao
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
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7
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Dunn J, Lenis VP, Hilton DA, Warta R, Herold-Mende C, Hanemann CO, Futschik ME. Integration and Comparison of Transcriptomic and Proteomic Data for Meningioma. Cancers (Basel) 2020; 12:E3270. [PMID: 33167358 PMCID: PMC7694371 DOI: 10.3390/cancers12113270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/03/2020] [Indexed: 12/17/2022] Open
Abstract
Meningioma are the most frequent primary intracranial tumour. Management of aggressive meningioma is complex, and development of effective biomarkers or pharmacological interventions is hampered by an incomplete knowledge of molecular landscape. Here, we present an integrated analysis of two complementary omics studies to investigate alterations in the "transcriptome-proteome" profile of high-grade (III) compared to low-grade (I) meningiomas. We identified 3598 common transcripts/proteins and revealed concordant up- and downregulation in grade III vs. grade I meningiomas. Concordantly upregulated genes included FABP7, a fatty acid binding protein and the monoamine oxidase MAOB, the latter of which we validated at the protein level and established an association with Food and Drug Administration (FDA)-approved drugs. Notably, we derived a plasma signature of 21 discordantly expressed genes showing positive changes in protein but negative in transcript levels of high-grade meningiomas, including the validated genes CST3, LAMP2, PACS1 and HTRA1, suggesting the acquisition of these proteins by tumour from plasma. Aggressive meningiomas were enriched in processes such as oxidative phosphorylation and RNA metabolism, whilst concordantly downregulated genes were related to reduced cellular adhesion. Overall, our study provides the first transcriptome-proteome characterisation of meningioma, identifying several novel and previously described transcripts/proteins with potential grade III biomarker and therapeutic significance.
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Affiliation(s)
- Jemma Dunn
- Faculty of Health: Medicine, Dentistry and Human Sciences, The Institute of Translational and Stratified Medicine, University of Plymouth, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK;
| | - Vasileios P. Lenis
- School of Health & Life Sciences, Centuria Building, Teesside University, Middlesbrough, Tees Valley TS1 3BX, UK;
| | - David A. Hilton
- Cellular and Anatomical Pathology, Plymouth Hospitals NHS Trust, Derriford Road, Plymouth PL6 8BU, UK;
| | - Rolf Warta
- Department of Neurosurgery, Division of Experimental Neurosurgery, Heidelberg University Hospital, 69120 Heidelberg, Germany; (R.W.); (C.H.-M.)
| | - Christel Herold-Mende
- Department of Neurosurgery, Division of Experimental Neurosurgery, Heidelberg University Hospital, 69120 Heidelberg, Germany; (R.W.); (C.H.-M.)
| | - C. Oliver Hanemann
- Faculty of Health: Medicine, Dentistry and Human Sciences, The Institute of Translational and Stratified Medicine, University of Plymouth, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK;
| | - Matthias E. Futschik
- Faculty of Medicine, School of Public Health, Imperial College London, Medical School, St Mary’s Hospital, Praed Street, London W2 1NY, UK
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8
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Jia Z, Zhao C, Wang M, Zhao X, Zhang W, Han T, Xia Q, Han Z, Lin R, Li X. Hepatotoxicity assessment of Rhizoma Paridis in adult zebrafish through proteomes and metabolome. Biomed Pharmacother 2020; 121:109558. [DOI: 10.1016/j.biopha.2019.109558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 10/08/2019] [Accepted: 10/17/2019] [Indexed: 12/20/2022] Open
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9
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Díez P, Góngora R, Orfao A, Fuentes M. Functional proteomic insights in B-cell chronic lymphocytic leukemia. Expert Rev Proteomics 2016; 14:137-146. [DOI: 10.1080/14789450.2017.1275967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
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10
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Díez P, Fuentes M. Proteogenomics for the Comprehensive Analysis of Human Cellular and Serum Antibody Repertoires. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 926:153-162. [PMID: 27686811 DOI: 10.1007/978-3-319-42316-6_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The vast repertoire of immunoglobulins produced by the immune system is a consequence of the huge amount of antigens to which we are exposed every day. The diversity of these immunoglobulins is due to different mechanisms (including VDJ recombination, somatic hypermutation, and antigen selection). Understanding how the immune system is capable of generating this diversity and which are the molecular bases of the composition of immunoglobulins are key challenges in the immunological field. During the last decades, several techniques have emerged as promising strategies to achieve these goals, but it is their combination which appears to be the fruitful solution for increasing the knowledge about human cellular and serum antibody repertoires.In this chapter, we address the diverse strategies focused on the analysis of immunoglobulin repertoires as well as the characterization of the genomic and peptide sequences. Moreover, the advantages of combining various -omics approaches are discussed through review different published studies, showing the benefits in clinical areas.
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Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra, S/N 37007, Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra, S/N 37007, Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra, S/N 37007, Salamanca, Spain. .,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra, S/N 37007, Salamanca, Spain.
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11
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Poverennaya EV, Kopylov AT, Ponomarenko EA, Ilgisonis EV, Zgoda VG, Tikhonova OV, Novikova SE, Farafonova TE, Kiseleva YY, Radko SP, Vakhrushev IV, Yarygin KN, Moshkovskii SA, Kiseleva OI, Lisitsa AV, Sokolov AS, Mazur AM, Prokhortchouk EB, Skryabin KG, Kostrjukova ES, Tyakht AV, Gorbachev AY, Ilina EN, Govorun VM, Archakov AI. State of the Art of Chromosome 18-Centric HPP in 2016: Transcriptome and Proteome Profiling of Liver Tissue and HepG2 Cells. J Proteome Res 2016; 15:4030-4038. [PMID: 27527821 DOI: 10.1021/acs.jproteome.6b00380] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A gene-centric approach was applied for a large-scale study of expression products of a single chromosome. Transcriptome profiling of liver tissue and HepG2 cell line was independently performed using two RNA-Seq platforms (SOLiD and Illumina) and also by Droplet Digital PCR (ddPCR) and quantitative RT-PCR. Proteome profiling was performed using shotgun LC-MS/MS as well as selected reaction monitoring with stable isotope-labeled standards (SRM/SIS) for liver tissue and HepG2 cells. On the basis of SRM/SIS measurements, protein copy numbers were estimated for the Chromosome 18 (Chr 18) encoded proteins in the selected types of biological material. These values were compared with expression levels of corresponding mRNA. As a result, we obtained information about 158 and 142 transcripts for HepG2 cell line and liver tissue, respectively. SRM/SIS measurements and shotgun LC-MS/MS allowed us to detect 91 Chr 18-encoded proteins in total, while an intersection between the HepG2 cell line and liver tissue proteomes was ∼66%. In total, there were 16 proteins specifically observed in HepG2 cell line, while 15 proteins were found solely in the liver tissue. Comparison between proteome and transcriptome revealed a poor correlation (R2 ≈ 0.1) between corresponding mRNA and protein expression levels. The SRM and shotgun data sets (obtained during 2015-2016) are available in PASSEL (PASS00697) and ProteomeExchange/PRIDE (PXD004407). All measurements were also uploaded into the in-house Chr 18 Knowledgebase at http://kb18.ru/protein/matrix/416126 .
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Affiliation(s)
| | - Arthur T Kopylov
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Elena A Ponomarenko
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | | | - Victor G Zgoda
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Olga V Tikhonova
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Svetlana E Novikova
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Tatyana E Farafonova
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Yana Yu Kiseleva
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Igor V Vakhrushev
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Konstantin N Yarygin
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Sergei A Moshkovskii
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.,Pirogov Russian National Research Medical University , Ostrovitianov Str. 1, Moscow 117997, Russia
| | - Olga I Kiseleva
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Andrey V Lisitsa
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Alexey S Sokolov
- Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia
| | - Alexander M Mazur
- Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia
| | - Egor B Prokhortchouk
- Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia
| | - Konstantin G Skryabin
- Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia
| | - Elena S Kostrjukova
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Alexander V Tyakht
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Alexey Yu Gorbachev
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Elena N Ilina
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Vadim M Govorun
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Alexander I Archakov
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
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12
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Paik YK, Omenn GS, Overall CM, Deutsch EW, Hancock WS. Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light. J Proteome Res 2016; 14:3409-14. [PMID: 26337862 DOI: 10.1021/acs.jproteome.5b00785] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - Gilbert S Omenn
- Center for Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan 48109, United States.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z3, Canada.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - Eric W Deutsch
- Institute for Systems Biology , Seattle, Washington 98109, United States.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - William S Hancock
- Department of Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
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13
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Sallou O, Duek PD, Darde TA, Collin O, Lane L, Chalmel F. PepPSy: a web server to prioritize gene products in experimental and biocuration workflows. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw070. [PMID: 27173522 PMCID: PMC4865363 DOI: 10.1093/database/baw070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 04/13/2016] [Indexed: 12/03/2022]
Abstract
Among the 20 000 human gene products predicted from genome annotation, about 3000 still lack validation at protein level. We developed PepPSy, a user-friendly gene expression-based prioritization system, to help investigators to determine in which human tissues they should look for an unseen protein. PepPSy can also be used by biocurators to revisit the annotation of specific categories of proteins based on the ‘omics’ data housed by the system. In this study, it was used to prioritize 21 dubious protein-coding genes among the 616 annotated in neXtProt for reannotation. PepPSy is freely available at http://peppsy.genouest.org. Database URL:http://peppsy.genouest.org.
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Affiliation(s)
- Olivier Sallou
- Genouest Bioinformatics Platform, IRISA, Campus de Beaulieu, Rennes 35042, France
| | - Paula D Duek
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, CMU, Michel Servet 1, Geneva 1211, Switzerland
| | - Thomas A Darde
- Genouest Bioinformatics Platform, IRISA, Campus de Beaulieu, Rennes 35042, France IRSET, Inserm U1085, 9 avenue du Professeur Léon Bernard, Rennes 35000, France
| | - Olivier Collin
- Genouest Bioinformatics Platform, IRISA, Campus de Beaulieu, Rennes 35042, France
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, CMU, Michel Servet 1, Geneva 1211, Switzerland Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, CMU, Michel Servet 1, Geneva 1211, Switzerland
| | - Frédéric Chalmel
- IRSET, Inserm U1085, 9 avenue du Professeur Léon Bernard, Rennes 35000, France
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14
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Gioria S, Lobo Vicente J, Barboro P, La Spina R, Tomasi G, Urbán P, Kinsner-Ovaskainen A, François R, Chassaigne H. A combined proteomics and metabolomics approach to assess the effects of gold nanoparticles in vitro. Nanotoxicology 2016; 10:736-48. [PMID: 26647645 PMCID: PMC4898143 DOI: 10.3109/17435390.2015.1121412] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Omics technologies, such as proteomics or metabolomics, have to date been applied in the field of nanomaterial safety assessment to a limited extent. To address this dearth, we developed an integrated approach combining the two techniques to study the effects of two sizes, 5 and 30 nm, of gold nanoparticles (AuNPs) in Caco-2 cells. We observed differences in cells exposed for 72 h to each size of AuNPs: 61 responsive (up/down-regulated) proteins were identified and 35 metabolites in the cell extract were tentatively annotated. Several altered biological pathways were highlighted by integrating the obtained multi-omics data with bioinformatic tools. This provided a unique set of molecular information on the effects of nanomaterials at cellular level. This information was supported by complementary data obtained by immunochemistry, microscopic analysis, and multiplexed assays. A part from increasing our knowledge on how the cellular processes and pathways are affected by nanomaterials (NMs), these findings could be used to identify specific biomarkers of toxicity or to support the safe-by-design concept in the development of new nanomedicines.
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Affiliation(s)
- Sabrina Gioria
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
| | - Joana Lobo Vicente
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
| | - Paola Barboro
- b IRCCS Azienda Ospedaliera Universitaria San Martino - IST Istituto Nazionale per la Ricerca sul Cancro , Genova , Italy
| | - Rita La Spina
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
| | - Giorgio Tomasi
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
| | - Patricia Urbán
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
| | | | - Rossi François
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
| | - Hubert Chassaigne
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
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