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Wu D, Zheng K, Yin W, Hu B, Yu M, Yu Q, Wei X, Deng J, Zhang C. Enhanced osteochondral regeneration with a 3D-Printed biomimetic scaffold featuring a calcified interfacial layer. Bioact Mater 2024; 36:317-329. [PMID: 38496032 PMCID: PMC10940945 DOI: 10.1016/j.bioactmat.2024.03.004] [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: 11/14/2023] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
The integrative regeneration of both articular cartilage and subchondral bone remains an unmet clinical need due to the difficulties of mimicking spatial complexity in native osteochondral tissues for artificial implants. Layer-by-layer fabrication strategies, such as 3D printing, have emerged as a promising technology replicating the stratified zonal architecture and varying microstructures and mechanical properties. However, the dynamic and circulating physiological environments, such as mass transportation or cell migration, usually distort the pre-confined biological properties in the layered implants, leading to undistinguished spatial variations and subsequently inefficient regenerations. This study introduced a biomimetic calcified interfacial layer into the scaffold as a compact barrier between a cartilage layer and a subchondral bone layer to facilitate osteogenic-chondrogenic repair. The calcified interfacial layer consisting of compact polycaprolactone (PCL), nano-hydroxyapatite, and tasquinimod (TA) can physically and biologically separate the cartilage layer (TA-mixed, chondrocytes-load gelatin methacrylate) from the subchondral bond layer (porous PCL). This introduction preserved the as-designed independent biological environment in each layer for both cartilage and bone regeneration, successfully inhibiting vascular invasion into the cartilage layer and preventing hyaluronic cartilage calcification owing to devascularization of TA. The improved integrative regeneration of cartilage and subchondral bone was validated through gross examination, micro-computed tomography (micro-CT), and histological and immunohistochemical analyses based on an in vivo rat model. Moreover, gene and protein expression studies identified a key role of Caveolin (CAV-1) in promoting angiogenesis through the Wnt/β-catenin pathway and indicated that TA in the calcified layer blocked angiogenesis by inhibiting CAV-1.
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Affiliation(s)
- Di Wu
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.600 Yishan Road, Shanghai, 200233, China
| | - Kaiwen Zheng
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.600 Yishan Road, Shanghai, 200233, China
| | - Wenjing Yin
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.600 Yishan Road, Shanghai, 200233, China
| | - Bin Hu
- Institute of Microsurgery on Extremities, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.600 Yishan Road, Shanghai, 200233, China
| | - Mingzhao Yu
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.600 Yishan Road, Shanghai, 200233, China
| | - Qingxiao Yu
- Shanghai Uniorlechnology Corporation, No. 258 Xinzhuan Road, Shanghai, 201612, China
| | - Xiaojuan Wei
- Institute of Microsurgery on Extremities, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.600 Yishan Road, Shanghai, 200233, China
| | - Jue Deng
- Academy for Engineering & Technology, Fudan University, No. 220 Handan Road, Shanghai, 200433, China
| | - Changqing Zhang
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.600 Yishan Road, Shanghai, 200233, China
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2
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Giusti SA, Pino NS, Pannunzio C, Ogando MB, Armando NG, Garrett L, Zimprich A, Becker L, Gimeno ML, Lukin J, Merino FL, Pardi MB, Pedroncini O, Di Mauro GC, Durner VG, Fuchs H, de Angelis MH, Patop IL, Turck CW, Deussing JM, Vogt Weisenhorn DM, Jahn O, Kadener S, Hölter SM, Brose N, Giesert F, Wurst W, Marin-Burgin A, Refojo D. A brain-enriched circular RNA controls excitatory neurotransmission and restricts sensitivity to aversive stimuli. SCIENCE ADVANCES 2024; 10:eadj8769. [PMID: 38787942 PMCID: PMC11122670 DOI: 10.1126/sciadv.adj8769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/22/2024] [Indexed: 05/26/2024]
Abstract
Circular RNAs (circRNAs) are a large class of noncoding RNAs. Despite the identification of thousands of circular transcripts, the biological significance of most of them remains unexplored, partly because of the lack of effective methods for generating loss-of-function animal models. In this study, we focused on circTulp4, an abundant circRNA derived from the Tulp4 gene that is enriched in the brain and synaptic compartments. By creating a circTulp4-deficient mouse model, in which we mutated the splice acceptor site responsible for generating circTulp4 without affecting the linear mRNA or protein levels, we were able to conduct a comprehensive phenotypic analysis. Our results demonstrate that circTulp4 is critical in regulating neuronal and brain physiology, modulating the strength of excitatory neurotransmission and sensitivity to aversive stimuli. This study provides evidence that circRNAs can regulate biologically relevant functions in neurons, with modulatory effects at multiple levels of the phenotype, establishing a proof of principle for the regulatory role of circRNAs in neural processes.
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Affiliation(s)
- Sebastian A. Giusti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Buenos Aires, Argentina
- Molecular Neurobiology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Natalia S. Pino
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Camila Pannunzio
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Mora B. Ogando
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Natalia G. Armando
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Lillian Garrett
- German Mouse Clinic, Helmholtz Zentrum München, Munich, Germany
| | - Annemarie Zimprich
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Mouse Clinic, Helmholtz Zentrum München, Munich, Germany
- Chair of Developmental Genetics, Munich School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Lore Becker
- German Mouse Clinic, Helmholtz Zentrum München, Munich, Germany
| | - Maria L. Gimeno
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Jeronimo Lukin
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Florencia L. Merino
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - M. Belen Pardi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Olivia Pedroncini
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Giuliana C. Di Mauro
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | | | - Helmut Fuchs
- German Mouse Clinic, Helmholtz Zentrum München, Munich, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Helmholtz Zentrum München, Munich, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | | | - Christoph W. Turck
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Jan M. Deussing
- Molecular Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Daniela M. Vogt Weisenhorn
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Chair of Developmental Genetics, Munich School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Olaf Jahn
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg-August-University, Göttingen, Germany
| | | | - Sabine M. Hölter
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Chair of Developmental Genetics, Munich School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE) Site Munich, Munich, Germany
| | - Antonia Marin-Burgin
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Damian Refojo
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Buenos Aires, Argentina
- Molecular Neurobiology, Max Planck Institute of Psychiatry, Munich, Germany
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3
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Duława-Kobeluszczyk J, Strzałka A, Tracz M, Bartyńska M, Pawlikiewicz K, Łebkowski T, Wróbel S, Szymczak J, Zarek A, Małecki T, Jakimowicz D, Szafran MJ. The activity of CobB1 protein deacetylase contributes to nucleoid compaction in Streptomyces venezuelae spores by increasing HupS affinity for DNA. Nucleic Acids Res 2024:gkae418. [PMID: 38783097 DOI: 10.1093/nar/gkae418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Streptomyces are soil bacteria with complex life cycle. During sporulation Streptomyces linear chromosomes become highly compacted so that the genetic material fits within limited spore volume. The key players in this process are nucleoid-associated proteins (NAPs). Among them, HU (heat unstable) proteins are the most abundant NAPs in the cell and the most conserved in bacteria. HupS, one of the two HU homologues encoded by the Streptomyces genome, is the best-studied spore-associated NAP. In contrast to other HU homologues, HupS contains a long, C-terminal domain that is extremely rich in lysine repeats (LR domain) similar to eukaryotic histone H2B and mycobacterial HupB protein. Here, we have investigated, whether lysine residues in HupS are posttranslationally modified by reversible lysine acetylation. We have confirmed that Streptomyces venezuelae HupS is acetylated in vivo. We showed that HupS binding to DNA in vitro is controlled by the acetylation. Moreover, we identified that CobB1, one of two Sir2 homologues in Streptomyces, controls HupS acetylation levels in vivo. We demonstrate that the elimination of CobB1 increases HupS mobility, reduces chromosome compaction in spores, and affects spores maturation. Thus, our studies indicate that HupS acetylation affects its function by diminishing DNA binding and disturbing chromosome organization.
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Affiliation(s)
| | | | - Michał Tracz
- Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
| | | | | | - Tomasz Łebkowski
- Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
| | - Sara Wróbel
- Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
| | - Justyna Szymczak
- Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
| | - Anna Zarek
- Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
| | - Tomasz Małecki
- Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
| | | | - Marcin J Szafran
- Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
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4
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Wang J, Tan H, Fu Y, Mishra A, Sun H, Wang Z, Wu Z, Wang X, Serrano GE, Beach TG, Peng J, High AA. Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 38754071 DOI: 10.1021/jasms.4c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Accurate and precise quantification is crucial in modern proteomics, particularly in the context of exploring low-amount samples. While the innovative 4D-data-independent acquisition (DIA) quantitative proteomics facilitated by timsTOF mass spectrometers gives enhanced sensitivity and selectivity for protein identification, the diaPASEF (parallel accumulation-serial fragmentation combined with data-independent acquisition) parameters have not been systematically optimized, and a comprehensive evaluation of the quantification is currently lacking. In this study, we conducted a thorough optimization of key parameters on a timsTOF SCP instrument, including sample loading amount (50 ng), ramp/accumulation time (140 ms), isolation window width (20 m/z), and gradient time (60 min). To further improve the identification of proteins in low-amount samples, we utilized different column settings and introduced 0.02% n-dodecyl-β-d-maltoside (DDM) in the sample reconstitution solution, resulting in a remarkable 19-fold increase in protein identification at the single-cell-equivalent level. Moreover, a comprehensive comparison of protein quantification using a tandem mass tag reporter (TMT-reporter), complement TMT ions (TMTc), and diaPASEF revealed a strong correlation between these methods. Both diaPASEF and TMTc have effectively addressed the issue of ratio compression, highlighting the diaPASEF method's effectiveness in achieving accurate quantification data compared to TMT reporter quantification. Additionally, an in-depth analysis of in-group variation positioned diaPASEF between the TMT-reporter and TMTc methods. Therefore, diaPASEF quantification on the timsTOF SCP instrument emerges as a precise and accurate methodology for quantitative proteomics, especially for samples with small amounts.
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Affiliation(s)
- Ju Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yingxue Fu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Huan Sun
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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5
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da Paschoa RP, Pinto VB, Pereira JP, Cavatte PC, Garbin ML, Godinho T, Xavier LR, Carrijo TT, Silveira V. Proteomic and physiological signatures of altitude adaptation in a Myrsine coriacea population under common garden conditions. J Proteomics 2024; 299:105156. [PMID: 38467267 DOI: 10.1016/j.jprot.2024.105156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 03/13/2024]
Abstract
Plants exhibit phenotypic plasticity in response to environmental variations, which can lead to stable genetic and physiological adaptations if exposure to specific conditions is prolonged. Myrsine coriacea demonstrates this through its ability to thrive in diverse environments. The objective of the article is to investigate potential differences in protein accumulation and physiological responses of M. coriacea by cultivating plants from seeds collected from four populations at different altitudes in a common garden experiment. Additionally, we aim to evaluate whether these differences exhibit genetic fixation. Through integrated physiological and proteomic analyses, we identified 170 differentially accumulated proteins and observed significant physiological differences among the populations. The high-altitude population (POP1) exhibited a unique proteomic profile with significant down-regulation of proteins involved in carbon fixation and energy metabolism, suggesting a potential reduction in photosynthetic efficiency. Physiological analyses showed lower leaf nitrogen content, net CO2 assimilation rate, specific leaf area, and relative growth rate in stem height for POP1, alongside higher leaf carbon isotopic composition (δ13C) and leaf carbon (C) content. These findings provide insight into the complex interplay between proteomic and physiological adaptations in M. coriacea and underscore the importance of local adaptations. SIGNIFICANCE: We investigate the adaptive responses of M. coriacea, a shrub with a broad phenotypic range, by cultivating plants from seeds collected at four different altitudes in a common garden experiment. These findings provide insight into the complex interplay between proteomic and physiological adaptations in M. coriacea and underscore the importance of local adaptations in the face of climate change. This study contributes to advancing our understanding of the influence of altitude-specific selection pressures on the molecular biology and physiology of plants in natural populations. Our findings provide valuable insights that enhance our ability to predict and comprehend how plants respond to climate change.
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Affiliation(s)
- Roberta Pena da Paschoa
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Brazil
| | | | - Jéssica Priscilla Pereira
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Depto. Biologia, Lab. Botânica, Alto Universitário, Guararema, Alegre, ES, Brazil
| | - Paulo Cezar Cavatte
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Depto. Biologia, Lab. Botânica, Alto Universitário, Guararema, Alegre, ES, Brazil
| | - Mário Luís Garbin
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Depto. Biologia, Lab. Botânica, Alto Universitário, Guararema, Alegre, ES, Brazil
| | - Tiago Godinho
- Reserva Natural Vale, Rodovia BR 101, km 122 s/n Zona Rural, Linhares, ES 29900-111, Brazil
| | - Lucas Rodrigues Xavier
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Brazil
| | - Tatiana Tavares Carrijo
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Depto. Biologia, Lab. Botânica, Alto Universitário, Guararema, Alegre, ES, Brazil.
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Brazil.
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6
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Marassi V, La Rocca G, Placci A, Muntiu A, Vincenzoni F, Vitali A, Desiderio C, Maraldi T, Beretti F, Russo E, Miceli V, Conaldi PG, Papait A, Romele P, Cargnoni A, Silini AR, Alviano F, Parolini O, Giordani S, Zattoni A, Reschiglian P, Roda B. Native characterization and QC profiling of human amniotic mesenchymal stromal cell vesicular fractions for secretome-based therapy. Talanta 2024; 276:126216. [PMID: 38761653 DOI: 10.1016/j.talanta.2024.126216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/09/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024]
Abstract
Human amniotic mesenchymal stromal cells (hAMSCs) have unique immunomodulatory properties making them attractive candidates for regenerative applications in inflammatory diseases. Most of their beneficial properties are mediated through their secretome. The bioactive factors concurring to its therapeutic activity are still unknown. Evidence suggests synergy between the two main components of the secretome, soluble factors and vesicular fractions, pivotal in shifting inflammation and promoting self-healing. Biological variability and the absence of quality control (QC) protocols hinder secretome-based therapy translation to clinical applications. Moreover, vesicular secretome contains a multitude of particles with varying size, cargos and functions whose complexity hinders full characterization and comprehension. This study achieved a significant advancement in secretome characterization by utilizing native, FFF-based separation and characterizing extracellular vesicles derived from hAMSCs. This was accomplished by obtaining dimensionally homogeneous fractions then characterized based on their protein content, potentially enabling the identification of subpopulations with diverse functionalities. This method proved to be successful as an independent technique for secretome profiling, with the potential to contribute to the standardization of a qualitative method. Additionally, it served as a preparative separation tool, streamlining populations before ELISA and LC-MS characterization. This approach facilitated the categorization of distinctive and recurring proteins, along with the identification of clusters associated with vesicle activity and functions. However, the presence of proteins unique to each fraction obtained through the FFF separation tool presents a challenge for further analysis of the protein content within these cargoes.
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Affiliation(s)
- Valentina Marassi
- Department of Chemistry G. Ciamician, University of Bologna, Italy; byFlow srl, Bologna, Italy
| | - Giampiero La Rocca
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127, Palermo, Italy
| | - Anna Placci
- Department of Chemistry G. Ciamician, University of Bologna, Italy
| | - Alexandra Muntiu
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", Consiglio Nazionale delle Ricerche, 00168, Rome, Italy
| | - Federica Vincenzoni
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Alberto Vitali
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", Consiglio Nazionale delle Ricerche, 00168, Rome, Italy
| | - Claudia Desiderio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", Consiglio Nazionale delle Ricerche, 00168, Rome, Italy
| | - Tullia Maraldi
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Francesca Beretti
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Eleonora Russo
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127, Palermo, Italy
| | - Vitale Miceli
- Research Department, IRCCS ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad alta Specializzazione), 90127, Palermo, Italy
| | - Pier Giulio Conaldi
- Research Department, IRCCS ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad alta Specializzazione), 90127, Palermo, Italy
| | - Andrea Papait
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy; Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Pietro Romele
- Centro di Ricerca E. Menni, Fondazione Poliambulanza Istituto Ospedaliero, 25124, Brescia, Italy
| | - Anna Cargnoni
- Centro di Ricerca E. Menni, Fondazione Poliambulanza Istituto Ospedaliero, 25124, Brescia, Italy
| | - Antonietta Rosa Silini
- Centro di Ricerca E. Menni, Fondazione Poliambulanza Istituto Ospedaliero, 25124, Brescia, Italy
| | - Francesco Alviano
- Department of Biomedical and Neuromotor Science, University of Bologna, Bologna, Italy
| | - Ornella Parolini
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy; Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Stefano Giordani
- Department of Chemistry G. Ciamician, University of Bologna, Italy
| | - Andrea Zattoni
- Department of Chemistry G. Ciamician, University of Bologna, Italy; byFlow srl, Bologna, Italy
| | - Pierluigi Reschiglian
- Department of Chemistry G. Ciamician, University of Bologna, Italy; byFlow srl, Bologna, Italy
| | - Barbara Roda
- Department of Chemistry G. Ciamician, University of Bologna, Italy; byFlow srl, Bologna, Italy.
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7
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Abiola J, Berg AM, Aiyelaagbe O, Adeyi A, König S. Dabsylated Bradykinin Is Cleaved by Snake Venom Proteases from Echis ocellatus. Biomedicines 2024; 12:1027. [PMID: 38790989 PMCID: PMC11118064 DOI: 10.3390/biomedicines12051027] [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: 03/04/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
The vasoactive peptide bradykinin (BK) is an important member of the renin-angiotensin system. Its discovery is tightly interwoven with snake venom research, because it was first detected in plasma following the addition of viper venom. While the fact that venoms liberate BK from a serum globulin fraction is well described, its destruction by the venom has largely gone unnoticed. Here, BK was found to be cleaved by snake venom metalloproteinases in the venom of Echis ocellatus, one of the deadliest snakes, which degraded its dabsylated form (DBK) in a few minutes after Pro7 (RPPGFSP↓FR). This is a common cleavage site for several mammalian proteases such as ACE, but is not typical for matrix metalloproteinases. Residual protease activity < 5% after addition of EDTA indicated that DBK is also cleaved by serine proteases to a minor extent. Mass spectrometry-based protein analysis provided spectral proof for several peptides of zinc metalloproteinase-disintegrin-like Eoc1, disintegrin EO4A, and three serine proteases in the venom.
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Affiliation(s)
- Julius Abiola
- IZKF Core Unit Proteomics, Interdisciplinary Center for Clinical Research, University of Münster, Röntgenstr. 21, 48149 Münster, Germany; (J.A.)
- Organic Unit, Department of Chemistry, University of Ibadan, Ibadan 200005, Nigeria
| | - Anna Maria Berg
- IZKF Core Unit Proteomics, Interdisciplinary Center for Clinical Research, University of Münster, Röntgenstr. 21, 48149 Münster, Germany; (J.A.)
| | - Olapeju Aiyelaagbe
- Organic Unit, Department of Chemistry, University of Ibadan, Ibadan 200005, Nigeria
| | - Akindele Adeyi
- Animal Physiology Unit, Department of Zoology, University of Ibadan, Ibadan 200005, Nigeria
| | - Simone König
- IZKF Core Unit Proteomics, Interdisciplinary Center for Clinical Research, University of Münster, Röntgenstr. 21, 48149 Münster, Germany; (J.A.)
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8
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Pereira Duarte R, Cancela Ramos HC, Rodrigues Xavier L, Azevedo Vimercati Pirovani A, Souza Rodrigues A, Turquetti-Moraes DK, Rodrigues da Silva Junior I, Motta Venâncio T, Silveira V, Gonzaga Pereira M. Comparative proteomic analysis of papaya bud flowers reveals metabolic signatures and pathways driving hermaphrodite development. Sci Rep 2024; 14:8867. [PMID: 38632280 PMCID: PMC11024100 DOI: 10.1038/s41598-024-59306-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Papaya (Carica papaya) is a trioecious species with female, male, and hermaphrodite plants. Given the sex segregation, selecting hermaphroditic plants is vital for orchard establishment due to their greater commercial value. However, selecting hermaphrodite plants through sexing is laborious and costly. Moreover, environmental stressors can exacerbate the issue by potentially inducing abnormal flower development, thus affecting fruit quality. Despite these challenges, the molecular mechanisms governing sex development in papaya remain poorly understood. Thus, this study aimed to identify proteins associated with sex development in female and hermaphrodite flowers of papaya through comparative proteomic analysis. Proteins from flower buds at the early and late developmental stages of three papaya genotypes (UENF-CALIMAN 01, JS12, and Sunrise Solo 72/12) were studied via proteomic analysis via the combination of the shotgun method and nanoESI-HDMSE technology. In buds at an early stage of development, 496 (35.9%) proteins exhibited significantly different abundances between sexes for the SS72/12 genotype, 139 (10%) for the JS12 genotype, and 165 (11.9%) for the UC-01 genotype. At the final stage of development, there were 181 (13.5%) for SS72/12, 113 (8.4%) for JS12, and 125 (9.1%) for UC-01. The large group of differentially accumulated proteins (DAPs) between the sexes was related to metabolism, as shown by the observation of only the proteins that exhibited the same pattern of accumulation in the three genotypes. Specifically, carbohydrate metabolism proteins were up-regulated in hermaphrodite flower buds early in development, while those linked to monosaccharide and amino acid metabolism increased during late development. Enrichment of sporopollenin and phenylpropanoid biosynthesis pathways characterizes hermaphrodite samples across developmental stages, with predicted protein interactions highlighting the crucial role of phenylpropanoids in sporopollenin biosynthesis for pollen wall formation. Most of the DAPs played key roles in pectin, cellulose, and lignin synthesis and were essential for cell wall formation and male flower structure development, notably in the pollen coat. These findings suggest that hermaphrodite flowers require more energy for development, likely due to complex pollen wall formation. Overall, these insights illuminate the molecular mechanisms of papaya floral development, revealing complex regulatory networks and energetic demands in the formation of male reproductive structures.
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Affiliation(s)
- Rafaela Pereira Duarte
- Laboratório de Melhoramento Genético Vegetal - LMGV, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil.
| | - Helaine Christine Cancela Ramos
- Laboratório de Melhoramento Genético Vegetal - LMGV, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Lucas Rodrigues Xavier
- Laboratório de Biotecnologia - LBT, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Adriana Azevedo Vimercati Pirovani
- Laboratório de Melhoramento Genético Vegetal - LMGV, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Alex Souza Rodrigues
- Laboratório de Melhoramento Genético Vegetal - LMGV, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Dayana Kelly Turquetti-Moraes
- Laboratório de Química e Função de Proteínas e Peptídeos - LQFPP, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Izaias Rodrigues da Silva Junior
- Laboratório de Melhoramento Genético Vegetal - LMGV, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Thiago Motta Venâncio
- Laboratório de Química e Função de Proteínas e Peptídeos - LQFPP, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia - LBT, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Messias Gonzaga Pereira
- Laboratório de Melhoramento Genético Vegetal - LMGV, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
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9
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de Souza WM, Fumagalli MJ, de Lima STS, Parise PL, Carvalho DCM, Hernandez C, de Jesus R, Delafiori J, Candido DS, Carregari VC, Muraro SP, Souza GF, Simões Mello LM, Claro IM, Díaz Y, Kato RB, Trentin LN, Costa CHS, Maximo ACBM, Cavalcante KF, Fiuza TS, Viana VAF, Melo MEL, Ferraz CPM, Silva DB, Duarte LMF, Barbosa PP, Amorim MR, Judice CC, Toledo-Teixeira DA, Ramundo MS, Aguilar PV, Araújo ELL, Costa FTM, Cerqueira-Silva T, Khouri R, Boaventura VS, Figueiredo LTM, Fang R, Moreno B, López-Vergès S, Mello LP, Skaf MS, Catharino RR, Granja F, Martins-de-Souza D, Plante JA, Plante KS, Sabino EC, Diamond MS, Eugenin E, Proença-Módena JL, Faria NR, Weaver SC. Pathophysiology of chikungunya virus infection associated with fatal outcomes. Cell Host Microbe 2024; 32:606-622.e8. [PMID: 38479396 PMCID: PMC11018361 DOI: 10.1016/j.chom.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/08/2023] [Accepted: 02/16/2024] [Indexed: 03/28/2024]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes acute, subacute, and chronic human arthritogenic diseases and, in rare instances, can lead to neurological complications and death. Here, we combined epidemiological, virological, histopathological, cytokine, molecular dynamics, metabolomic, proteomic, and genomic analyses to investigate viral and host factors that contribute to chikungunya-associated (CHIK) death. Our results indicate that CHIK deaths are associated with multi-organ infection, central nervous system damage, and elevated serum levels of pro-inflammatory cytokines and chemokines compared with survivors. The histopathologic, metabolite, and proteomic signatures of CHIK deaths reveal hemodynamic disorders and dysregulated immune responses. The CHIKV East-Central-South-African lineage infecting our study population causes both fatal and survival cases. Additionally, CHIKV infection impairs the integrity of the blood-brain barrier, as evidenced by an increase in permeability and altered tight junction protein expression. Overall, our findings improve the understanding of CHIK pathophysiology and the causes of fatal infections.
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Affiliation(s)
- William M de Souza
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, College of Medicine, Lexington, KY, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Global Virus Network, Baltimore, MD, USA.
| | - Marcilio J Fumagalli
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Shirlene T S de Lima
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil; Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Pierina L Parise
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Deyse C M Carvalho
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Laboratory of Immunobiotechnology, Biotechnology Center, Federal University of Paraíba, João Pessoa, Paraíba, Brazil
| | - Cristian Hernandez
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ronaldo de Jesus
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jeany Delafiori
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Darlan S Candido
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Victor C Carregari
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Stefanie P Muraro
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Gabriela F Souza
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Ingra M Claro
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Yamilka Díaz
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama
| | - Rodrigo B Kato
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lucas N Trentin
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Clauber H S Costa
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - Tayna S Fiuza
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil; Programa de Pós Graduação em Bioinformática, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Vânia A F Viana
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil
| | | | | | - Débora B Silva
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil
| | | | - Priscilla P Barbosa
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Mariene R Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Carla C Judice
- Laboratory of Tropical Diseases, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Daniel A Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Mariana S Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Patricia V Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Center for Tropical Diseases, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Emerson L L Araújo
- Coordenação Geral de Atenção às Doenças Transmissíveis na Atenção Primária, Departamento de Gestão ao cuidado Integral, Secretaria de Atenção Primária à Saúde, Ministério da Saúde, Brasília, Brazil
| | - Fabio T M Costa
- Laboratory of Tropical Diseases, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Thiago Cerqueira-Silva
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil
| | - Ricardo Khouri
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil
| | - Viviane S Boaventura
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil; Hospital Santa Izabel, Santa Casa de Misericórdia da Bahia, Serviço de Otorrinolaringologia, Salvador, Bahia, Brazil
| | - Luiz Tadeu M Figueiredo
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rong Fang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Brechla Moreno
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama
| | - Sandra López-Vergès
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama; Sistema Nacional de Investigación from SENACYT, Panama, Panama
| | | | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Rodrigo R Catharino
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; Biodiversity Research Centre, Federal University of Roraima, Boa Vista, Roraima, Brazil
| | - Daniel Martins-de-Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; D'Or Institute for Research and Education, São Paulo, São Paulo, Brazil; Experimental Medicine Research Cluster, University of Campinas, Campinas, São Paulo, Brazil
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Eliseo Eugenin
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX, USA
| | - José Luiz Proença-Módena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Global Virus Network, Baltimore, MD, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
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10
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Carregari VC, Reis-de-Oliveira G, Crunfli F, Smith BJ, de Souza GF, Muraro SP, Saia-Cereda VM, Vendramini PH, Baldasso PA, Silva-Costa LC, Zuccoli GS, Brandão-Teles C, Antunes A, Valença AF, Davanzo GG, Virgillio-da-Silva JV, Dos Reis Araújo T, Guimarães RC, Chaim FDM, Chaim EA, Kawagosi Onodera CM, Ludwig RG, Saccon TD, Damásio ARL, Leiria LOS, Vinolo MAR, Farias AS, Moraes-Vieira PM, Mori MA, Módena JLP, Martins-de-Souza D. Diving into the proteomic atlas of SARS-CoV-2 infected cells. Sci Rep 2024; 14:7375. [PMID: 38548777 PMCID: PMC10978884 DOI: 10.1038/s41598-024-56328-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/05/2024] [Indexed: 04/01/2024] Open
Abstract
The COVID-19 pandemic was initiated by the rapid spread of a SARS-CoV-2 strain. Though mainly classified as a respiratory disease, SARS-CoV-2 infects multiple tissues throughout the human body, leading to a wide range of symptoms in patients. To better understand how SARS-CoV-2 affects the proteome from cells with different ontologies, this work generated an infectome atlas of 9 cell models, including cells from brain, blood, digestive system, and adipocyte tissue. Our data shows that SARS-CoV-2 infection mainly trigger dysregulations on proteins related to cellular structure and energy metabolism. Despite these pivotal processes, heterogeneity of infection was also observed, highlighting many proteins and pathways uniquely dysregulated in one cell type or ontological group. These data have been made searchable online via a tool that will permit future submissions of proteomic data ( https://reisdeoliveira.shinyapps.io/Infectome_App/ ) to enrich and expand this knowledgebase.
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Affiliation(s)
- Victor C Carregari
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Guilherme Reis-de-Oliveira
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Fernanda Crunfli
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Bradley J Smith
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Gabriela Fabiano de Souza
- Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Stéfanie Primon Muraro
- Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Veronica M Saia-Cereda
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Pedro H Vendramini
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Paulo A Baldasso
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Lícia C Silva-Costa
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Giuliana S Zuccoli
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Caroline Brandão-Teles
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - André Antunes
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Aline F Valença
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Gustavo G Davanzo
- Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - João Victor Virgillio-da-Silva
- Department of Pharmacology, Ribeirão Preto Medical School (FMRP), University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto, SP, Brazil
| | | | - Raphael Campos Guimarães
- Center for Research in Inflammatory Diseases, Ribeirão Preto, SP, Brazil
- Obesity and Comorbidities Research Center (OCRC), Campinas, São Paulo, Brazil
| | | | - Elinton Adami Chaim
- Department of Surgery, Faculty of Medical Sciences, University of Campinas, Campinas, SP, Brazil
| | | | - Raissa Guimarães Ludwig
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Tatiana Dandolini Saccon
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - André R L Damásio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Luiz Osório S Leiria
- Department of Pharmacology, Ribeirão Preto Medical School (FMRP), University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto, SP, Brazil
| | - Marco Aurélio R Vinolo
- Obesity and Comorbidities Research Center (OCRC), Campinas, São Paulo, Brazil
- Hematology-Hemotherapy Center, University of Campinas, Campinas, SP, Brazil
- Laboratory of Immunoinflammation, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Alessandro S Farias
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Científico e Tecnológico, São Paulo, 05403-000, Brazil
- D'Or Institute for Research and Education (IDOR), São Paulo, 04501-000, Brazil
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Pedro M Moraes-Vieira
- Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
- Obesity and Comorbidities Research Center (OCRC), Campinas, São Paulo, Brazil
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Department of Pharmacology, Ribeirão Preto Medical School (FMRP), University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
- Laboratory of Immunoinflammation, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - José Luiz P Módena
- Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
- D'Or Institute for Research and Education (IDOR), São Paulo, 04501-000, Brazil.
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
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11
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Conforti JM, Ziegler AM, Worth CS, Nambiar AM, Bailey JT, Taube JH, Gallagher ES. Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584881. [PMID: 38559195 PMCID: PMC10980087 DOI: 10.1101/2024.03.13.584881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The goal of proteomics experiments is to identify proteins to observe changes in cellular processes and diseases. One challenge in proteomics is the removal of contaminants following protein extraction, which can limit protein identification. Single-pot, solid-phase-enhanced sample preparation (SP3) is a clean-up technique in which proteins are captured on carboxylate-modified particles through a proposed hydrophilic-interaction-liquid-chromatography (HILIC)-like mechanism. However, recent results have suggested that proteins are captured in SP3 due to a protein-aggregation mechanism. Thus, solvent precipitation, single-pot, solid-phase-enhanced sample preparation (SP4) is a newer clean-up technique that employs protein-aggregation to capture proteins without modified particles. SP4 has previously enriched low-solubility proteins, though differences in protein capture could affect which proteins are detected and identified. We hypothesize that the mechanisms of capture for SP3 and SP4 are distinct. Herein, we assess the proteins identified and enriched using SP3 versus SP4 for MCF7 subcellular fractions and correlate protein capture in each method to protein hydrophobicity. Our results indicate that SP3 captures more hydrophilic proteins through a combination of HILIC-like and protein-aggregation mechanisms, while SP4 captures more hydrophobic proteins through a protein-aggregation mechanism. From these results, we recommend clean-up techniques based on protein-sample hydrophobicity to yield high proteome coverage in biological samples.
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Affiliation(s)
- Jessica M. Conforti
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Amanda M. Ziegler
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Charli S. Worth
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Adhwaitha M. Nambiar
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Jacob T. Bailey
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Joseph H. Taube
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Elyssia S. Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
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12
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König S, Schork K, Eisenacher M. Observations from the Proteomics Bench. Proteomes 2024; 12:6. [PMID: 38390966 PMCID: PMC10885119 DOI: 10.3390/proteomes12010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
Many challenges in proteomics result from the high-throughput nature of the experiments. This paper first presents pre-analytical problems, which still occur, although the call for standardization in omics has been ongoing for many years. This article also discusses aspects that affect bioinformatic analysis based on three sets of reference data measured with different orbitrap instruments. Despite continuous advances in mass spectrometer technology as well as analysis software, data-set-wise quality control is still necessary, and decoy-based estimation, although challenged by modern instruments, should be utilized. We draw attention to the fact that numerous young researchers perceive proteomics as a mature, readily applicable technology. However, it is important to emphasize that the maximum potential of the technology can only be realized by an educated handling of its limitations.
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Affiliation(s)
- Simone König
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
| | - Karin Schork
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Ruhr-University Bochum, 44801 Bochum, Germany
- Core Unit for Bioinformatics (CUBiMed.RUB), Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Ruhr-University Bochum, 44801 Bochum, Germany
- Core Unit for Bioinformatics (CUBiMed.RUB), Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
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13
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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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14
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Little AS, Younker IT, Schechter MS, Bernardino PN, Méheust R, Stemczynski J, Scorza K, Mullowney MW, Sharan D, Waligurski E, Smith R, Ramanswamy R, Leiter W, Moran D, McMillin M, Odenwald MA, Iavarone AT, Sidebottom AM, Sundararajan A, Pamer EG, Eren AM, Light SH. Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. Nat Microbiol 2024; 9:55-69. [PMID: 38177297 PMCID: PMC11055453 DOI: 10.1038/s41564-023-01560-2] [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: 01/11/2023] [Accepted: 11/14/2023] [Indexed: 01/06/2024]
Abstract
Respiratory reductases enable microorganisms to use molecules present in anaerobic ecosystems as energy-generating respiratory electron acceptors. Here we identify three taxonomically distinct families of human gut bacteria (Burkholderiaceae, Eggerthellaceae and Erysipelotrichaceae) that encode large arsenals of tens to hundreds of respiratory-like reductases per genome. Screening species from each family (Sutterella wadsworthensis, Eggerthella lenta and Holdemania filiformis), we discover 22 metabolites used as respiratory electron acceptors in a species-specific manner. Identified reactions transform multiple classes of dietary- and host-derived metabolites, including bioactive molecules resveratrol and itaconate. Products of identified respiratory metabolisms highlight poorly characterized compounds, such as the itaconate-derived 2-methylsuccinate. Reductase substrate profiling defines enzyme-substrate pairs and reveals a complex picture of reductase evolution, providing evidence that reductases with specificities for related cinnamate substrates independently emerged at least four times. These studies thus establish an exceptionally versatile form of anaerobic respiration that directly links microbial energy metabolism to the gut metabolome.
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Affiliation(s)
- Alexander S Little
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Isaac T Younker
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Matthew S Schechter
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Paola Nol Bernardino
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Raphaël Méheust
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Joshua Stemczynski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Kaylie Scorza
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | | | - Deepti Sharan
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Emily Waligurski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Rita Smith
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | | | - William Leiter
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - David Moran
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Mary McMillin
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Matthew A Odenwald
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Section of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
- Section of Infectious Diseases & Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenbug, Germany
| | - Samuel H Light
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
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15
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Muntiu A, Papait A, Vincenzoni F, Vitali A, Lattanzi W, Romele P, Cargnoni A, Silini A, Parolini O, Desiderio C. Disclosing the molecular profile of the human amniotic mesenchymal stromal cell secretome by filter-aided sample preparation proteomic characterization. Stem Cell Res Ther 2023; 14:339. [PMID: 38012707 PMCID: PMC10683150 DOI: 10.1186/s13287-023-03557-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND The secretome of mesenchymal stromal cells isolated from the amniotic membrane (hAMSCs) has been extensively studied for its in vitro immunomodulatory activity as well as for the treatment of several preclinical models of immune-related disorders. The bioactive molecules within the hAMSCs secretome are capable of modulating the immune response and thus contribute to stimulating regenerative processes. At present, only a few studies have attempted to define the composition of the secretome, and several approaches, including multi-omics, are underway in an attempt to precisely define its composition and possibly identify key factors responsible for the therapeutic effect. METHODS In this study, we characterized the protein composition of the hAMSCs secretome by a filter-aided sample preparation (FASP) digestion and liquid chromatography-high resolution mass spectrometry (LC-MS) approach. Data were processed for gene ontology classification and functional protein interaction analysis by bioinformatics tools. RESULTS Proteomic analysis of the hAMSCs secretome resulted in the identification of 1521 total proteins, including 662 unique elements. A number of 157 elements, corresponding to 23.7%, were found as repeatedly characterizing the hAMSCs secretome, and those that resulted as significantly over-represented were involved in immunomodulation, hemostasis, development and remodeling of the extracellular matrix molecular pathways. CONCLUSIONS Overall, our characterization enriches the landscape of hAMSCs with new information that could enable a better understanding of the mechanisms of action underlying the therapeutic efficacy of the hAMSCs secretome while also providing a basis for its therapeutic translation.
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Affiliation(s)
- Alexandra Muntiu
- Istituto di Scienze e Tecnologie Chimiche (SCITEC) ''Giulio Natta'', Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Andrea Papait
- Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario ''Agostino Gemelli'' Istituto di Ricovero e Cura a Carattere Scientifico, IRCCS, Rome, Italy
| | - Federica Vincenzoni
- Fondazione Policlinico Universitario ''Agostino Gemelli'' Istituto di Ricovero e Cura a Carattere Scientifico, IRCCS, Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alberto Vitali
- Istituto di Scienze e Tecnologie Chimiche (SCITEC) ''Giulio Natta'', Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Wanda Lattanzi
- Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario ''Agostino Gemelli'' Istituto di Ricovero e Cura a Carattere Scientifico, IRCCS, Rome, Italy
| | - Pietro Romele
- Centro di Ricerca E. Menni, Fondazione Poliambulanza Istituto Ospedaliero, Brescia, Italy
| | - Anna Cargnoni
- Centro di Ricerca E. Menni, Fondazione Poliambulanza Istituto Ospedaliero, Brescia, Italy
| | - Antonietta Silini
- Centro di Ricerca E. Menni, Fondazione Poliambulanza Istituto Ospedaliero, Brescia, Italy
| | - Ornella Parolini
- Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy.
- Fondazione Policlinico Universitario ''Agostino Gemelli'' Istituto di Ricovero e Cura a Carattere Scientifico, IRCCS, Rome, Italy.
| | - Claudia Desiderio
- Istituto di Scienze e Tecnologie Chimiche (SCITEC) ''Giulio Natta'', Consiglio Nazionale delle Ricerche, Rome, Italy.
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16
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Marzano V, Levi Mortera S, Vernocchi P, Del Chierico F, Marangelo C, Guarrasi V, Gardini S, Dentici ML, Capolino R, Digilio MC, Di Donato M, Spasari I, Abreu MT, Dallapiccola B, Putignani L. Williams-Beuren syndrome shapes the gut microbiota metaproteome. Sci Rep 2023; 13:18963. [PMID: 37923896 PMCID: PMC10624682 DOI: 10.1038/s41598-023-46052-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023] Open
Abstract
Williams-Beuren syndrome (WBS) is a rare genetic neurodevelopmental disorder with multi-systemic manifestations. The evidence that most subjects with WBS face gastrointestinal (GI) comorbidities, have prompted us to carry out a metaproteomic investigation of their gut microbiota (GM) profile compared to age-matched healthy subjects (CTRLs). Metaproteomic analysis was carried out on fecal samples collected from 41 individuals with WBS, and compared with samples from 45 CTRLs. Stool were extracted for high yield in bacterial protein group (PG) content, trypsin-digested and analysed by nanoLiquid Chromatography-Mass Spectrometry. Label free quantification, taxonomic assignment by the lowest common ancestor (LCA) algorithm and functional annotations by COG and KEGG databases were performed. Data were statistically interpreted by multivariate and univariate analyses. A WBS GM functional dissimilarity respect to CTRLs, regardless age distribution, was reported. The alterations in function of WBSs GM was primarily based on bacterial pathways linked to carbohydrate transport and metabolism and energy production. Influence of diet, obesity, and GI symptoms was assessed, highlighting changes in GM biochemical patterns, according to WBS subsets' stratification. The LCA-derived ecology unveiled WBS-related functionally active bacterial signatures: Bacteroidetes related to over-expressed PGs, and Firmicutes, specifically the specie Faecalibacterium prausnitzii, linked to under-expressed PGs, suggesting a depletion of beneficial bacteria. These new evidences on WBS gut dysbiosis may offer novel targets for tailored interventions.
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Affiliation(s)
- Valeria Marzano
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Stefano Levi Mortera
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Del Chierico
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chiara Marangelo
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valerio Guarrasi
- GenomeUp s.r.l., Rome, Italy
- Unit of Computer Systems and Bioinformatics, Department of Engineering, University Campus Bio-Medico of Rome, Rome, Italy
| | | | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rossella Capolino
- Genetics and Rare Diseases Research Division, Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maddalena Di Donato
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Iolanda Spasari
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Teresa Abreu
- Division of Digestive Health and Liver Diseases, Department of Medicine, Crohn's and Colitis Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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17
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Will A, Oliinyk D, Bleiholder C, Meier F. Peptide collision cross sections of 22 post-translational modifications. Anal Bioanal Chem 2023; 415:6633-6645. [PMID: 37758903 PMCID: PMC10598134 DOI: 10.1007/s00216-023-04957-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 07/13/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023]
Abstract
Recent advances have rekindled the interest in ion mobility as an additional dimension of separation in mass spectrometry (MS)-based proteomics. Ion mobility separates ions according to their size and shape in the gas phase. Here, we set out to investigate the effect of 22 different post-translational modifications (PTMs) on the collision cross section (CCS) of peptides. In total, we analyzed ~4300 pairs of matching modified and unmodified peptide ion species by trapped ion mobility spectrometry (TIMS). Linear alignment based on spike-in reference peptides resulted in highly reproducible CCS values with a median coefficient of variation of 0.26%. On a global level, we observed a redistribution in the m/z vs. ion mobility space for modified peptides upon changes in their charge state. Pairwise comparison between modified and unmodified peptides of the same charge state revealed median shifts in CCS between -1.4% (arginine citrullination) and +4.5% (O-GlcNAcylation). In general, increasing modified peptide masses were correlated with higher CCS values, in particular within homologous PTM series. However, investigating the ion populations in more detail, we found that the change in CCS can vary substantially for a given PTM and is partially correlated with the gas phase structure of its unmodified counterpart. In conclusion, our study shows PTM- and sequence-specific effects on the cross section of peptides, which could be further leveraged for proteome-wide PTM analysis.
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Affiliation(s)
- Andreas Will
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Denys Oliinyk
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32304, USA
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.
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18
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Kitata RB, Yang JC, Chen YJ. Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape. MASS SPECTROMETRY REVIEWS 2023; 42:2324-2348. [PMID: 35645145 DOI: 10.1002/mas.21781] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
Abstract
The data-independent acquisition mass spectrometry (DIA-MS) has rapidly evolved as a powerful alternative for highly reproducible proteome profiling with a unique strength of generating permanent digital maps for retrospective analysis of biological systems. Recent advancements in data analysis software tools for the complex DIA-MS/MS spectra coupled to fast MS scanning speed and high mass accuracy have greatly expanded the sensitivity and coverage of DIA-based proteomics profiling. Here, we review the evolution of the DIA-MS techniques, from earlier proof-of-principle of parallel fragmentation of all-ions or ions in selected m/z range, the sequential window acquisition of all theoretical mass spectra (SWATH-MS) to latest innovations, recent development in computation algorithms for data informatics, and auxiliary tools and advanced instrumentation to enhance the performance of DIA-MS. We further summarize recent applications of DIA-MS and experimentally-derived as well as in silico spectra library resources for large-scale profiling to facilitate biomarker discovery and drug development in human diseases with emphasis on the proteomic profiling coverage. Toward next-generation DIA-MS for clinical proteomics, we outline the challenges in processing multi-dimensional DIA data set and large-scale clinical proteomics, and continuing need in higher profiling coverage and sensitivity.
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Affiliation(s)
| | - Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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19
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Sandbaumhüter F, Nezhyva M, Andrén PE, Jansson ET. Label-Free Quantitative Thermal Proteome Profiling Reveals Target Transcription Factors with Activities Modulated by MC3R Signaling. Anal Chem 2023; 95:15400-15408. [PMID: 37804223 PMCID: PMC10585664 DOI: 10.1021/acs.analchem.3c03643] [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: 08/15/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023]
Abstract
Thermal proteome profiling with label-free quantitation using ion-mobility-enhanced LC-MS offers versatile data sets, providing information on protein differential expression, thermal stability, and the activities of transcription factors. We developed a multidimensional data analysis workflow for label-free quantitative thermal proteome profiling (TPP) experiments that incorporates the aspects of gene set enrichment analysis, differential protein expression analysis, and inference of transcription factor activities from LC-MS data. We applied it to study the signaling processes downstream of melanocortin 3 receptor (MC3R) activation by endogenous agonists derived from the proopiomelanocortin prohormone: ACTH, α-MSH, and γ-MSH. The obtained information was used to map signaling pathways downstream of MC3R and to deduce transcription factors responsible for cellular response to ligand treatment. Using our workflow, we identified differentially expressed proteins and investigated their thermal stability. We found in total 298 proteins with altered thermal stability, resulting from MC3R activation. Out of these, several proteins were transcription factors, indicating them as being downstream target regulators that take part in the MC3R signaling cascade. We found transcription factors CCAR2, DDX21, HMGB2, SRSF7, and TET2 to have altered thermal stability. These apparent target transcription factors within the MC3R signaling cascade play important roles in immune responses. Additionally, we inferred the activities of the transcription factors identified in our data set. This was done with Bayesian statistics using the differential expression data we obtained with label-free quantitative LC-MS. The inferred transcription factor activities were validated in our bioinformatic pipeline by the phosphorylated peptide abundances that we observed, highlighting the importance of post-translational modifications in transcription factor regulation. Our multidimensional data analysis workflow allows for a comprehensive characterization of the signaling processes downstream of MC3R activation. It provides insights into protein differential expression, thermal stability, and activities of key transcription factors. All proteomic data generated in this study are publicly available at DOI: 10.6019/PXD039945.
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Affiliation(s)
| | - Mariya Nezhyva
- Department
of Pharmaceutical Biosciences, Uppsala University, 751 24 Uppsala, Sweden
| | - Per E. Andrén
- Department
of Pharmaceutical Biosciences, Uppsala University, 751 24 Uppsala, Sweden
- Science
for Life Laboratory, Spatial Mass Spectrometry, Uppsala University, 751 24 Uppsala, Sweden
| | - Erik T. Jansson
- Department
of Pharmaceutical Biosciences, Uppsala University, 751 24 Uppsala, Sweden
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20
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Davalieva K, Kiprijanovska S, Ivanovski O, Trifunovski A, Saidi S, Dimovski A, Popov Z. Proteomics Profiling of Bladder Cancer Tissues from Early to Advanced Stages Reveals NNMT and GALK1 as Biomarkers for Early Detection and Prognosis of BCa. Int J Mol Sci 2023; 24:14938. [PMID: 37834386 PMCID: PMC10573217 DOI: 10.3390/ijms241914938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 10/15/2023] Open
Abstract
The high recurrence rate and invasive diagnostic and monitoring methods in bladder cancer (BCa) clinical management require the development of new non-invasive molecular tools for early detection, particularly for low-grade and low-stage BCa as well as for risk stratification. By using an in-solution digestion method and label-free data-independent LC-MS/MS coupled with ion mobility, we profiled the BCa tissues from initiation to advanced stages and confidently identified and quantified 1619 proteins (≥2 peptides). A statistically significant difference in abundance (Anova ≤ 0.05) showed 494 proteins. Significant correlation with stage with steady up or down with BCa stages showed 15 proteins. Testing of NNMT, GALK1, and HTRA1 in urine samples showed excellent diagnostic potential for NNMT and GALK1 with AUC of 1.000 (95% CI: 1.000-1.000; p < 0.0001) and 0.801 (95% CI: 0.655-0.947; p < 0.0001), respectively. NNMT and GALK1 also showed very good potential in discriminating non-invasive low-grade from invasive high-grade BCa with AUC of 0.763 (95% CI: 0.606-0.921; p = 0.001) and 0.801 (95% CI: 0.653-0.950; p < 0.0001), respectively. The combination of NNMT and GALK1 increased prognostic accuracy (AUC = 0.813). Our results broaden the range of potential novel candidates for non-invasive BCa diagnosis and prognosis.
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Affiliation(s)
- Katarina Davalieva
- Research Centre for Genetic Engineering and Biotechnology “Georgi D Efremov”, Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia; (S.K.); (A.D.)
| | - Sanja Kiprijanovska
- Research Centre for Genetic Engineering and Biotechnology “Georgi D Efremov”, Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia; (S.K.); (A.D.)
| | - Ognen Ivanovski
- Clinical Centre “Mother Theresa”, University Clinic for Urology, 1000 Skopje, North Macedonia; (O.I.); (A.T.); (S.S.)
| | - Aleksandar Trifunovski
- Clinical Centre “Mother Theresa”, University Clinic for Urology, 1000 Skopje, North Macedonia; (O.I.); (A.T.); (S.S.)
| | - Skender Saidi
- Clinical Centre “Mother Theresa”, University Clinic for Urology, 1000 Skopje, North Macedonia; (O.I.); (A.T.); (S.S.)
| | - Aleksandar Dimovski
- Research Centre for Genetic Engineering and Biotechnology “Georgi D Efremov”, Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia; (S.K.); (A.D.)
- Faculty of Pharmacy, University “St. Cyril and Methodius”, 1000 Skopje, North Macedonia
| | - Zivko Popov
- Clinical Hospital “Acibadem Sistina”, 1000 Skopje, North Macedonia;
- Medical Faculty, University “St. Cyril and Methodius”, 1000 Skopje, North Macedonia
- Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia
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21
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Shettima A, Ishak IH, Lau B, Abu Hasan H, Miswan N, Othman N. Quantitative proteomics analysis of permethrin and temephos-resistant Ae. aegypti revealed diverse differentially expressed proteins associated with insecticide resistance from Penang Island, Malaysia. PLoS Negl Trop Dis 2023; 17:e0011604. [PMID: 37721966 PMCID: PMC10538732 DOI: 10.1371/journal.pntd.0011604] [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: 11/17/2022] [Revised: 09/28/2023] [Accepted: 08/18/2023] [Indexed: 09/20/2023] Open
Abstract
Synthetic insecticides are the primary vector control method used globally. However, the widespread use of insecticides is a major cause of insecticide-resistance in mosquitoes. Hence, this study aimed at elucidating permethrin and temephos-resistant protein expression profiles in Ae. aegypti using quantitative proteomics. In this study, we evaluated the susceptibility of Ae. aegypti from Penang Island dengue hotspot and non-hotspot against 0.75% permethrin and 31.25 mg/l temephos using WHO bioassay method. Protein extracts from the mosquitoes were then analysed using LC-ESI-MS/MS for protein identification and quantification via label-free quantitative proteomics (LFQ). Next, Perseus 1.6.14.0 statistical software was used to perform differential protein expression analysis using ANOVA and Student's t-test. The t-test selected proteins with≥2.0-fold change (FC) and ≥2 unique peptides for gene expression validation via qPCR. Finally, STRING software was used for functional ontology enrichment and protein-protein interactions (PPI). The WHO bioassay showed resistance with 28% and 53% mortalities in adult mosquitoes exposed to permethrin from the hotspot and non-hotspot areas. Meanwhile, the susceptibility of Ae. aegypti larvae revealed high resistance to temephos in hotspot and non-hotspot regions with 80% and 91% mortalities. The LFQ analyses revealed 501 and 557 (q-value <0.05) differentially expressed proteins in adults and larvae Ae. aegypti. The t-test showed 114 upregulated and 74 downregulated proteins in adult resistant versus laboratory strains exposed to permethrin. Meanwhile, 13 upregulated and 105 downregulated proteins were observed in larvae resistant versus laboratory strains exposed to temephos. The t-test revealed the upregulation of sodium/potassium-dependent ATPase β2 in adult permethrin resistant strain, H15 domain-containing protein, 60S ribosomal protein, and PB protein in larvae temephos resistant strain. The downregulation of troponin I, enolase phosphatase E1, glucosidase 2β was observed in adult permethrin resistant strain and tubulin β chain in larvae temephos resistant strain. Furthermore, the gene expression by qPCR revealed similar gene expression patterns in the above eight differentially expressed proteins. The PPI of differentially expressed proteins showed a p-value at <1.0 x 10-16 in permethrin and temephos resistant Ae. aegypti. Significantly enriched pathways in differentially expressed proteins revealed metabolic pathways, oxidative phosphorylation, carbon metabolism, biosynthesis of amino acids, glycolysis, and citrate cycle. In conclusion, this study has shown differentially expressed proteins and highlighted upregulated and downregulated proteins associated with insecticide resistance in Ae. aegypti. The validated differentially expressed proteins merit further investigation as a potential protein marker to monitor and predict insecticide resistance in field Ae. aegypti. The LC-MS/MS data were submitted into the MASSIVE database with identifier no: MSV000089259.
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Affiliation(s)
- Abubakar Shettima
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
- Department of Microbiology, University of Maiduguri, Maiduguri, Nigeria
| | - Intan Haslina Ishak
- School of Biological Sciences (SBS), Universiti Sains Malaysia, Gelugor, Malaysia
- Vector Control Research Unit (VCRU), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Benjamin Lau
- Proteomics and Metabolomics (PROMET) laboratory, Malaysian Palm Oil Board (MPOB), Kajang, Malaysia
| | - Hadura Abu Hasan
- School of Biological Sciences (SBS), Universiti Sains Malaysia, Gelugor, Malaysia
- Vector Control Research Unit (VCRU), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Noorizan Miswan
- Center for Chemical Biology (CCB), Universiti Sains Malaysia, Bayan Lepas, Malaysia
| | - Nurulhasanah Othman
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
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22
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Vavlukis A, Mladenovska K, Davalieva K, Vavlukis M, Dimovski A. Rosuvastatin effects on the HDL proteome in hyperlipidemic patients. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2023; 73:363-384. [PMID: 37708957 DOI: 10.2478/acph-2023-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/07/2023] [Indexed: 09/16/2023]
Abstract
The advancements in proteomics have provided a better understanding of the functionality of apolipoproteins and lipoprotein-associated proteins, with the HDL lipoprotein fraction being the most studied. The focus of this study was to evaluate the HDL proteome in dyslipidemic subjects without an established cardiovascular disease, as well as to test whether rosuvastatin treatment alters the HDL proteome. Patients with primary hypercholesterolemia or mixed dyslipidemia were assigned to 20 mg/day rosuvastatin and blood samples were drawn at study entry and after 12 weeks of treatment. A label-free LC-MS/MS protein profiling was conducted, coupled with bioinformatics analysis. Sixty-nine HDL proteins were identified, belonging to four main biological function clusters: lipid transport and metabolism; platelet activation, degranulation, and aggregation, wound response and wound healing; immune response; inflammatory and acute phase response. Five HDL proteins showed statistically significant differences in the abundance (Anova ≤ 0.05), before and after rosuvastatin treatment. Platelet factor 4 variant (PF4V1), Pregnancy-specific beta-1-glycoprotein 2 (PSG2), Profilin-1 (PFN1) and Keratin type II cytoskeletal 2 epidermal (KRT2) showed decreased expressions, while Integrin alpha-IIb (ITGA2B) showed an increased expression after treatment with rosuvastatin. The ELISA validation of PFN1 segregated the subjects into responders and non-responders, as PFN1 levels after rosuvastatin were shown to mostly depend on the subjects' inflammatory phenotype. Findings from this study introduce novel insights into the HDL proteome and statin pleiotropism.
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Affiliation(s)
- Ana Vavlukis
- University Ss Cyril and Methodius Faculty of Pharmacy, 1000 Skopje RN Macedonia
| | | | - Katarina Davalieva
- Macedonian Academy of Sciences and Arts, Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov", 1000 Skopje RN Macedonia
| | - Marija Vavlukis
- University Ss Cyril and Methodius Faculty of Medicine, 1000 Skopje RN Macedonia
| | - Aleksandar Dimovski
- University Ss Cyril and Methodius Faculty of Pharmacy, 1000 Skopje RN Macedonia
- Macedonian Academy of Sciences and Arts, Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov", 1000 Skopje RN Macedonia
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23
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Brockbals L, Garrett-Rickman S, Fu S, Ueland M, McNevin D, Padula MP. Estimating the time of human decomposition based on skeletal muscle biopsy samples utilizing an untargeted LC-MS/MS-based proteomics approach. Anal Bioanal Chem 2023; 415:5487-5498. [PMID: 37423904 PMCID: PMC10444689 DOI: 10.1007/s00216-023-04822-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/11/2023]
Abstract
Accurate estimation of the postmortem interval (PMI) is crucial in forensic medico-legal investigations to understand case circumstances (e.g. narrowing down list of missing persons or include/exclude suspects). Due to the complex decomposition chemistry, estimation of PMI remains challenging and currently often relies on the subjective visual assessment of gross morphological/taphonomic changes of a body during decomposition or entomological data. The aim of the current study was to investigate the human decomposition process up to 3 months after death and propose novel time-dependent biomarkers (peptide ratios) for the estimation of decomposition time. An untargeted liquid chromatography tandem mass spectrometry-based bottom-up proteomics workflow (ion mobility separated) was utilized to analyse skeletal muscle, collected repeatedly from nine body donors decomposing in an open eucalypt woodland environment in Australia. Additionally, general analytical considerations for large-scale proteomics studies for PMI determination are raised and discussed. Multiple peptide ratios (human origin) were successfully proposed (subgroups < 200 accumulated degree days (ADD), < 655 ADD and < 1535 ADD) as a first step towards generalised, objective biochemical estimation of decomposition time. Furthermore, peptide ratios for donor-specific intrinsic factors (sex and body mass) were found. Search of peptide data against a bacterial database did not yield any results most likely due to the low abundance of bacterial proteins within the collected human biopsy samples. For comprehensive time-dependent modelling, increased donor number would be necessary along with targeted confirmation of proposed peptides. Overall, the presented results provide valuable information that aid in the understanding and estimation of the human decomposition processes.
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Affiliation(s)
- Lana Brockbals
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Samara Garrett-Rickman
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Shanlin Fu
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Maiken Ueland
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Dennis McNevin
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Matthew P Padula
- School of Life Sciences, Faculty of Science, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.
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24
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Demeuse J, Massonnet P, Schoumacher M, Grifnée E, Huyghebaert L, Dubrowski T, Peeters S, Le Goff C, Cavalier E. Innovative workflow for the identification of cathepsin K cleavage sites in type I collagen. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1228:123864. [PMID: 37634391 DOI: 10.1016/j.jchromb.2023.123864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/09/2023] [Accepted: 08/19/2023] [Indexed: 08/29/2023]
Abstract
Since the late 1990s, cathepsin K cleavage sites in type I collagen have been extensively studied due to its ability to release bone resorption biomarkers such as CTX and NTX. However, gel-based methods and N-sequencing used in these studies lack sensitivity, especially for small to medium peptides. In this work, we propose a degradomics mass spectrometry-based workflow that combines protein digestion, Nano-LC-UDMSE, and several software tools to identify cathepsin K cleavage sites. This workflow not only identified previously known cleavage sites, but also discovered new ones. Multiple cleavage hotspots were found and described in type I α1 and type I α2 collagen, many of which coincided with pyridinoline crosslinks, known to stabilize the triple helix. Our results allowed us to establish a chronology of digestion and conclude that cathepsin K preferentially cleaves the extremities of type I collagen before the helical part. We also found that cathepsin K preferentially cleaves amino acid residues with long and hydrophobic lateral chains at the beginning of digestion, whereas no preferred amino acid residues were identified later in the digestion. In conclusion, our workflow successfully identified new cleavage sites and can be easily applied to other proteins or proteases.
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Affiliation(s)
- Justine Demeuse
- Department of Clinical Chemistry, CIRM, University of Liège, 4000 Liège, Belgium.
| | - Philippe Massonnet
- Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
| | - Matthieu Schoumacher
- Department of Clinical Chemistry, CIRM, University of Liège, 4000 Liège, Belgium
| | - Elodie Grifnée
- Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
| | - Loreen Huyghebaert
- Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
| | - Thomas Dubrowski
- Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
| | - Stéphanie Peeters
- Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
| | - Caroline Le Goff
- Department of Clinical Chemistry, CIRM, University of Liège, 4000 Liège, Belgium; Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
| | - Etienne Cavalier
- Department of Clinical Chemistry, CIRM, University of Liège, 4000 Liège, Belgium; Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
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25
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Brunetti NS, Davanzo GG, de Moraes D, Ferrari AJR, Souza GF, Muraro SP, Knittel TL, Boldrini VO, Monteiro LB, Virgílio-da-Silva JV, Profeta GS, Wassano NS, Nunes Santos L, Carregari VC, Dias AHS, Veras FP, Tavares LA, Forato J, Castro IMS, Silva-Costa LC, Palma AC, Mansour E, Ulaf RG, Bernardes AF, Nunes TA, Ribeiro LC, Agrela MV, Moretti ML, Buscaratti LI, Crunfli F, Ludwig RG, Gerhardt JA, Munhoz-Alves N, Marques AM, Sesti-Costa R, Amorim MR, Toledo-Teixeira DA, Parise PL, Martini MC, Bispos-Dos-Santos K, Simeoni CL, Granja F, Silvestrini VC, de Oliveira EB, Faca VM, Carvalho M, Castelucci BG, Pereira AB, Coimbra LD, Dias MMG, Rodrigues PB, Gomes ABSP, Pereira FB, Santos LMB, Bloyet LM, Stumpf S, Pontelli MC, Whelan S, Sposito AC, Carvalho RF, Vieira AS, Vinolo MAR, Damasio A, Velloso L, Figueira ACM, da Silva LLP, Cunha TM, Nakaya HI, Marques-Souza H, Marques RE, Martins-de-Souza D, Skaf MS, Proenca-Modena JL, Moraes-Vieira PMM, Mori MA, Farias AS. SARS-CoV-2 uses CD4 to infect T helper lymphocytes. eLife 2023; 12:e84790. [PMID: 37523305 PMCID: PMC10390044 DOI: 10.7554/elife.84790] [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: 11/30/2022] [Accepted: 07/13/2023] [Indexed: 08/02/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent of a major global outbreak of respiratory tract disease known as Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 infects mainly lungs and may cause several immune-related complications, such as lymphocytopenia and cytokine storm, which are associated with the severity of the disease and predict mortality. The mechanism by which SARS-CoV-2 infection may result in immune system dysfunction is still not fully understood. Here, we show that SARS-CoV-2 infects human CD4+ T helper cells, but not CD8+ T cells, and is present in blood and bronchoalveolar lavage T helper cells of severe COVID-19 patients. We demonstrated that SARS-CoV-2 spike glycoprotein (S) directly binds to the CD4 molecule, which in turn mediates the entry of SARS- CoV-2 in T helper cells. This leads to impaired CD4 T cell function and may cause cell death. SARS-CoV-2-infected T helper cells express higher levels of IL-10, which is associated with viral persistence and disease severity. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may contribute to a poor immune response in COVID-19 patients.
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Grants
- #2295/20 Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas
- #2021/08354-2 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2015/15626-8 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/14465-1 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #465489/2014-1 Instituto Nacional de Ciência e Tecnologia em Neuroimunomodulação
- #01.20.0003.00 Financiadora de Estudos e Projetos
- #306248/2017-4 Conselho Nacional de Desenvolvimento Científico e Tecnológico
- #2019/17007-4 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/04726-2 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2319/20 Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas
- #2274/20 Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas
- #2266/20 Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas
- #2458/20 Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas
- #2019/16116-4 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/06372-3 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2020/04583-4 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2013/08293-7 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2020/04579-7 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2018/14933-2 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2020/04746-0 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/00098-7 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2020/04919-2 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2017/01184-9 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2020/04558-0 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2016/00194-8 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2016/18031- 8 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/22398-2 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/13552-8 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/05155-9 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/06459-1 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2017/23920-9 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2016/24163-4 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2016/23328-0 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #310287/2018-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico
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Affiliation(s)
- Natalia S Brunetti
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Gustavo G Davanzo
- Laboratory of Immunometabolism, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Diogo de Moraes
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Department of Structural and Functional Biology, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Allan J R Ferrari
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas (UNICAMP), Campinas, Brazil
| | - Gabriela F Souza
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Stéfanie Primon Muraro
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Thiago L Knittel
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Vinicius O Boldrini
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Lauar B Monteiro
- Laboratory of Immunometabolism, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - João Victor Virgílio-da-Silva
- Laboratory of Immunometabolism, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Gerson S Profeta
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Natália S Wassano
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Luana Nunes Santos
- Brazilian Laboratory on Silencing Technologies (BLaST), Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Victor C Carregari
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Artur H S Dias
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas (UNICAMP), Campinas, Brazil
| | - Flavio P Veras
- Center of Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto,, São Paulo, Brazil
| | - Lucas A Tavares
- Department of Cell and Molecular Biology, Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Julia Forato
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Icaro M S Castro
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lícia C Silva-Costa
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - André C Palma
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Eli Mansour
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Raisa G Ulaf
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Ana F Bernardes
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Thyago A Nunes
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Luciana C Ribeiro
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Marcus V Agrela
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Maria Luiza Moretti
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Lucas I Buscaratti
- Brazilian Laboratory on Silencing Technologies (BLaST), Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fernanda Crunfli
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Raissa G Ludwig
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Jaqueline A Gerhardt
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Natália Munhoz-Alves
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Ana Maria Marques
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Renata Sesti-Costa
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Hematology and Hemotherapy Center, University of Campinas (UNICAMP), Campinas, Brazil
| | - Mariene R Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel A Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Pierina Lorencini Parise
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Matheus Cavalheiro Martini
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Karina Bispos-Dos-Santos
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Camila L Simeoni
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Virgínia C Silvestrini
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Eduardo B de Oliveira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Vitor M Faca
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Murilo Carvalho
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Bianca G Castelucci
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Alexandre B Pereira
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Laís D Coimbra
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Marieli M G Dias
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Patricia B Rodrigues
- Laboratory of Immunoinflammation, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil;, Campinas, Brazil
| | - Arilson Bernardo S P Gomes
- Laboratory of Immunoinflammation, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil;, Campinas, Brazil
| | - Fabricio B Pereira
- Hematology and Hemotherapy Center, University of Campinas (UNICAMP), Campinas, Brazil
| | - Leonilda M B Santos
- Neuroimmunology Unit, Department of Genetics, Microbiology and Immunology, University of Campinas (UNICAMP), Campinas, Brazil
- National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM) - Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Louis-Marie Bloyet
- Washington University in St Louis, Department of Molecular Microbiology, St. Louis, United States
| | - Spencer Stumpf
- Washington University in St Louis, Department of Molecular Microbiology, St. Louis, United States
| | - Marjorie C Pontelli
- Washington University in St Louis, Department of Molecular Microbiology, St. Louis, United States
| | - Sean Whelan
- Washington University in St Louis, Department of Molecular Microbiology, St. Louis, United States
| | - Andrei C Sposito
- Laboratory of Vascular Biology and Arteriosclerosis, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Robson F Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - André S Vieira
- Laboratory of Electrophysiology, Neurobiology and Behavior, University of Campinas (UNICAMP), Campinas, Brazil
| | - Marco A R Vinolo
- Laboratory of Immunoinflammation, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil;, Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas (UNICAMP), Campinas, Brazil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
| | - Licio Velloso
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas (UNICAMP), Campinas, Brazil
| | - Ana Carolina M Figueira
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Luis L P da Silva
- Center of Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thiago Mattar Cunha
- Center of Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto,, São Paulo, Brazil
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Henrique Marques-Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Brazilian Laboratory on Silencing Technologies (BLaST), Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Rafael E Marques
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil
- National Institute of Science and Technology in Biomarkers for Neuropsychiatry (INCTINBION), São Paulo, Brazil
| | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas (UNICAMP), Campinas, Brazil
| | - Jose Luiz Proenca-Modena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
| | - Pedro M M Moraes-Vieira
- Laboratory of Immunometabolism, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas (UNICAMP), Campinas, Brazil
| | - Marcelo A Mori
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas (UNICAMP), Campinas, Brazil
| | - Alessandro S Farias
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Washington University in St Louis, Department of Molecular Microbiology, St. Louis, United States
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas (UNICAMP), Campinas, Brazil
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26
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Kirschner F, Arnold-Schild D, Leps C, Łącki MK, Klein M, Chen Y, Ludt A, Marini F, Kücük C, Stein L, Distler U, Sielaff M, Michna T, Riegel K, Rajalingam K, Bopp T, Tenzer S, Schild H. Modulation of cellular transcriptome and proteome composition by azidohomoalanine-implications on click chemistry-based secretome analysis. J Mol Med (Berl) 2023; 101:855-867. [PMID: 37231147 PMCID: PMC10300158 DOI: 10.1007/s00109-023-02333-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/25/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
The analysis of the secretome provides important information on proteins defining intercellular communication and the recruitment and behavior of cells in specific tissues. Especially in the context of tumors, secretome data can support decisions for diagnosis and therapy. The mass spectrometry-based analysis of cell-conditioned media is widely used for the unbiased characterization of cancer secretomes in vitro. Metabolic labeling using azide-containing amino acid analogs in combination with click chemistry facilitates this type of analysis in the presence of serum, preventing serum starvation-induced effects. The modified amino acid analogs, however, are less efficiently incorporated into newly synthesized proteins and may perturb protein folding. Combining transcriptome and proteome analysis, we elucidate in detail the effects of metabolic labeling with the methionine analog azidohomoalanine (AHA) on gene and protein expression. Our data reveal that 15-39% of the proteins detected in the secretome displayed changes in transcript and protein expression induced by AHA labeling. Gene Ontology (GO) analyses indicate that metabolic labeling using AHA leads to induction of cellular stress and apoptosis-related pathways and provide first insights on how this affects the composition of the secretome on a global scale. KEY MESSAGES: Azide-containing amino acid analogs affect gene expression profiles. Azide-containing amino acid analogs influence cellular proteome. Azidohomoalanine labeling induces cellular stress and apoptotic pathways. Secretome consists of proteins with dysregulated expression profiles.
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Affiliation(s)
- Friederike Kirschner
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Danielle Arnold-Schild
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Christian Leps
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Mateusz Krzysztof Łącki
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Matthias Klein
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Yannic Chen
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany
| | - Annekathrin Ludt
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Can Kücük
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany
| | - Lara Stein
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Malte Sielaff
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Thomas Michna
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Kristina Riegel
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tobias Bopp
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- University Cancer Center Mainz, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany.
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany.
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany.
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany.
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
- University Cancer Center Mainz, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
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27
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Lanas A, Tacconelli S, Contursi A, Piazuelo E, Bruno A, Ronci M, Marcone S, Dovizio M, Sopeña F, Falcone L, Milillo C, Mucci M, Ballerini P, Patrignani P. Biomarkers of Response to Low-Dose Aspirin in Familial Adenomatous Polyposis Patients. Cancers (Basel) 2023; 15:cancers15092457. [PMID: 37173923 PMCID: PMC10177499 DOI: 10.3390/cancers15092457] [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: 03/27/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND The results of Aspirin prevention of colorectal adenomas in patients with familial adenomatous polyposis (FAP) are controversial. METHODS We conducted a biomarker-based clinical study in eight FAP patients treated with enteric-coated low-dose Aspirin (100 mg daily for three months) to explore whether the drug targets mainly platelet cyclooxygenase (COX)-1 or affects extraplatelet cellular sources expressing COX-isozymes and/or off-target effects in colorectal adenomas. RESULTS In FAP patients, low-dose Aspirin-acetylated platelet COX-1 at Serine529 (>70%) was associated with an almost complete inhibition of platelet thromboxane (TX) B2 generation ex vivo (serum TXB2). However, enhanced residual urinary 11-dehydro-TXB2 and urinary PGEM, primary metabolites of TXA2 and prostaglandin (PG)E2, respectively, were detected in association with incomplete acetylation of COX-1 in normal colorectal biopsies and adenomas. Proteomics of adenomas showed that Aspirin significantly modulated only eight proteins. The upregulation of vimentin and downregulation of HBB (hemoglobin subunit beta) distinguished two groups with high vs. low residual 11-dehydro-TXB2 levels, possibly identifying the nonresponders and responders to Aspirin. CONCLUSIONS Although low-dose Aspirin appropriately inhibited the platelet, persistently high systemic TXA2 and PGE2 biosynthesis were found, plausibly for a marginal inhibitory effect on prostanoid biosynthesis in the colorectum. Novel chemotherapeutic strategies in FAP can involve blocking the effects of TXA2 and PGE2 signaling with receptor antagonists.
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Affiliation(s)
- Angel Lanas
- University Hospital LB, Aragon Health Research Institute (IISAragon), CIBERehd, University of Zaragoza, 50009 Zaragoza, Spain
| | - Stefania Tacconelli
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University, 66100 Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, "G. d'Annunzio" University, 66100 Chieti, Italy
| | - Annalisa Contursi
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University, 66100 Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, "G. d'Annunzio" University, 66100 Chieti, Italy
| | - Elena Piazuelo
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
| | - Annalisa Bruno
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University, 66100 Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, "G. d'Annunzio" University, 66100 Chieti, Italy
| | - Maurizio Ronci
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University, 66100 Chieti, Italy
| | - Simone Marcone
- Trinity Translational Medicine Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Melania Dovizio
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University, 66100 Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, "G. d'Annunzio" University, 66100 Chieti, Italy
| | - Federico Sopeña
- University Hospital LB, Aragon Health Research Institute (IISAragon), CIBERehd, University of Zaragoza, 50009 Zaragoza, Spain
| | - Lorenza Falcone
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University, 66100 Chieti, Italy
- Department of Innovative Technologies in Medicine and Dentistry, "G. d'Annunzio" University, 66100 Chieti, Italy
| | - Cristina Milillo
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University, 66100 Chieti, Italy
- Department of Innovative Technologies in Medicine and Dentistry, "G. d'Annunzio" University, 66100 Chieti, Italy
| | - Matteo Mucci
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University, 66100 Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, "G. d'Annunzio" University, 66100 Chieti, Italy
| | - Patrizia Ballerini
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University, 66100 Chieti, Italy
- Department of Innovative Technologies in Medicine and Dentistry, "G. d'Annunzio" University, 66100 Chieti, Italy
| | - Paola Patrignani
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University, 66100 Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, "G. d'Annunzio" University, 66100 Chieti, Italy
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28
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Gaspar RS, Delafiori J, Zuccoli G, Carregari VC, Prado TP, Morari J, Sidarta-Oliveira D, Solon CS, Catharino RR, Araujo EP, Martins-de-Souza D, Velloso LA. Exogenous succinate impacts mouse brown adipose tissue mitochondrial proteome and potentiates body mass reduction induced by liraglutide. Am J Physiol Endocrinol Metab 2023; 324:E226-E240. [PMID: 36724126 DOI: 10.1152/ajpendo.00231.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Obesity is one of the leading noncommunicable diseases in the world. Despite intense efforts to develop strategies to prevent and treat obesity, its prevalence continues to rise worldwide. A recent study has shown that the tricarboxylic acid intermediate succinate increases body energy expenditure by promoting brown adipose tissue thermogenesis through the activation of uncoupling protein-1; this has generated interest surrounding its potential usefulness as an approach to treat obesity. It is currently unknown how succinate impacts brown adipose tissue protein expression, and how exogenous succinate impacts body mass reduction promoted by a drug approved to treat human obesity, the glucagon-like-1 receptor agonist, liraglutide. In the first part of this study, we used bottom-up shotgun proteomics to determine the acute impact of exogenous succinate on the brown adipose tissue. We show that succinate rapidly affects the expression of 177 brown adipose tissue proteins, which are mostly associated with mitochondrial structure and function. In the second part of this study, we performed a short-term preclinical pharmacological intervention, treating diet-induced obese mice with a combination of exogenous succinate and liraglutide. We show that the combination was more efficient than liraglutide alone in promoting body mass reduction, food energy efficiency reduction, food intake reduction, and an increase in body temperature. Using serum metabolomics analysis, we showed that succinate, but not liraglutide, promoted a significant increase in the blood levels of several medium and long-chain fatty acids. In conclusion, exogenous succinate promotes rapid changes in brown adipose tissue mitochondrial proteins, and when used in association with liraglutide, increases body mass reduction.NEW & NOTEWORTHY Exogenous succinate induces major changes in brown adipose tissue protein expression affecting particularly mitochondrial respiration and structural proteins. When given exogenously in drinking water, succinate mitigates body mass gain in a rodent model of diet-induced obesity; in addition, when given in association with the glucagon-like peptide-1 receptor agonist, liraglutide, succinate increases body mass reduction promoted by liraglutide alone.
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Affiliation(s)
- Rodrigo S Gaspar
- Laboratory of Cell Signaling-Obesity and Comorbidities Research Center, University of Campinas, Campinas, Brazil
- National Institute of Science and Technology on Neuroimmunomodulation, Rio de Janeiro, Brazil
| | - Jeany Delafiori
- INNOVARE Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, Brazil
| | - Giuliana Zuccoli
- Laboratory of Neuroproteomics, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - Thais P Prado
- Laboratory of Cell Signaling-Obesity and Comorbidities Research Center, University of Campinas, Campinas, Brazil
| | - Joseane Morari
- Laboratory of Cell Signaling-Obesity and Comorbidities Research Center, University of Campinas, Campinas, Brazil
| | - Davi Sidarta-Oliveira
- Laboratory of Cell Signaling-Obesity and Comorbidities Research Center, University of Campinas, Campinas, Brazil
| | - Carina S Solon
- Laboratory of Cell Signaling-Obesity and Comorbidities Research Center, University of Campinas, Campinas, Brazil
| | - Rodrigo R Catharino
- INNOVARE Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, Brazil
| | - Eliana P Araujo
- Laboratory of Cell Signaling-Obesity and Comorbidities Research Center, University of Campinas, Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Institute of Biology, University of Campinas, Campinas, Brazil
- D'Or Institute for Research and Education, São Paulo, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, Brazil
- National Institute of Biomarkers in Neuropsychiatry, National Council for Scientific and Technological Development, São Paulo, Brazil
| | - Licio A Velloso
- Laboratory of Cell Signaling-Obesity and Comorbidities Research Center, University of Campinas, Campinas, Brazil
- National Institute of Science and Technology on Neuroimmunomodulation, Rio de Janeiro, Brazil
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29
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Nickelsen A, Götz C, Lenz F, Niefind K, König S, Jose J. Analyzing the interactome of human CK2β in prostate carcinoma cells reveals HSP70-1 and Rho guanin nucleotide exchange factor 12 as novel interaction partners. FASEB Bioadv 2023; 5:114-130. [PMID: 36876296 PMCID: PMC9983076 DOI: 10.1096/fba.2022-00098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/19/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
CK2β is the non-catalytic modulating part of the S/T-protein kinase CK2. However, the overall function of CK2β is poorly understood. Here, we report on the identification of 38 new interaction partners of the human CK2β from lysates of DU145 prostate cancer cells using photo-crosslinking and mass spectrometry, whereby HSP70-1 was identified with high abundance. The KD value of its interaction with CK2β was determined as 0.57 μM by microscale thermophoresis, this being the first time, to our knowledge, that a KD value of CK2β with another protein than CK2α or CK2α' was quantified. Phosphorylation studies excluded HSP70-1 as a substrate or activity modulator of CK2, suggesting a CK2 activity independent interaction of HSP70-1 with CK2β. Co-immunoprecipitation experiments in three different cancer cell lines confirmed the interaction of HSP70-1 with CK2β in vivo. A second identified CK2β interaction partner was Rho guanin nucleotide exchange factor 12, indicating an involvement of CK2β in the Rho-GTPase signal pathway, described here for the first time to our knowledge. This points to a role of CK2β in the interaction network affecting the organization of the cytoskeleton.
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Affiliation(s)
- Anna Nickelsen
- Institute of Pharmaceutical and Medicinal Chemistry University of Münster Münster Germany
| | - Claudia Götz
- Department of Medical Biochemistry and Molecular Biology Saarland University Homburg Germany
| | - Florian Lenz
- Institute of Pharmaceutical and Medicinal Chemistry University of Münster Münster Germany
| | - Karsten Niefind
- Department of Chemistry, Institute of Biochemistry University of Cologne Köln Germany
| | - Simone König
- Interdisciplinary Center for Clinical Research, Core Unit Proteomics, Medical Faculty University of Münster Münster Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry University of Münster Münster Germany
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30
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Rizzo AJ, Palacios MB, Vale EM, Zelada AM, Silveira V, Burrieza HP. Snapshot of four mature quinoa ( Chenopodium quinoa) seeds: a shotgun proteomics analysis with emphasis on seed maturation, reserves and early germination. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:319-334. [PMID: 37033760 PMCID: PMC10073371 DOI: 10.1007/s12298-023-01295-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/10/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Chenopodium quinoa Willd. is a crop species domesticated over 5000 years ago. This species is highly diverse, with a geographical distribution that covers more than 5000 km from Colombia to Chile, going through a variety of edaphoclimatic conditions. Quinoa grains have great nutritional quality, raising interest at a worldwide level. In this work, by using shotgun proteomics and in silico analysis, we present an overview of mature quinoa seed proteins from a physiological context and considering the process of seed maturation and future seed germination. For this purpose, we selected grains from four contrasting quinoa cultivars (Amarilla de Maranganí, Chadmo, Sajama and Nariño) with different edaphoclimatic and geographical origins. The results give insight on the most important metabolic pathways for mature quinoa seeds including: starch synthesis, protein bodies and lipid bodies composition, reserves and their mobilization, redox homeostasis, and stress related proteins like heat-shock proteins (HSPs) and late embryogenesis abundant proteins (LEAs), as well as evidence for capped and uncapped mRNA translation. LEAs present in our analysis show a specific pattern of expression matching that of other species. Overall, this work presents a complete snapshot of quinoa seeds physiological context, providing a reference point for further studies. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01295-8.
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Affiliation(s)
- Axel Joel Rizzo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Biología del Desarrollo de las Plantas, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Belén Palacios
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Biología del Desarrollo de las Plantas, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ellen Moura Vale
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, RJ Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos Dos Goytacazes, RJ Brazil
| | - Alicia Mercedes Zelada
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Agrobiotecnología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, RJ Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos Dos Goytacazes, RJ Brazil
| | - Hernán Pablo Burrieza
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Biología del Desarrollo de las Plantas, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
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31
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Rivera-Lugo R, Huang S, Lee F, Méheust R, Iavarone AT, Sidebottom AM, Oldfield E, Portnoy DA, Light SH. Distinct Energy-Coupling Factor Transporter Subunits Enable Flavin Acquisition and Extracytosolic Trafficking for Extracellular Electron Transfer in Listeria monocytogenes. mBio 2023; 14:e0308522. [PMID: 36744898 PMCID: PMC9973259 DOI: 10.1128/mbio.03085-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 02/07/2023] Open
Abstract
A variety of electron transfer mechanisms link bacterial cytosolic electron pools with functionally diverse redox activities in the cell envelope and extracellular space. In Listeria monocytogenes, the ApbE-like enzyme FmnB catalyzes extracytosolic protein flavinylation, covalently linking a flavin cofactor to proteins that transfer electrons to extracellular acceptors. L. monocytogenes uses an energy-coupling factor (ECF) transporter complex that contains distinct substrate-binding, transmembrane, ATPase A, and ATPase A' subunits (RibU, EcfT, EcfA, and EcfA') to import environmental flavins, but the basis of extracytosolic flavin trafficking for FmnB flavinylation remains poorly defined. In this study, we show that the EetB and FmnA proteins are related to ECF transporter substrate-binding and transmembrane subunits, respectively, and are essential for exporting flavins from the cytosol for flavinylation. Comparisons of the flavin import versus export capabilities of L. monocytogenes strains lacking different ECF transporter subunits demonstrate a strict directionality of substrate-binding subunit transport but partial functional redundancy of transmembrane and ATPase subunits. Based on these results, we propose that ECF transporter complexes with different subunit compositions execute directional flavin import/export through a broadly conserved mechanism. Finally, we present genomic context analyses that show that related ECF exporter genes are distributed across members of the phylum Firmicutes and frequently colocalize with genes encoding flavinylated extracytosolic proteins. These findings clarify the basis of ECF transporter export and extracytosolic flavin cofactor trafficking in Firmicutes. IMPORTANCE Bacteria import vitamins and other essential compounds from their surroundings but also traffic related compounds from the cytosol to the cell envelope where they serve various functions. Studying the foodborne pathogen Listeria monocytogenes, we find that the modular use of subunits from a prominent class of bacterial transporters enables the import of environmental vitamin B2 cofactors and the extracytosolic trafficking of a vitamin B2-derived cofactor that facilitates redox reactions in the cell envelope. These studies clarify the basis of bidirectional small-molecule transport across the cytoplasmic membrane and the assembly of redox-active proteins within the cell envelope and extracellular space.
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Affiliation(s)
- Rafael Rivera-Lugo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Shuo Huang
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Frank Lee
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Raphaël Méheust
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Anthony T. Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, California, USA
| | | | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Samuel H. Light
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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32
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Polesi LG, Fraga HPDF, Almeida FA, Silveira V, Guerra MP. Comparative proteomic analysis and antioxidant enzyme activity provide new insights into the embryogenic competence of Guadua chacoensis (Bambusoideae, Poaceae). J Proteomics 2023; 273:104790. [PMID: 36535623 DOI: 10.1016/j.jprot.2022.104790] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/21/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
Somatic embryogenesis (SE) involves modifications of cellular, biochemical, genetic, and epigenetic patterns. Our work investigated proteins as markers of embryogenic response and characterized the redox state of embryogenic cultures (EC) of Guadua chacoensis. We identified a total of 855 proteins; 129 were up- and 136 down-accumulated in EC as compared with non-embryogenic culture (NEC). Additionally, 37 and 22 proteins were identified as unique in EC and NEC, respectively. Heat-shock proteins as unique proteins and increased activity in Superoxide Dismutase and Guaiacol Peroxidase in EC suggest that the embryogenic response requires activation of the stress response mechanism. Ribosomal, translational, and glycolytic proteins in EC seem to be associated with protein synthesis and energy sources for embryo development, respectively. Accumulation of cell wall-related proteins, such as Arabinogalactan and Polygalacturonase inhibitors, and signaling transduction proteins, including Chitinase, Phospholipase, and Guanine nucleotide-binding proteins in EC seems to be associated with embryogenic response. Enhancement of H2O2 content in EC compared to NEC suggests a possible role as a secondary messenger in SE. Altogether, the present study identified marker proteins of embryogenic response in G. chacoensis and revealed the activation of ROS scavenging enzymes to assure cell redox homeostasis and SE responses. SIGNIFICANCE: Somatic embryogenesis is a promising technique for the propagation and conservation of bamboo species; however, this route has been the least understood and studied until now. This study corresponds to the first work approaching proteomics complemented with biochemical analyses in the somatic embryogenesis of bamboo, bringing robust and precise information that can improve our understanding of this complex morphogenetic route.
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Affiliation(s)
- Luiza Giacomolli Polesi
- Graduate Program in Plant Genetic Resources, Laboratory of Plant Developmental Physiology and Genetics, Federal University of Santa Catarina, Florianópolis, SC 88034-000, Brazil
| | | | - Felipe Astolpho Almeida
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ 28013-602, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ 28013-602, Brazil
| | - Miguel Pedro Guerra
- Graduate Program in Plant Genetic Resources, Laboratory of Plant Developmental Physiology and Genetics, Federal University of Santa Catarina, Florianópolis, SC 88034-000, Brazil; Graduate Program in Agricultural and Natural Ecosystems, Federal University of Santa Catarina, Curitibanos Campus, Ulysses Gaboardi Road, km 3, 89520-000 Curitibanos, Brazil.
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33
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Garlapati V, Molitor M, Michna T, Harms GS, Finger S, Jung R, Lagrange J, Efentakis P, Wild J, Knorr M, Karbach S, Wild S, Vujacic-Mirski K, Münzel T, Daiber A, Brandt M, Gori T, Milting H, Tenzer S, Ruf W, Wenzel P. Targeting myeloid cell coagulation signaling blocks MAP kinase/TGF-β1-driven fibrotic remodeling in ischemic heart failure. J Clin Invest 2023; 133:156436. [PMID: 36548062 PMCID: PMC9927945 DOI: 10.1172/jci156436] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Despite major advances in acute interventions for myocardial infarction (MI), adverse cardiac remodeling and excess fibrosis after MI causing ischemic heart failure (IHF) remain a leading cause of death worldwide. Here we identify a profibrotic coagulation signaling pathway that can be targeted for improved cardiac function following MI with persistent ischemia. Quantitative phosphoproteomics of cardiac tissue revealed an upregulated mitogen-activated protein kinase (MAPK) pathway in human IHF. Intervention in this pathway with trametinib improves myocardial function and prevents fibrotic remodeling in a murine model of non-reperfused MI. MAPK activation in MI requires myeloid cell signaling of protease-activated receptor 2 linked to the cytoplasmic domain of the coagulation initiator tissue factor (TF). They act upstream of pro-oxidant NOX2 NADPH oxidase, ERK1/2 phosphorylation, and activation of profibrotic TGF-β1. Specific targeting with the TF inhibitor nematode anticoagulant protein c2 (NAPc2) starting 1 day after established experimental MI averts IHF. Increased TF cytoplasmic domain phosphorylation in circulating monocytes from patients with subacute MI identifies a potential thromboinflammatory biomarker reflective of increased risk for IHF and suitable for patient selection to receive targeted TF inhibition therapy.
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Affiliation(s)
- Venkata Garlapati
- Center for Thrombosis and Hemostasis and.,Department of Cardiology, University Medical Center Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Michael Molitor
- Center for Thrombosis and Hemostasis and.,Department of Cardiology, University Medical Center Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Thomas Michna
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany
| | - Gregory S Harms
- Cell Biology Unit, University Medical Center Mainz, Mainz, Germany and.,Departments of Biology and Physics, Wilkes University, Wilkes-Barre, Pennsylvania, USA
| | - Stefanie Finger
- Center for Thrombosis and Hemostasis and.,Department of Cardiology, University Medical Center Mainz, Mainz, Germany
| | - Rebecca Jung
- Center for Thrombosis and Hemostasis and.,Department of Cardiology, University Medical Center Mainz, Mainz, Germany.,Institute for Molecular Medicine, University Medical Center Mainz, Mainz, Germany
| | | | | | - Johannes Wild
- Center for Thrombosis and Hemostasis and.,Department of Cardiology, University Medical Center Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Maike Knorr
- Center for Thrombosis and Hemostasis and.,Department of Cardiology, University Medical Center Mainz, Mainz, Germany
| | - Susanne Karbach
- Center for Thrombosis and Hemostasis and.,Department of Cardiology, University Medical Center Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Sabine Wild
- Center for Thrombosis and Hemostasis and.,Department of Cardiology, University Medical Center Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | | | - Thomas Münzel
- Center for Thrombosis and Hemostasis and.,Department of Cardiology, University Medical Center Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Andreas Daiber
- Department of Cardiology, University Medical Center Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Moritz Brandt
- Center for Thrombosis and Hemostasis and.,Department of Cardiology, University Medical Center Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Tommaso Gori
- Department of Cardiology, University Medical Center Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Hendrik Milting
- Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Herz- und Diabeteszentrum NRW, Bad Oeynhausen, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany.,Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Germany and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfram Ruf
- Center for Thrombosis and Hemostasis and.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany.,Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
| | - Philip Wenzel
- Center for Thrombosis and Hemostasis and.,Department of Cardiology, University Medical Center Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
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34
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Ramić D, Jug B, Šimunović K, Tušek Žnidarič M, Kunej U, Toplak N, Kovač M, Fournier M, Jamnik P, Smole Možina S, Klančnik A. The Role of luxS in Campylobacter jejuni Beyond Intercellular Signaling. Microbiol Spectr 2023; 11:e0257222. [PMID: 36722966 PMCID: PMC10100756 DOI: 10.1128/spectrum.02572-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/07/2023] [Indexed: 02/02/2023] Open
Abstract
The full role of the luxS gene in the biological processes, such as essential amino acid synthesis, nitrogen and pyruvate metabolism, and flagellar assembly, of Campylobacter jejuni has not been clearly described to date. Therefore, in this study, we used a comprehensive approach at the cellular and molecular levels, including transcriptomics and proteomics, to investigate the key role of the luxS gene and compared C. jejuni 11168ΔluxS (luxS mutant) and C. jejuni NCTC 11168 (wild type) strains. Transcriptomic analysis of the luxS mutant grown under optimal conditions revealed upregulation of luxS mutant metabolic pathways when normalized to wild type, including oxidative phosphorylation, carbon metabolism, citrate cycle, biosynthesis of secondary metabolites, and biosynthesis of various essential amino acids. Interestingly, induction of these metabolic pathways was also confirmed by proteomic analysis, indicating their important role in energy production and the growth of C. jejuni. In addition, genes important for the stress response of C. jejuni, including nutrient starvation and oxidative stress, were upregulated. This was also evident in the better survival of the luxS mutant under starvation conditions than the wild type. At the molecular level, we confirmed that metabolic pathways were upregulated under optimal conditions in the luxS mutant, including those important for the biosynthesis of several essential amino acids. This also modulated the utilization of various carbon and nitrogen sources, as determined by Biolog phenotype microarray analysis. In summary, transcriptomic and proteomic analysis revealed key biological differences in tricarboxylic acid (TCA) cycle, pyruvate, nitrogen, and thiamine metabolism as well as lipopolysaccharide biosynthesis in the luxS mutant. IMPORTANCE Campylobacter jejuni is the world's leading foodborne bacterial pathogen of gastrointestinal disease in humans. C. jejuni is a fastidious but widespread organism and the most frequently reported zoonotic pathogen in the European Union since 2005. This led us to believe that C. jejuni, which is highly sensitive to stress factors (starvation and oxygen concentration) and has a low growth rate, benefits significantly from the luxS gene. The role of this gene in the life cycle of C. jejuni is well known, and the expression of luxS regulates many phenotypes, including motility, biofilm formation, host colonization, virulence, autoagglutination, cellular adherence and invasion, oxidative stress, and chemotaxis. Surprisingly, this study confirmed for the first time that the deletion of the luxS gene strongly affects the central metabolic pathway of C. jejuni, which improves its survival, showing its role beyond the intercellular signaling system.
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Affiliation(s)
- Dina Ramić
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Jug
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Katarina Šimunović
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and System Biology, National institute of Biology, Ljubljana, Slovenia
| | - Urban Kunej
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | | | - Marjorie Fournier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Polona Jamnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sonja Smole Možina
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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35
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Räuber S, Schroeter CB, Strippel C, Nelke C, Ruland T, Dik A, Golombeck KS, Regner-Nelke L, Paunovic M, Esser D, Münch C, Rosenow F, van Duijn M, Henes A, Ruck T, Amit I, Leypoldt F, Titulaer MJ, Wiendl H, Meuth SG, Meyer Zu Hörste G, Melzer N. Cerebrospinal fluid proteomics indicates immune dysregulation and neuronal dysfunction in antibody associated autoimmune encephalitis. J Autoimmun 2023; 135:102985. [PMID: 36621173 DOI: 10.1016/j.jaut.2022.102985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/15/2022] [Indexed: 01/09/2023]
Abstract
Autoimmune Encephalitis (AE) spans a group of non-infectious inflammatory conditions of the central nervous system due to an imbalanced immune response. Aiming to elucidate the pathophysiological mechanisms of AE, we applied an unsupervised proteomic approach to analyze the cerebrospinal fluid (CSF) protein profile of AE patients with autoantibodies against N-methyl-d-aspartate receptor (NMDAR) (n = 9), leucine-rich glioma-inactivated protein 1 (LGI1) (n = 9), or glutamate decarboxylase 65 (GAD65) (n = 8) compared to 9 patients with relapsing-remitting multiple sclerosis as inflammatory controls, and 10 patients with somatic symptom disorder as non-inflammatory controls. We found a dysregulation of the complement system, a disbalance between pro-inflammatory and anti-inflammatory proteins on the one hand, and dysregulation of proteins involved in synaptic transmission, synaptogenesis, brain connectivity, and neurodegeneration on the other hand to a different extent in all AE subtypes compared to non-inflammatory controls. Furthermore, elevated levels of several proteases and reduction in protease inhibitors could be detected in all AE subtypes compared to non-inflammatory controls. Moreover, the different AE subtypes showed distinct protein profiles compared to each other and inflammatory controls which may facilitate future identification of disease-specific biomarkers. Overall, CSF proteomics provides insights into the complex pathophysiological mechanisms of AE, including immune dysregulation, neuronal dysfunction, neurodegeneration, and altered protease function.
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Affiliation(s)
- Saskia Räuber
- Department of Neurology with Institute of Translational Neurology, University of Münster, 48149, Münster, Germany; Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Christina B Schroeter
- Department of Neurology with Institute of Translational Neurology, University of Münster, 48149, Münster, Germany; Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Christine Strippel
- Department of Neurology with Institute of Translational Neurology, University of Münster, 48149, Münster, Germany
| | - Christopher Nelke
- Department of Neurology with Institute of Translational Neurology, University of Münster, 48149, Münster, Germany; Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Tillmann Ruland
- Department of Psychiatry, University of Münster, 48149, Münster, Germany; Department of Psychiatry, Maria Brunn Hospital, 48163, Münster, Germany
| | - Andre Dik
- Department of Neurology with Institute of Translational Neurology, University of Münster, 48149, Münster, Germany; Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Kristin S Golombeck
- Department of Neurology with Institute of Translational Neurology, University of Münster, 48149, Münster, Germany; Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Liesa Regner-Nelke
- Department of Neurology with Institute of Translational Neurology, University of Münster, 48149, Münster, Germany; Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Manuela Paunovic
- Department of Neurology, Erasmus MC University Medical Center, 3015 GD, Rotterdam, the Netherlands
| | - Daniela Esser
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, 24105, Kiel, Lübeck, Germany
| | - Christian Münch
- Institute of Biochemistry II, Goethe University Frankfurt, Faculty of Medicine, Theodor-Stern-Kai 7, Building 75, 60590, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Frankfurt am Main, Germany; Cardio-Pulmonary Institute, Frankfurt am Main, Germany
| | - Felix Rosenow
- Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital Frankfurt, Goethe University Frankfurt, 60528 Frankfurt am Main, Germany; LOEWE Center for Personalized Translational Epilepsy Research (CePTER), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Martijn van Duijn
- Department of Neurology, Erasmus MC University Medical Center, 3015 GD, Rotterdam, the Netherlands
| | - Antonia Henes
- Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Tobias Ruck
- Department of Neurology with Institute of Translational Neurology, University of Münster, 48149, Münster, Germany; Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Frank Leypoldt
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, 24105, Kiel, Lübeck, Germany; Department of Neurology, Faculty of Medicine, Kiel University, 24105, Kiel, Germany
| | - Maarten J Titulaer
- Department of Neurology, Erasmus MC University Medical Center, 3015 GD, Rotterdam, the Netherlands
| | - Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University of Münster, 48149, Münster, Germany
| | - Sven G Meuth
- Department of Neurology with Institute of Translational Neurology, University of Münster, 48149, Münster, Germany; Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Gerd Meyer Zu Hörste
- Department of Neurology with Institute of Translational Neurology, University of Münster, 48149, Münster, Germany
| | - Nico Melzer
- Department of Neurology with Institute of Translational Neurology, University of Münster, 48149, Münster, Germany; Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany.
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36
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Greco MF, Rizzuto AS, Zarà M, Cafora M, Favero C, Solazzo G, Giusti I, Adorni MP, Zimetti F, Dolo V, Banfi C, Ferri N, Sirtori CR, Corsini A, Barbieri SS, Pistocchi A, Bollati V, Macchi C, Ruscica M. PCSK9 Confers Inflammatory Properties to Extracellular Vesicles Released by Vascular Smooth Muscle Cells. Int J Mol Sci 2022; 23:13065. [PMID: 36361853 PMCID: PMC9655172 DOI: 10.3390/ijms232113065] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 10/20/2023] Open
Abstract
Vascular smooth muscle cells (VSMCs) are key participants in both early- and late-stage atherosclerosis and influence neighbouring cells possibly by means of bioactive molecules, some of which are packed into extracellular vesicles (EVs). Proprotein convertase subtilisin/kexin type 9 (PCSK9) is expressed and secreted by VSMCs. This study aimed to unravel the role of PCSK9 on VSMCs-derived EVs in terms of content and functionality. EVs were isolated from human VSMCs overexpressing human PCSK9 (VSMCPCSK9-EVs) and tested on endothelial cells, monocytes, macrophages and in a model of zebrafish embryos. Compared to EVs released from wild-type VSMCs, VSMCPCSK9-EVs caused a rise in the expression of adhesion molecules in endothelial cells and of pro-inflammatory cytokines in monocytes. These acquired an increased migratory capacity, a reduced oxidative phosphorylation and secreted proteins involved in immune response and immune effector processes. Concerning macrophages, VSMCPCSK9-EVs enhanced inflammatory milieu and uptake of oxidized low-density lipoproteins, whereas the migratory capacity was reduced. When injected into zebrafish embryos, VSMCPCSK9-EVs favoured the recruitment of macrophages toward the site of injection. The results of the present study provide evidence that PCSK9 plays an inflammatory role by means of EVs, at least by those derived from smooth muscle cells of vascular origin.
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Affiliation(s)
- Maria Francesca Greco
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Alessandra Stefania Rizzuto
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Marta Zarà
- Centro Cardiologico Monzino, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 20133 Milan, Italy
| | - Marco Cafora
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20133 Milan, Italy
| | - Chiara Favero
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20133 Milan, Italy
| | - Giulia Solazzo
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20133 Milan, Italy
| | - Ilaria Giusti
- Department of Life, Health and Environmental Sciences, Università degli Studi dell'Aquila, 67100 L'Aquila, Italy
| | - Maria Pia Adorni
- Unit of Neuroscience, Department of Medicine and Surgery, Università degli Studi di Parma, 43124 Parma, Italy
| | - Francesca Zimetti
- Department of Food and Drug, Università degli Studi di Parma, 43124 Parma, Italy
| | - Vincenza Dolo
- Department of Life, Health and Environmental Sciences, Università degli Studi dell'Aquila, 67100 L'Aquila, Italy
| | - Cristina Banfi
- Centro Cardiologico Monzino, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 20133 Milan, Italy
| | - Nicola Ferri
- Department of Medicine, Università degli Studi di Padova, 35100 Padua, Italy
| | - Cesare R Sirtori
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Alberto Corsini
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Silvia Stella Barbieri
- Centro Cardiologico Monzino, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 20133 Milan, Italy
| | - Anna Pistocchi
- Department of Medical Biotechnology and Translational, Università degli Studi di Milano, L.I.T.A., 20133 Milan, Italy
| | - Valentina Bollati
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20133 Milan, Italy
| | - Chiara Macchi
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Massimiliano Ruscica
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
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37
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SARS-CoV-2 infects adipose tissue in a fat depot- and viral lineage-dependent manner. Nat Commun 2022; 13:5722. [PMID: 36175400 PMCID: PMC9521555 DOI: 10.1038/s41467-022-33218-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/08/2022] [Indexed: 01/08/2023] Open
Abstract
Visceral adiposity is a risk factor for severe COVID-19, and a link between adipose tissue infection and disease progression has been proposed. Here we demonstrate that SARS-CoV-2 infects human adipose tissue and undergoes productive infection in fat cells. However, susceptibility to infection and the cellular response depends on the anatomical origin of the cells and the viral lineage. Visceral fat cells express more ACE2 and are more susceptible to SARS-CoV-2 infection than their subcutaneous counterparts. SARS-CoV-2 infection leads to inhibition of lipolysis in subcutaneous fat cells, while in visceral fat cells, it results in higher expression of pro-inflammatory cytokines. Viral load and cellular response are attenuated when visceral fat cells are infected with the SARS-CoV-2 gamma variant. A similar degree of cell death occurs 4-days after SARS-CoV-2 infection, regardless of the cell origin or viral lineage. Hence, SARS-CoV-2 infects human fat cells, replicating and altering cell function and viability in a depot- and viral lineage-dependent fashion. Visceral adiposity is a risk factor for severe COVID-19, and infection of adipose tissue by SARS-CoV-2 has been reported. Here the authors confirm that human adipose tissue is a possible site for SARS-CoV-2 infection, but the degree of adipose tissue infection and the way adipocytes respond to the virus depend on the adipose tissue depot and the viral strain.
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38
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Düking T, Spieth L, Berghoff SA, Piepkorn L, Schmidke AM, Mitkovski M, Kannaiyan N, Hosang L, Scholz P, Shaib AH, Schneider LV, Hesse D, Ruhwedel T, Sun T, Linhoff L, Trevisiol A, Köhler S, Pastor AM, Misgeld T, Sereda M, Hassouna I, Rossner MJ, Odoardi F, Ischebeck T, de Hoz L, Hirrlinger J, Jahn O, Saher G. Ketogenic diet uncovers differential metabolic plasticity of brain cells. SCIENCE ADVANCES 2022; 8:eabo7639. [PMID: 36112685 PMCID: PMC9481126 DOI: 10.1126/sciadv.abo7639] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
To maintain homeostasis, the body, including the brain, reprograms its metabolism in response to altered nutrition or disease. However, the consequences of these challenges for the energy metabolism of the different brain cell types remain unknown. Here, we generated a proteome atlas of the major central nervous system (CNS) cell types from young and adult mice, after feeding the therapeutically relevant low-carbohydrate, high-fat ketogenic diet (KD) and during neuroinflammation. Under steady-state conditions, CNS cell types prefer distinct modes of energy metabolism. Unexpectedly, the comparison with KD revealed distinct cell type-specific strategies to manage the altered availability of energy metabolites. Astrocytes and neurons but not oligodendrocytes demonstrated metabolic plasticity. Moreover, inflammatory demyelinating disease changed the neuronal metabolic signature in a similar direction as KD. Together, these findings highlight the importance of the metabolic cross-talk between CNS cells and between the periphery and the brain to manage altered nutrition and neurological disease.
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Affiliation(s)
- Tim Düking
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Lena Spieth
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Stefan A. Berghoff
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Lars Piepkorn
- Neuroproteomics Group, Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Translational Neuroproteomics Group, Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Annika M. Schmidke
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Miso Mitkovski
- City Campus Light Microscopy Facility, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Nirmal Kannaiyan
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Leon Hosang
- Institute for Neuroimmunology and Multiple Sclerosis Research, University Medical Center Göttingen, Göttingen, Germany
| | - Patricia Scholz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Ali H. Shaib
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Lennart V. Schneider
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Dörte Hesse
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Neuroproteomics Group, Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Torben Ruhwedel
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Electron Microscopy Core Unit, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ting Sun
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Lisa Linhoff
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
- Translational Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Andrea Trevisiol
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Susanne Köhler
- Carl-Ludwig-Institute for Physiology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Adrian Marti Pastor
- Institute of Neuronal Cell Biology, Technische Universität München, Cluster for Systems Neurology (SyNergy), German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Thomas Misgeld
- Institute of Neuronal Cell Biology, Technische Universität München, Cluster for Systems Neurology (SyNergy), German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Michael Sereda
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
- Translational Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Imam Hassouna
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Moritz J. Rossner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Francesca Odoardi
- Institute for Neuroimmunology and Multiple Sclerosis Research, University Medical Center Göttingen, Göttingen, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
- Institute of Plant Biology and Biotechnology (IBBP), Green Biotechnology, University of Münster, Münster, Germany
| | - Livia de Hoz
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Neurowissenschafliches Forschungszentrum, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes Hirrlinger
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Carl-Ludwig-Institute for Physiology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Olaf Jahn
- Neuroproteomics Group, Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Translational Neuroproteomics Group, Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Gesine Saher
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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van der Kooij MA, Rojas-Charry L, Givehchi M, Wolf C, Bueno D, Arndt S, Tenzer S, Mattioni L, Treccani G, Hasch A, Schmeisser MJ, Vianello C, Giacomello M, Methner A. Chronic social stress disrupts the intracellular redistribution of brain hexokinase 3 induced by shifts in peripheral glucose levels. J Mol Med (Berl) 2022; 100:1441-1453. [PMID: 35943566 PMCID: PMC9470722 DOI: 10.1007/s00109-022-02235-x] [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: 02/01/2022] [Revised: 06/06/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022]
Abstract
Abstract
Chronic stress has the potential to impair health and may increase the vulnerability for psychiatric disorders. Emerging evidence suggests that specific neurometabolic dysfunctions play a role herein. In mice, chronic social defeat (CSD) stress reduces cerebral glucose uptake despite hyperglycemia. We hypothesized that this metabolic decoupling would be reflected by changes in contact sites between mitochondria and the endoplasmic reticulum, important intracellular nutrient sensors, and signaling hubs. We thus analyzed the proteome of their biochemical counterparts, mitochondria-associated membranes (MAMs) from whole brain tissue obtained from CSD and control mice. This revealed a lack of the glucose-metabolizing enzyme hexokinase 3 (HK3) in MAMs from CSD mice. In controls, HK3 protein abundance in MAMs and also in striatal synaptosomes correlated positively with peripheral blood glucose levels, but this connection was lost in CSD. We conclude that the ability of HK3 to traffic to sites of need, such as MAMs or synapses, is abolished upon CSD and surmise that this contributes to a cellular dysfunction instigated by chronic stress.
Key messages Chronic social defeat (CSD) alters brain glucose metabolism CSD depletes hexokinase 3 (HK3) from mitochondria-associated membranes (MAMs) CSD results in loss of positive correlation between blood glucose and HK3 in MAMs and synaptosomes
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Affiliation(s)
| | - Liliana Rojas-Charry
- Institute for Molecular Medicine, Johannes Gutenberg University Mainz, Mainz, 55131, Germany.,Institute of Anatomy, Johannes Gutenberg University Mainz, Mainz, 55131, Germany
| | - Maryam Givehchi
- Leibniz Institute for Resilience Research (LIR), Mainz, 55122, Germany
| | - Christina Wolf
- Institute for Molecular Medicine, Johannes Gutenberg University Mainz, Mainz, 55131, Germany
| | - Diones Bueno
- Institute for Molecular Medicine, Johannes Gutenberg University Mainz, Mainz, 55131, Germany
| | - Sabine Arndt
- Institute for Immunology, Johannes Gutenberg University Mainz, Mainz, 55131, Germany
| | - Stefan Tenzer
- Institute for Immunology, Johannes Gutenberg University Mainz, Mainz, 55131, Germany
| | - Lorenzo Mattioni
- Institute of Anatomy, Johannes Gutenberg University Mainz, Mainz, 55131, Germany
| | - Giulia Treccani
- Institute of Anatomy, Johannes Gutenberg University Mainz, Mainz, 55131, Germany.,Department of Psychiatry and Psychotherapy, Translational Psychiatry, University Medical Center, Johannes Gutenberg University Mainz, Mainz, 55131, Germany
| | - Annika Hasch
- Leibniz Institute for Resilience Research (LIR), Mainz, 55122, Germany
| | - Michael J Schmeisser
- Institute of Anatomy, Johannes Gutenberg University Mainz, Mainz, 55131, Germany
| | - Caterina Vianello
- Institute for Molecular Medicine, Johannes Gutenberg University Mainz, Mainz, 55131, Germany.,Department of Biology, University of Padua, Padua, 35121, Italy
| | | | - Axel Methner
- Institute for Molecular Medicine, Johannes Gutenberg University Mainz, Mainz, 55131, Germany.
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40
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Flomm FJ, Soh TK, Schneider C, Wedemann L, Britt HM, Thalassinos K, Pfitzner S, Reimer R, Grünewald K, Bosse JB. Intermittent bulk release of human cytomegalovirus. PLoS Pathog 2022; 18:e1010575. [PMID: 35925870 PMCID: PMC9352052 DOI: 10.1371/journal.ppat.1010575] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/06/2022] [Indexed: 01/24/2023] Open
Abstract
Human Cytomegalovirus (HCMV) can infect a variety of cell types by using virions of varying glycoprotein compositions. It is still unclear how this diversity is generated, but spatio-temporally separated envelopment and egress pathways might play a role. So far, one egress pathway has been described in which HCMV particles are individually enveloped into small vesicles and are subsequently exocytosed continuously. However, some studies have also found enveloped virus particles inside multivesicular structures but could not link them to productive egress or degradation pathways. We used a novel 3D-CLEM workflow allowing us to investigate these structures in HCMV morphogenesis and egress at high spatio-temporal resolution. We found that multiple envelopment events occurred at individual vesicles leading to multiviral bodies (MViBs), which subsequently traversed the cytoplasm to release virions as intermittent bulk pulses at the plasma membrane to form extracellular virus accumulations (EVAs). Our data support the existence of a novel bona fide HCMV egress pathway, which opens the gate to evaluate divergent egress pathways in generating virion diversity.
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Affiliation(s)
- Felix J. Flomm
- Centre for Structural Systems Biology, Hamburg, Germany
- Hannover Medical School, Institute of Virology, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
| | - Timothy K. Soh
- Centre for Structural Systems Biology, Hamburg, Germany
- Hannover Medical School, Institute of Virology, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
| | | | - Linda Wedemann
- Centre for Structural Systems Biology, Hamburg, Germany
- Hannover Medical School, Institute of Virology, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
| | - Hannah M. Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | | | | | - Kay Grünewald
- Centre for Structural Systems Biology, Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- University of Hamburg, Department of Chemistry, Hamburg, Germany
| | - Jens B. Bosse
- Centre for Structural Systems Biology, Hamburg, Germany
- Hannover Medical School, Institute of Virology, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
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41
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Davalieva K, Rusevski A, Velkov M, Noveski P, Kubelka-Sabit K, Filipovski V, Plaseski T, Dimovski A, Plaseska-Karanfilska D. Comparative proteomics analysis of human FFPE testicular tissues reveals new candidate biomarkers for distinction among azoospermia types and subtypes. J Proteomics 2022; 267:104686. [PMID: 35914715 DOI: 10.1016/j.jprot.2022.104686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 10/16/2022]
Abstract
Understanding molecular mechanisms that underpin azoospermia and discovery of biomarkers that could enable reliable, non-invasive diagnosis is highly needed. Using label-free data-independent LC-MS/MS acquisition coupled with ion mobility, we compared the FFPE testicular proteome of patients with obstructive (OA) and non-obstructive azoospermia (NOA) subtypes hypospermatogenesis (Hyp) and Sertoli cell-only syndrome (SCO). Out of 2044 proteins identified based on ≥2 peptides, 61 proteins had the power to quantitatively discriminate OA from NOA and 30 to quantitatively discriminate SCO from Hyp and OA. Among these, H1-6, RANBP1 and TKTL2 showed superior potential for quantitative discrimination among OA, Hyp and SCO. Integrin signaling pathway, adherens junction, planar cell polarity/convergent extension pathway and Dectin-1 mediated noncanonical NF-kB signaling were significantly associated with the proteins that could discriminate OA from NOA. Comparison with 2 transcriptome datasets revealed 278 and 55 co-differentially expressed proteins/genes with statistically significant positive correlation. Gene expression analysis by qPCR of 6 genes (H1-6, RANBP1, TKTL2, TKTL1, H2BC1, and ACTL7B) with the highest discriminatory power on protein level and the same regulation trend with transcriptomic datasets, confirmed proteomics results. In summary, our results suggest some underlying pathways in azoospermia and broaden the range of potential novel candidates for diagnosis. SIGNIFICANCE: Using a comparative proteomics approach on testicular tissue we have identified several pathways associated with azoospermia and a number of testis-specific and germ cell-specific proteins that have the potential to pinpoint the type of spermatogenesis failure. Furthermore, comparison with transcriptomics datasets based on genome-wide gene expression analyses of human testis specimens from azoospermia patients identified proteins that could discriminate between obstructive and non-obstructive azoospermia subtypes on both protein and mRNA levels. Up to our knowledge, this is the first integrated comparative analysis of proteomics and transcriptomics data from testicular tissues. We believe that the data from our study contributes significantly to increase the knowledge of molecular mechanisms of azoospermia and pave the way for new investigations in regards to non-invasive diagnosis.
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Affiliation(s)
- Katarina Davalieva
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia, Macedonia.
| | - Aleksandar Rusevski
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia, Macedonia
| | - Milan Velkov
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia, Macedonia
| | - Predrag Noveski
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia, Macedonia
| | - Katerina Kubelka-Sabit
- Laboratory for Histopathology, Clinical Hospital "Sistina", 1000 Skopje, North Macedonia, Macedonia
| | - Vanja Filipovski
- Laboratory for Histopathology, Clinical Hospital "Sistina", 1000 Skopje, North Macedonia, Macedonia
| | - Toso Plaseski
- Faculty of Medicine, Endocrinology and Metabolic Disorders Clinic, 1000 Skopje, North Macedonia, Macedonia
| | - Aleksandar Dimovski
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia, Macedonia; Faculty of Pharmacy, University "St. Cyril and Methodius", 1000 Skopje, North Macedonia, Macedonia
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, 1000 Skopje, North Macedonia, Macedonia.
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42
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de Oliveira LG, de Souza Angelo Y, Yamamoto P, Carregari VC, Crunfli F, Reis-de-Oliveira G, Costa L, Vendramini PH, Almeida ÉD, Dos Santos NB, Firmino EM, Paiva IM, Almeida GM, Sebollela A, Polonio CM, Zanluqui NG, de Oliveira MG, da Silva P, Gastão Davanzo G, Ayupe MC, Loureiro Salgado C, de Souza Filho AF, de Araújo MV, Silva-Pereira TT, de Almeida Campos AC, Góes LGB, Dos Passos Cunha M, Caldini EG, Lima MRDI, Fonseca DM, de Sá Guimarães AM, Minoprio PC, Munhoz CD, Mori CMC, Moraes-Vieira PM, Cunha TM, Martins-de-Souza D, Peron JPS. SARS-CoV-2 Infection Impacts Carbon Metabolism and Depends on Glutamine for Replication in Syrian Hamster Astrocytes. J Neurochem 2022; 163:113-132. [PMID: 35880385 PMCID: PMC9350388 DOI: 10.1111/jnc.15679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 01/08/2023]
Abstract
COVID‐19 causes more than million deaths worldwide. Although much is understood about the immunopathogenesis of the lung disease, a lot remains to be known on the neurological impact of COVID‐19. Here we evaluated immunometabolic changes using astrocytes in vitro and dissected brain areas of SARS‐CoV‐2 infected Syrian hamsters. We show that SARS‐CoV‐2 alters proteins of carbon metabolism, glycolysis, and synaptic transmission, many of which are altered in neurological diseases. Real‐time respirometry evidenced hyperactivation of glycolysis, further confirmed by metabolomics, with intense consumption of glucose, pyruvate, glutamine, and alpha ketoglutarate. Consistent with glutamine reduction, the blockade of glutaminolysis impaired viral replication and inflammatory response in vitro. SARS‐CoV‐2 was detected in vivo in hippocampus, cortex, and olfactory bulb of intranasally infected animals. Our data evidence an imbalance in important metabolic molecules and neurotransmitters in infected astrocytes. We suggest this may correlate with the neurological impairment observed during COVID‐19, as memory loss, confusion, and cognitive impairment.
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Affiliation(s)
- Lilian Gomes de Oliveira
- Neuroimmune Interactions Laboratory, Institute of Biomedical Science, Department of Immunology, University of São Paulo, São Paulo, SP, Brazil.,Neuroimmunology of Arboviruses Laboratory, Scientific Platform Pasteur, University of São Paulo, São Paulo, SP, Brazil
| | - Yan de Souza Angelo
- Neuroimmune Interactions Laboratory, Institute of Biomedical Science, Department of Immunology, University of São Paulo, São Paulo, SP, Brazil.,Neuroimmunology of Arboviruses Laboratory, Scientific Platform Pasteur, University of São Paulo, São Paulo, SP, Brazil
| | - Pedro Yamamoto
- Neuroimmune Interactions Laboratory, Institute of Biomedical Science, Department of Immunology, University of São Paulo, São Paulo, SP, Brazil.,Neuroimmunology of Arboviruses Laboratory, Scientific Platform Pasteur, University of São Paulo, São Paulo, SP, Brazil
| | - Victor Corasolla Carregari
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Fernanda Crunfli
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Guilherme Reis-de-Oliveira
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Lícia Costa
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Pedro Henrique Vendramini
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Érica Duque Almeida
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Barreto Dos Santos
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Egidi Mayara Firmino
- Center for Research in Inflammatory Diseases (CRID); Department of Pharmacology - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Isadora Marques Paiva
- Center for Research in Inflammatory Diseases (CRID); Department of Pharmacology - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Glaucia Maria Almeida
- Department of Biocehmistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Adriano Sebollela
- Department of Biocehmistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Carolina Manganeli Polonio
- Neuroimmune Interactions Laboratory, Institute of Biomedical Science, Department of Immunology, University of São Paulo, São Paulo, SP, Brazil.,Neuroimmunology of Arboviruses Laboratory, Scientific Platform Pasteur, University of São Paulo, São Paulo, SP, Brazil
| | - Nagela Ghabdan Zanluqui
- Neuroimmune Interactions Laboratory, Institute of Biomedical Science, Department of Immunology, University of São Paulo, São Paulo, SP, Brazil.,Neuroimmunology of Arboviruses Laboratory, Scientific Platform Pasteur, University of São Paulo, São Paulo, SP, Brazil
| | - Marília Garcia de Oliveira
- Neuroimmune Interactions Laboratory, Institute of Biomedical Science, Department of Immunology, University of São Paulo, São Paulo, SP, Brazil
| | - Patrick da Silva
- Neuroimmune Interactions Laboratory, Institute of Biomedical Science, Department of Immunology, University of São Paulo, São Paulo, SP, Brazil.,Neuroimmunology of Arboviruses Laboratory, Scientific Platform Pasteur, University of São Paulo, São Paulo, SP, Brazil
| | - Gustavo Gastão Davanzo
- Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Marina Caçador Ayupe
- Laboratory of Mucosal Immunology, Department of Immunology - Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Caio Loureiro Salgado
- Laboratory of Mucosal Immunology, Department of Immunology - Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Antônio Francisco de Souza Filho
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Marcelo Valdemir de Araújo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | | | | | | | - Elia Garcia Caldini
- Laboratory of Cellular Biology (LIM 59), School of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | | | - Denise Morais Fonseca
- Laboratory of Mucosal Immunology, Department of Immunology - Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Ana Márcia de Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | | | - Carolina Demarchi Munhoz
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Cláudia Madalena Cabrera Mori
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, São Paulo, SP, Brazil
| | - Pedro Manoel Moraes-Vieira
- Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Thiago Mattar Cunha
- Center for Research in Inflammatory Diseases (CRID); Department of Pharmacology - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, Brazil.,D'Or Institute for Research and Education (IDOR), São Paulo, SP, Brazil.,Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Científico e Tecnológico, São Paulo, SP, Brazil
| | - Jean Pierre Schatzmann Peron
- Neuroimmune Interactions Laboratory, Institute of Biomedical Science, Department of Immunology, University of São Paulo, São Paulo, SP, Brazil.,Neuroimmunology of Arboviruses Laboratory, Scientific Platform Pasteur, University of São Paulo, São Paulo, SP, Brazil.,Immunopathology and Allergy Post Graduate Program, School of Medicine, University of São Paulo, São Paulo, SP, Brazil
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43
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Bob K, Teschner D, Kemmer T, Gomez-Zepeda D, Tenzer S, Schmidt B, Hildebrandt A. Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data. BMC Bioinformatics 2022; 23:287. [PMID: 35858828 PMCID: PMC9301846 DOI: 10.1186/s12859-022-04833-5] [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: 07/01/2021] [Accepted: 07/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Mass spectrometry is an important experimental technique in the field of proteomics. However, analysis of certain mass spectrometry data faces a combination of two challenges: first, even a single experiment produces a large amount of multi-dimensional raw data and, second, signals of interest are not single peaks but patterns of peaks that span along the different dimensions. The rapidly growing amount of mass spectrometry data increases the demand for scalable solutions. Furthermore, existing approaches for signal detection usually rely on strong assumptions concerning the signals properties. Results In this study, it is shown that locality-sensitive hashing enables signal classification in mass spectrometry raw data at scale. Through appropriate choice of algorithm parameters it is possible to balance false-positive and false-negative rates. On synthetic data, a superior performance compared to an intensity thresholding approach was achieved. Real data could be strongly reduced without losing relevant information. Our implementation scaled out up to 32 threads and supports acceleration by GPUs. Conclusions Locality-sensitive hashing is a desirable approach for signal classification in mass spectrometry raw data. Availability Generated data and code are available at https://github.com/hildebrandtlab/mzBucket. Raw data is available at https://zenodo.org/record/5036526. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04833-5.
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Affiliation(s)
- Konstantin Bob
- Institute of Computer Science, Johannes Gutenberg University Mainz, D-55128, Mainz, Germany
| | - David Teschner
- Institute of Computer Science, Johannes Gutenberg University Mainz, D-55128, Mainz, Germany
| | - Thomas Kemmer
- Institute of Computer Science, Johannes Gutenberg University Mainz, D-55128, Mainz, Germany
| | - David Gomez-Zepeda
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, D-55128, Mainz, Germany.,Immunoproteomics Unit, Helmholtz-Institute for Translational Oncology (HI-TRON) Mainz, D-55131, Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, D-55128, Mainz, Germany.,Immunoproteomics Unit, Helmholtz-Institute for Translational Oncology (HI-TRON) Mainz, D-55131, Mainz, Germany
| | - Bertil Schmidt
- Institute of Computer Science, Johannes Gutenberg University Mainz, D-55128, Mainz, Germany
| | - Andreas Hildebrandt
- Institute of Computer Science, Johannes Gutenberg University Mainz, D-55128, Mainz, Germany.
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44
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She X, Zou C, Zheng Z. Differences in Vitreous Protein Profiles in Patients With Proliferative Diabetic Retinopathy Before and After Ranibizumab Treatment. Front Med (Lausanne) 2022; 9:776855. [PMID: 35721061 PMCID: PMC9198965 DOI: 10.3389/fmed.2022.776855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/29/2022] [Indexed: 01/09/2023] Open
Abstract
Proliferative diabetic retinopathy (PDR) accounts for severe impact on vision, its mechanism is still poorly understood. To compare the differences of vitreous protein profiles in PDR patients before and after a complete anti-vascular endothelial growth factor (VEGF) loading dose with ranibizumab treatment. Twelve vitreous humor (VH) samples were collected from six PDR patients before (set as pre group) and after (set as post group) intravitreal injection of ranibizumab (IVR) treatment. LC-MS/MS and bioinformatics analysis were performed to identify differentially expressed proteins. Proteins were validated with targeted proteomics using parallel reaction monitoring (PRM) in a validation set consisting of samples from the above patients. A total of 2680 vitreous proteins were identified. Differentially expressed proteins were filtrated with fold change ≥2.0 (post group/ pre group protein abundance ratio ≥2 or ≤ 0.5) and p-value <0.05. 11 proteins were up-regulated and 17 proteins were down-regulated, while consistent presence/absence expression profile group contains one elevated protein and nine reduced proteins, among which seven proteins were identified as potential biomarkers for IVR treatment through PRM assays. Bioinformatics analysis indicated the up-regulated proteins were significantly enriched in "GnRH secretion" and "Circadian rhythm" signaling pathway. This report represents the first description of combined label-free quantitative proteomics and PRM analysis of targeted proteins for discovery of different proteins before and after IVR treatment in the same patient. IVR treatment may protect against PDR by promoting SPP1 expression through "GnRH secretion" and "Circadian rhythm" signaling pathway.
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Affiliation(s)
- Xinping She
- Shanghai Key Laboratory of Ocular Fundus Diseases, Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Eye Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
| | - Chen Zou
- Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhi Zheng
- Shanghai Key Laboratory of Ocular Fundus Diseases, Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Eye Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China,*Correspondence: Zhi Zheng
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Aziz S, Rasheed F, Zahra R, König S. Gastric Cancer Pre-Stage Detection and Early Diagnosis of Gastritis Using Serum Protein Signatures. Molecules 2022; 27:molecules27092857. [PMID: 35566209 PMCID: PMC9099457 DOI: 10.3390/molecules27092857] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Background: A gastric cancer (GC) diagnosis relies on histopathology. Endoscopy rates are increasing. Helicobacter pylori infection is a major GC risk factor. In an effort to elucidate abundant blood biomarkers, and potentially reduce the number of diagnostic surgical interventions, we investigated sera and biopsies from a cohort of 219 H. pylori positive and negative patients diagnosed with GC, gastritis, and ulcers. This allowed the comparative investigation of the different gastroduodenal diseases, and the exclusion of protein changes resulting from bacterial infection or inflammation of the gastric mucosa when searching for GC-dependent proteins. Methods: High-definition mass spectrometry-based expression analysis of tryptically digested proteins was performed, followed by multivariate statistical and network analyses for the different disease groups, with respect to H. pylori infection status. Significantly regulated proteins differing more than two-fold between groups were shortlisted, and their role in gastritis and GC discussed. Results: We present data of comparative protein analyses of biopsies and sera from patients suffering from mild to advanced gastritis, ulcers, and early to advanced GC, in conjunction with a wealth of metadata, clinical information, histopathological evaluation, and H. pylori infection status. We used samples from pre-malignant stages to extract prospective serum markers for early-stage GC, and present a 29-protein marker panel containing, amongst others, integrin β-6 and glutathione peroxidase. Furthermore, ten serum markers specific for advanced GC, independent of H. pylori infection, are provided. They include CRP, protein S100A9, and kallistatin. The majority of these proteins were previously discussed in the context of cancer or GC. In addition, we detected hypoalbuminemia and increased fibrinogen serum levels in gastritis. Conclusion: Two protein panels were suggested for the development of multiplex tests for GC serum diagnostics. For most of the elements contained in these panels, individual commercial tests are available. Thus, we envision the design of multi-protein assays, incorporating several to all of the panel members, in order to gain a level of specificity that cannot be achieved by testing a single protein alone. As their development and validation will take time, gastritis diagnosis based on the fibrinogen to albumin serum ratio may be a quick way forward. Its determination at the primary/secondary care level for early diagnosis could significantly reduce the number of referrals to endoscopy. Preventive measures are in high demand. The protein marker panels presented in this work will contribute to improved GC diagnostics, once they have been transferred from a research result to a practical tool.
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Affiliation(s)
- Shahid Aziz
- BreathMAT Lab, Pakistan Institute of Nuclear Science and Technology (PINSTEC), Islamabad 44000, Pakistan; (S.A.); (F.R.)
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
| | - Faisal Rasheed
- BreathMAT Lab, Pakistan Institute of Nuclear Science and Technology (PINSTEC), Islamabad 44000, Pakistan; (S.A.); (F.R.)
| | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Simone König
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
- Correspondence:
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The Dysregulation of the Renin–Angiotensin System in COVID-19 Studied by Serum Proteomics: Angiotensinogen Increases with Disease Severity. Molecules 2022; 27:molecules27082495. [PMID: 35458690 PMCID: PMC9025241 DOI: 10.3390/molecules27082495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 01/25/2023] Open
Abstract
(1) Background: ACE and CPN serum activity correlated with disease severity in an earlier study of 45 hospitalized COVID-19 patients. The serum protein profile was investigated in the same cohort here to shed more light on the involvement of the renin–angiotensin system (RAS). (2) Methods: High-definition mass spectrometry-based protein expression analysis was performed, followed by multivariate statistical and network analyses. (3) Results: The protein profiles of hospitalized patients (HoP) differed significantly from those of convalescent and healthy probands. Surprisingly, HoP samples separated into six groups according to their protein profiles: group (G) 1 represented the youngest and the least afflicted patients, and G6 the oldest and critically ill patients. At least two major pathophysiological schemes were indicated based on differing involvement of the kallikrein-kinin system (KKS), the RAS and complement activation. The serum angiotensinogen concentration increased with disease severity. (4) Conclusions: The important role of the RAS in the response to COVID-19 infection was substantiated, but other pathways such as the KKS, plasminogen activation and complement activation influence the systemic response to the infection.
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Faita MR, Chaves A, Corrêa CCG, Silveira V, Nodari RO. Proteomic profiling of royal jelly produced by Apis mellifera L. exposed to food containing herbicide-based glyphosate. CHEMOSPHERE 2022; 292:133334. [PMID: 34958784 DOI: 10.1016/j.chemosphere.2021.133334] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Royal jelly (RJ) is rich in protective elements associated with collective immune defenses in the hive of Apis mellifera. Exposure of bees to glyphosate-based herbicides causes ultrastructural changes in the hypopharyngeal glands and a reduction in the production of RJ. However, the effects of glyphosate-based herbicides on the protein composition of RJ and consequences for the hive are unknown. Thus, we performed proteomic profiling of royal jelly produced in hives of A. mellifera exposed to food containing 1,5 μL of Roundup® (2.16 mg. g-1 of glyphosate). The production of RJ was carried out in six hives, following the method of artificial production of queens. The combs containing 80 grafting cells were introduced into the hives, and the collection of royal jelly was performed after 72 h. Two treatments were determined based on hive feeding and the hive as the experimental unit: Control and "Roundup®". Royal jelly from the Roundup® treatment hives was compared to the Control hives. Proteins with differences in expression were identified by mass spectrometry. Only the proteins present in all three biological replicates were considered in the differential abundance analysis, using Student's t-test (p-value < 0.05, two-tailed). Hives that received food containing Roundup®, analysis showed alterations in protein profile in the RJ produced therein. In total, 24 proteins were identified, and the accumulation of Major royal jelly protein 3 (MRJP3) was downregulated, showing a significant reduction in hives exposed to food containing Roundup® in relation to control hives (t = 0.0017). MRJP3 acts analogously to polyclonal antigen-antibody reactions, performing functions related to immunity in bees of different ages and castes. To the best of our knowledge, this is the first study to demonstrate changes in the proteomic profile of RJ caused by glyphosate-based herbicides, indicating its negative effects on the nutrition and social immunity of bees.
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Affiliation(s)
- Márcia Regina Faita
- Universidade Federal de Santa Catarina - UFSC, Programa de Pós-graduação em Recursos Genéticos Vegetais - PPGRGV, Rodovia Admar Gonzaga, 1346 - Bairro Itacorubi, 88.034-001, Florianópolis, Santa Catarina, Brazil.
| | - Adriana Chaves
- Universidade Federal de Santa Catarina - UFSC, Programa de Pós-graduação em Recursos Genéticos Vegetais - PPGRGV, Rodovia Admar Gonzaga, 1346 - Bairro Itacorubi, 88.034-001, Florianópolis, Santa Catarina, Brazil.
| | - Caio Cézar Guedes Corrêa
- Laboratório de Biotecnologia, Unidade de Biologia Integrativa, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Avenida Alberto Lamego 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil.
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Unidade de Biologia Integrativa, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Avenida Alberto Lamego 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil.
| | - Rubens Onofre Nodari
- Universidade Federal de Santa Catarina - UFSC, Programa de Pós-graduação em Recursos Genéticos Vegetais - PPGRGV, Rodovia Admar Gonzaga, 1346 - Bairro Itacorubi, 88.034-001, Florianópolis, Santa Catarina, Brazil.
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Yu X, Zhao X, Yang Y, Li Z. Quantitative Proteomics Reveals SOS2-Related Proteins in Arabidopsis Under
Salt Stress. CURR PROTEOMICS 2022. [DOI: 10.2174/1570164618666210413105907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Soil salinity is a major issue that seriously affects plant growth and cultivated
land utilization. Salt tolerance is one of the most fundamental biological processes that ensures
plant’s survival. SOS2 is one of the most important components of the Salt Overly Sensitive
(SOS) signaling pathway, which maintains plant ion homeostasis under salt stress. The SOS2-related
signaling pathways remain incompletely exploited especially at the proteomics level.
Objective:
In this paper, proteins potentially interacting with and regulated by SOS2 in Arabidopsis
were identified.
Methods:
The proteomes of Arabidopsis Wild Type (WT) and SOS2-deficient mutant (sos2-2) exposed
to 100 mM NaCl for 6 h were compared, proteins were identified using data-independent acquisition-
based quantitative proteomics strategy.
Results:
A total of 7470 proteins were identified and quantified, 372 Differentially Expressed Proteins
(DEP) were detected between WT and sos2-2 mutant under normal condition and 179 DEPs
were identified under salt treatment. Functional analysis showed that the DEPs were mainly involved
in protein binding and catalytic activity. Among the DEPs under salt stress, the protein expressions
of AVP1, Photosystem II reaction center protein A, B, C, and stress-responsive protein
(KIN2) were significantly up-regulated. LHCA1, LHCA2, LHCA4, ATPD and ATPE were significantly
down-regulated. These proteins were involved in biological processes including: stress response,
photosynthesis, transport and heat shock.
Conclusion:
These results revealed complexity of the functions of SOS2 in maintaining intracellular
homeostasis, in addition to its function in sodium homeostasis. Plant salt resistance is not independent
but closely related to metabolic processes including photosystem, ATP synthase, transport
and other stress resistances.
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Affiliation(s)
- Xiang Yu
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoyun Zhao
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yongqing Yang
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Li
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
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The caspase-2 substrate p54nrb exhibits a multifaceted role in tumor cell death susceptibility via gene regulatory functions. Cell Death Dis 2022; 13:386. [PMID: 35444189 PMCID: PMC9021192 DOI: 10.1038/s41419-022-04829-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 12/18/2022]
Abstract
Caspase-2 represents an evolutionary conserved caspase, which plays a role in genotoxic stress-induced apoptosis, ageing-related metabolic changes, and in deleting aneuploid cells in tumors. Genetic deletion of caspase-2 leads to increased tumor susceptibility in vivo. The exact downstream signaling mechanism by which caspase-2 accomplishes its specific tumor suppressor functions is not clear. Caspase-2, uniquely among caspases, resides in the nucleus and other cellular compartments. In this study, we identify a nuclear caspase-2 specific substrate, p54nrb, which is selectively cleaved by caspase-2 at D422, leading to disruption of the C-terminal site, the putative DNA binding region of the protein. P54nrb is an RNA and DNA binding protein, which plays a role in RNA editing, transport, and transcriptional regulation of genes. Overexpression of p54nrb is observed in several human tumor types, such as cervix adenocarcinoma, melanoma, and colon carcinoma. In contrast, the loss of p54nrb in tumor cell lines leads to increased cell death susceptibility and striking decrease in tumorigenic potential. By employing high resolution quantitative proteomics, we demonstrate that the loss/cleavage of p54nrb results in altered expression of oncogenic genes, among which the downregulation of the tumorigenic protease cathepsin-Z and the anti-apoptotic gelsolin can be detected universally across three tumor cell types, including adenocarcinoma, melanoma and colon carcinoma. Finally, we demonstrate that p54nrb interacts with cathepsin-Z and gelsolin DNA, but not RNA. Taken together, this study uncovers a so far not understood mechanism of caspase-2 tumor suppressor function in human tumor cells. ![]()
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GABA A Receptor-Stabilizing Protein Ubqln1 Affects Hyperexcitability and Epileptogenesis after Traumatic Brain Injury and in a Model of In Vitro Epilepsy in Mice. Int J Mol Sci 2022; 23:ijms23073902. [PMID: 35409261 PMCID: PMC8999075 DOI: 10.3390/ijms23073902] [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: 02/28/2022] [Revised: 03/23/2022] [Accepted: 03/30/2022] [Indexed: 11/16/2022] Open
Abstract
Posttraumatic epilepsy (PTE) is a major public health concern and strongly contributes to human epilepsy cases worldwide. However, an effective treatment and prevention remains a matter of intense research. The present study provides new insights into the gamma aminobutyric acid A (GABAA)-stabilizing protein ubiquilin-1 (ubqln1) and its regulation in mouse models of traumatic brain injury (TBI) and in vitro epilepsy. We performed label-free quantification on isolated cortical GABAergic interneurons from GAD67-GFP mice that received unilateral TBI and discovered reduced expression of ubqln1 24 h post-TBI. To investigate the link between this regulation and the development of epileptiform activity, we further studied ubqln1 expression in hippocampal and cortical slices. Epileptiform events were evoked pharmacologically in acute brain slices by administration of picrotoxin (PTX, 50 μM) and kainic acid (KA, 500 nM) and recorded in the hippocampal CA1 subfield using Multi-electrode Arrays (MEA). Interestingly, quantitative Western blots revealed significant decreases in ubqln1 expression 1–7 h after seizure induction that could be restored by application of the non-selective monoamine oxidase inhibitor nialamide (NM, 10 μM). In picrotoxin-dependent dose–response relationships, NM administration alleviated the frequency and peak amplitude of seizure-like events (SLEs). These findings indicate a role of the monoamine transmitter systems and ubqln1 for cortical network activity during posttraumatic epileptogenesis.
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