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Domingos IF, Carvalho LB, Lodeiro C, Gerivaz R, Prag G, Micaglio E, Muchtar E, Santos HM, Capelo JL. Dithiothreitol-based protein equalisation in the context of multiple myeloma: Enhancing proteomic analysis and therapeutic insights. Talanta 2024; 279:126589. [PMID: 39116730 DOI: 10.1016/j.talanta.2024.126589] [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: 05/31/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024]
Abstract
In this study, we employed the dithiothreitol-based protein equalisation technique and analytical proteomics to better understand myeloma diseases by comparing the proteomes of pellets and supernatants formed upon application of DTT on serum samples. The number of unique proteins found in pellets was 252 for healthy individuals and 223 for multiple myeloma patients. The comparison of these proteomes showed 97 dysregulated proteins. The unique proteins found for supernatants were 264 for healthy individuals and 235 for multiple myeloma patients. The comparison of these proteomes showed 87 dysregulated proteins. The analytical proteomic comparison of both groups of dysregulated proteins is translated into parallel dysregulated pathways, including chaperone-mediated autophagy and protein folding, addressing potential therapeutic interventions. Future research endeavours in personalised medicine should prioritize refining analytical proteomic methodologies using serum dithiothreitol-based protein equalisation to explore innovative therapeutic strategies. We highlight the advanced insights gained from this analytical strategy in studying multiple myeloma, emphasising its complex nature and the critical role of personalised, targeted analytical techniques in enhancing therapeutic efficacy in personalised medicine.
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Affiliation(s)
- Ines F Domingos
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal
| | - Luis B Carvalho
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal
| | - Carlos Lodeiro
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal
| | - Rita Gerivaz
- Serviço de Hematologia, Hospital Garcia de Orta, Almada, Portugal
| | - Gali Prag
- School of Neurobiology, Biochemistry and Biophysics, the George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Israel
| | - Emanuele Micaglio
- Department of Arrhythmology, IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097, Milan, Italy
| | - Eli Muchtar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Hugo M Santos
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal; Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
| | - Jose L Capelo
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal.
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2
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Esposito A, Rossi A, Stabile M, Pinto G, De Fino I, Melessike M, Tamanini A, Cabrini G, Lippi G, Aureli M, Loberto N, Renda M, Galietta LJV, Amoresano A, Dechecchi MC, De Gregorio E, Bragonzi A, Guaragna A. Assessing the Potential of N-Butyl-l-deoxynojirimycin (l-NBDNJ) in Models of Cystic Fibrosis as a Promising Antibacterial Agent. ACS Pharmacol Transl Sci 2024; 7:1807-1822. [PMID: 38898954 PMCID: PMC11184606 DOI: 10.1021/acsptsci.4c00044] [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: 01/26/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 06/21/2024]
Abstract
Over the past few years, l-iminosugars have revealed attractive pharmacological properties for managing rare diseases including Cystic Fibrosis (CF). The iminosugar N-butyl-l-deoxynojirimycin (l-NBDNJ, ent-1), prepared by a carbohydrate-based route, was herein evaluated for its anti-inflammatory and anti-infective potential in models of CF lung disease infection. A significant decrease in the bacterial load in the airways was observed in the murine model of Pseudomonas aeruginosa chronic infection in the presence of l-NBDNJ, also accompanied by a modest reduction of inflammatory cells. Mechanistic insights into the observed activity revealed that l-NBDNJ interferes with the expression of proteins regulating cytoskeleton assembly and organization of the host cell, downregulates the main virulence factors of P. aeruginosa involved in the host response, and affects pathogen adhesion to human cells. These findings along with the observation of the absence of an in vitro bacteriostatic/bactericidal action of l-NBDNJ suggest the potential use of this glycomimetic as an antivirulence agent in the management of CF lung disease.
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Affiliation(s)
- Anna Esposito
- Department
of Chemical, Materials and Production Engineering, University of Naples Federico II, Naples I-80125, Italy
| | - Alice Rossi
- Infections
and Cystic Fibrosis Unit, Division of Immunology, Transplantation
and Infectious Diseases, IRCCS San Raffaele
Scientific Institute, Milan I-20132, Italy
| | - Maria Stabile
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples I-80131, Italy
| | - Gabriella Pinto
- Department
of Chemical Sciences, University of Naples
Federico II, Naples I-80126, Italy
| | - Ida De Fino
- Infections
and Cystic Fibrosis Unit, Division of Immunology, Transplantation
and Infectious Diseases, IRCCS San Raffaele
Scientific Institute, Milan I-20132, Italy
| | - Medede Melessike
- Infections
and Cystic Fibrosis Unit, Division of Immunology, Transplantation
and Infectious Diseases, IRCCS San Raffaele
Scientific Institute, Milan I-20132, Italy
| | - Anna Tamanini
- Section
of Clinical Biochemistry, Department of Engineering for Innovation
Medicine, University of Verona, Verona I-37134, Italy
| | - Giulio Cabrini
- Center on
Innovative Therapies for Cystic Fibrosis, Department of Life Sciences
and Biotechnology, University of Ferrara, Ferrara I-40121, Italy
| | - Giuseppe Lippi
- Section
of Clinical Biochemistry, Department of Engineering for Innovation
Medicine, University of Verona, Verona I-37134, Italy
| | - Massimo Aureli
- Department
of Medical Biotechnology and Translational Medicine, University of Milan, Milan I-20054, Italy
| | - Nicoletta Loberto
- Department
of Medical Biotechnology and Translational Medicine, University of Milan, Milan I-20054, Italy
| | - Mario Renda
- Telethon
Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples I-80078, Italy
| | - Luis J. V. Galietta
- Telethon
Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples I-80078, Italy
- Department
of Translational Medical Sciences (DISMET), University of Naples Federico II, Naples I-80131, Italy
| | - Angela Amoresano
- Department
of Chemical Sciences, University of Naples
Federico II, Naples I-80126, Italy
- Istituto
Nazionale Biostrutture e Biosistemi, Consorzio Interuniversitario, Rome I-00136, Italy
| | - Maria Cristina Dechecchi
- Section
of Clinical Biochemistry, Department of Engineering for Innovation
Medicine, University of Verona, Verona I-37134, Italy
| | - Eliana De Gregorio
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples I-80131, Italy
| | - Alessandra Bragonzi
- Infections
and Cystic Fibrosis Unit, Division of Immunology, Transplantation
and Infectious Diseases, IRCCS San Raffaele
Scientific Institute, Milan I-20132, Italy
| | - Annalisa Guaragna
- Department
of Chemical Sciences, University of Naples
Federico II, Naples I-80126, Italy
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3
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Dötsch L, Davies C, Hennes E, Schönfeld J, Kumar A, Guita CDC, Ehrler JH, Hiesinger K, Thavam S, Janning P, Sievers S, Knapp S, Proschak E, Ziegler S, Waldmann H. Discovery of the sEH Inhibitor Epoxykynin as a Potent Kynurenine Pathway Modulator. J Med Chem 2024; 67:4691-4706. [PMID: 38470246 PMCID: PMC10983002 DOI: 10.1021/acs.jmedchem.3c02245] [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: 11/29/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024]
Abstract
Disease-related phenotypic assays enable unbiased discovery of novel bioactive small molecules and may provide novel insights into physiological systems and unprecedented molecular modes of action (MMOA). Herein, we report the identification and characterization of epoxykynin, a potent inhibitor of the soluble epoxide hydrolase (sEH). Epoxykynin was discovered by means of a cellular assay monitoring modulation of kynurenine (Kyn) levels in BxPC-3 cells upon stimulation with the cytokine interferon-γ (IFN-γ) and subsequent target identification employing affinity-based chemical proteomics. Increased Kyn levels are associated with immune suppression in the tumor microenvironment and, thus, the Kyn pathway and its key player indoleamine 2,3-dioxygenase 1 (IDO1) are appealing targets in immuno-oncology. However, targeting IDO1 directly has led to limited success in clinical investigations, demonstrating that alternative approaches to reduce Kyn levels are in high demand. We uncover a cross-talk between sEH and the Kyn pathway that may provide new opportunities to revert cancer-induced immune tolerance.
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Affiliation(s)
- Lara Dötsch
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Department
of Chemical Biology, Technical University
of Dortmund, Otto-Hahn-Strasse
6, Dortmund 44227, Germany
| | - Caitlin Davies
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Elisabeth Hennes
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Julia Schönfeld
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Adarsh Kumar
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
- Structural
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, Frankfurt 60438, Germany
| | - Celine Da Cruz
Lopes Guita
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Johanna H.M. Ehrler
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Kerstin Hiesinger
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Sasikala Thavam
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Petra Janning
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sonja Sievers
- Compound
Management and Screening Center (COMAS), Otto-Hahn-Strasse 15, Dortmund 44227, Germany
| | - Stefan Knapp
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
- Structural
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, Frankfurt 60438, Germany
| | - Ewgenij Proschak
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Slava Ziegler
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Herbert Waldmann
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Department
of Chemical Biology, Technical University
of Dortmund, Otto-Hahn-Strasse
6, Dortmund 44227, Germany
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4
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Chen H, Wu L, Zhang Y, Ding W, Xiaofan Y. Steroid inhibited Serpina3n expression which was positively correlated with the degrees of spinal cord injury. Heliyon 2024; 10:e26649. [PMID: 38449654 PMCID: PMC10915347 DOI: 10.1016/j.heliyon.2024.e26649] [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: 06/23/2023] [Revised: 01/23/2024] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Aims The aim of our project was to identify proteins associated with the extent of spinal cord injury (SCI) and subsequent long-term neurological recovery. Methods Through proteomic analysis, we identified proteins that are differentially expressed specifically in the acute phase of injury. We analyzed the concentrations of differentially expressed proteins in serum and the injured spinal cord segment by ELISA. Results Serpina3n protein expression in the injured spinal cord segment was increased 101-fold at 12 h after severe SCI and 89-fold at 12 h after mild SCI, as determined by LC‒MS/MS. In the mild and severe SCI groups, serum Serpina3n levels began to increase at 12 h and peaked at 24 h. At 12 h, 24 h and 3 d after injury, serum Serpina3n protein levels were significantly correlated with the severity of injury (12 h: r = 0.6034, P = 0.008; 24 h: r = 0.7542, P = 0.0003; 3 d: r = 0.862, P < 0.001). Serum Serpina3n levels at 2 h, 24 h and 3 d post injury were significantly correlated with long-term neurological recovery at 28 d after SCI (2 h: r = -0.5781, P = 0.012; 24 h: r = -0.5912, P = 0.0098; 3 d: r = -0.7792, P < 0.0001). Methylprednisolone treatment would decrease the serum Serpina3n levels in mice with mild and severe SCI compared with those in placebo-group mice at 12 h and 24 h after SCI. The serum Serpina3n concentration in the severe SCI group was significantly reduced on the third day after steroid treatment. Conclusion Taken together, these data suggest that serpina3n may be a circulating biomarker of acute SCI and may be closely associated with injury severity and long-term motor function recovery.
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Affiliation(s)
- Haihong Chen
- Orthopaedic Department, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Liang Wu
- Orthopaedic Department, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Yue Zhang
- Rehabilitation Department, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Wang Ding
- Orthopaedic Department, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Yin Xiaofan
- Orthopaedic Department, Minhang Hospital, Fudan University, Shanghai, 201199, China
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5
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Akhmadi A, Yeskendir A, Dey N, Mussakhmetov A, Shatkenova Z, Kulyyassov A, Andreeva A, Utepbergenov D. DJ-1 protects proteins from acylation by catalyzing the hydrolysis of highly reactive cyclic 3-phosphoglyceric anhydride. Nat Commun 2024; 15:2004. [PMID: 38443379 PMCID: PMC10915168 DOI: 10.1038/s41467-024-46391-9] [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: 07/19/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
Mutations in the human PARK7 gene that encodes protein DJ-1 lead to familial Parkinsonism due to loss of dopaminergic neurons. However, the molecular function of DJ-1 underpinning its cytoprotective effects are unclear. Recently, DJ-1 has been shown to prevent acylation of amino groups of proteins and metabolites by 1,3-bisphosphoglycerate. This acylation is indirect and thought to proceed via the formation of an unstable intermediate, presumably a cyclic 3-phosphoglyceric anhydride (cPGA). Several lines of evidence indicate that DJ-1 destroys cPGA, however this enzymatic activity has not been directly demonstrated. Here, we report simple and effective procedures for synthesis and quantitation of cPGA and present a comprehensive characterization of this highly reactive acylating electrophile. We demonstrate that DJ-1 is an efficient cPGA hydrolase with kcat/Km = 5.9 × 106 M-1s-1. Experiments with DJ-1-null cells reveal that DJ-1 protects against accumulation of 3-phosphoglyceroyl-lysine residues in proteins. Our results establish a definitive cytoprotective function for DJ-1 that uses catalytic hydrolysis of cPGA to mitigate the damage from this glycolytic byproduct.
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Affiliation(s)
- Aizhan Akhmadi
- Ph.D. Program in Life Sciences, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Adilkhan Yeskendir
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan
- Master Program, School of Medicine, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Nelly Dey
- Master Program, School of Medicine, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Arman Mussakhmetov
- National Center for Biotechnology, Astana, 010000, Kazakhstan
- Ph.D. Program in Biology, L.N. Gumilyov Eurasian National University, Astana, 010000, Kazakhstan
| | - Zariat Shatkenova
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan
| | | | - Anna Andreeva
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Darkhan Utepbergenov
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan.
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6
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Huber L, Kuropka B, Doulidis PG, Baszler E, Martin L, Rosu A, Kulmer L, Frizzo Ramos C, Rodríguez-Rojas A, Burgener IA. Plasma proteome signature of canine acute haemorrhagic diarrhoea syndrome (AHDS). PLoS One 2024; 19:e0297924. [PMID: 38330002 PMCID: PMC10852219 DOI: 10.1371/journal.pone.0297924] [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: 11/22/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
Acute haemorrhagic diarrhoea is a common complaint in dogs. In addition to causes like intestinal parasites, dietary indiscretion, intestinal foreign bodies, canine parvovirus infection, or hypoadrenocorticism, acute haemorrhagic diarrhoea syndrome (AHDS) is an important and sometimes life-threatening differential diagnosis. There is some evidence supporting the link between Clostridium perfringens toxins and AHDS. These toxins may be partially responsible for the epithelial cell injury, but the pathogenesis of AHDS is still not fully understood. Recent studies have suggested that severe damage to the intestinal mucosa and associated barrier dysfunction can trigger chronic gastrointestinal illnesses. Besides bloodwork and classical markers for AHDS such as protein loss and intestinal bacterial dysbiosis, we focused mainly on the plasma-proteome to identify systemic pathological alterations during this disease and searched for potential biomarkers to improve the diagnosis. To accomplish the goals, we used liquid chromatography-mass spectrometry. We compared the proteomic profiles of 20 dogs with AHDS to 20 age-, breed-, and sex-matched control dogs. All dogs were examined, and several blood work parameters were determined and compared, including plasma biochemistry and cell counts. We identified and quantified (relative quantification) 207 plasmatic proteins, from which dozens showed significantly altered levels in AHDS. Serpina3, Lipopolysaccharide-binding protein, several Ig-like domain-containing proteins, Glyceraldehyde-3-phosphate dehydrogenase and Serum amyloid A were more abundant in plasma from AHDS affected dogs. In contrast, other proteins such as Paraoxonase, Selenoprotein, Amine oxidases, and Apolipoprotein C-IV were significantly less abundant. Many of the identified and quantified proteins are known to be associated with inflammation. Other proteins like Serpina3 and RPLP1 have a relevant role in oncogenesis. Some proteins and their roles have not yet been described in dogs with diarrhoea. Our study opens new avenues that could contribute to the understanding of the aetiology and pathophysiology of AHDS.
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Affiliation(s)
- Lukas Huber
- Department for Companion Animals, Small Animal Internal Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Pavlos G. Doulidis
- Department for Companion Animals, Small Animal Internal Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Elisabeth Baszler
- Department for Companion Animals, Small Animal Internal Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Lukas Martin
- Department for Companion Animals, Small Animal Internal Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Anda Rosu
- Department for Companion Animals, Small Animal Internal Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Lisa Kulmer
- Department for Companion Animals, Small Animal Internal Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Carolina Frizzo Ramos
- The Interuniversity Messerli Research Institute, Medical University Vienna and University of Veterinary Medicine Vienna, Vienna, Austria
| | - Alexandro Rodríguez-Rojas
- Department for Companion Animals, Small Animal Internal Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Iwan A. Burgener
- Department for Companion Animals, Small Animal Internal Medicine, University of Veterinary Medicine, Vienna, Austria
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7
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Graf A, Bassukas AEL, Xiao Y, Barbosa ICR, Mergner J, Grill P, Michalke B, Kuster B, Schwechheimer C. D6PK plasma membrane polarity requires a repeated CXX(X)P motif and PDK1-dependent phosphorylation. NATURE PLANTS 2024; 10:300-314. [PMID: 38278951 PMCID: PMC10881395 DOI: 10.1038/s41477-023-01615-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/15/2023] [Indexed: 01/28/2024]
Abstract
D6 PROTEIN KINASE (D6PK) is a polarly localized plasma-membrane-associated kinase from Arabidopsis thaliana that activates polarly distributed PIN-FORMED auxin transporters. D6PK moves rapidly to and from the plasma membrane, independent of its PIN-FORMED targets. The middle D6PK domain, an insertion between kinase subdomains VII and VIII, is required and sufficient for association and polarity of the D6PK plasma membrane. How D6PK polarity is established and maintained remains to be shown. Here we show that cysteines from repeated middle domain CXX(X)P motifs are S-acylated and required for D6PK membrane association. While D6PK S-acylation is not detectably regulated during intracellular transport, phosphorylation of adjacent serine residues, in part in dependence on the upstream 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE, promotes D6PK transport, controls D6PK residence time at the plasma membrane and prevents its lateral diffusion. We thus identify new mechanisms for the regulation of D6PK plasma membrane interaction and polarity.
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Affiliation(s)
- Alina Graf
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | | | - Yao Xiao
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Inês C R Barbosa
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Julia Mergner
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar, Center for Translational Cancer Research, Munich, Germany
| | - Peter Grill
- Helmholtz Zentrum München, German Research Center for Environmental Health, Analytical BioGeoChemistry, Neuherberg, Germany
| | - Bernhard Michalke
- Helmholtz Zentrum München, German Research Center for Environmental Health, Analytical BioGeoChemistry, Neuherberg, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Claus Schwechheimer
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany.
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8
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Luti S, Militello R, Pinto G, Illiano A, Marzocchini R, Santi A, Becatti M, Amoresano A, Gamberi T, Pellegrino A, Modesti A, Modesti PA. Chronic lactate exposure promotes cardiomyocyte cytoskeleton remodelling. Heliyon 2024; 10:e24719. [PMID: 38312589 PMCID: PMC10835305 DOI: 10.1016/j.heliyon.2024.e24719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 02/06/2024] Open
Abstract
We investigated the effect of growing on lactate instead of glucose in human cardiomyocyte assessing their viability, cell cycle activity, oxidative stress and metabolism by a proteomic and metabolomic approach. In previous studies performed on elite players, we found that adaptation to exercise is characterized by a chronic high plasma level of lactate. Lactate is considered not only an energy source but also a signalling molecule and is referred as "lactormone"; heart is one of the major recipients of exogenous lactate. With this in mind, we used a cardiac cell line AC16 to characterize the lactate metabolic profile and investigate the metabolic flexibility of the heart. Interestingly, our data indicated that cardiomyocytes grown on lactate (72 h) show change in several proteins and metabolites linked to cell hypertrophy and cytoskeleton remodelling. The obtained results could help to understand the effect of this metabolite on heart of high-performance athletes.
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Affiliation(s)
- Simone Luti
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Rosamaria Militello
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Gabriella Pinto
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Anna Illiano
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Riccardo Marzocchini
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Alice Santi
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Matteo Becatti
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Angela Amoresano
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Tania Gamberi
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Alessio Pellegrino
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alessandra Modesti
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Pietro Amedeo Modesti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
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9
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Maghe C, Trillet K, André-Grégoire G, Kerhervé M, Merlet L, Jacobs KA, Schauer K, Bidère N, Gavard J. The paracaspase MALT1 controls cholesterol homeostasis in glioblastoma stem-like cells through lysosome proteome shaping. Cell Rep 2024; 43:113631. [PMID: 38183651 DOI: 10.1016/j.celrep.2023.113631] [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: 03/24/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 01/08/2024] Open
Abstract
Glioblastoma stem-like cells (GSCs) compose a tumor-initiating and -propagating population remarkably vulnerable to variation in the stability and integrity of the lysosomal compartment. Previous work has shown that the expression and activity of the paracaspase MALT1 control GSC viability via lysosome abundance. However, the underlying mechanisms remain elusive. By combining RNA sequencing (RNA-seq) with proteome-wide label-free quantification, we now report that MALT1 repression in patient-derived GSCs alters the homeostasis of cholesterol, which accumulates in late endosomes (LEs)-lysosomes. This failure in cholesterol supply culminates in cell death and autophagy defects, which can be partially reverted by providing exogenous membrane-permeable cholesterol to GSCs. From a molecular standpoint, a targeted lysosome proteome analysis unraveled that Niemann-Pick type C (NPC) lysosomal cholesterol transporters are diluted when MALT1 is impaired. Accordingly, we found that NPC1/2 inhibition and silencing partially mirror MALT1 loss-of-function phenotypes. This supports the notion that GSC fitness relies on lysosomal cholesterol homeostasis.
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Affiliation(s)
- Clément Maghe
- Team SOAP, CRCI2NA, Nantes Université, INSERM, CNRS, Université d'Angers, 44000 Nantes, France; Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Kilian Trillet
- Team SOAP, CRCI2NA, Nantes Université, INSERM, CNRS, Université d'Angers, 44000 Nantes, France; Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Gwennan André-Grégoire
- Team SOAP, CRCI2NA, Nantes Université, INSERM, CNRS, Université d'Angers, 44000 Nantes, France; Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France; Institut de Cancérologie de l'Ouest (ICO), 44800 Saint-Herblain, France
| | - Mathilde Kerhervé
- Team SOAP, CRCI2NA, Nantes Université, INSERM, CNRS, Université d'Angers, 44000 Nantes, France; Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Laura Merlet
- Team SOAP, CRCI2NA, Nantes Université, INSERM, CNRS, Université d'Angers, 44000 Nantes, France; Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Kathryn A Jacobs
- Team SOAP, CRCI2NA, Nantes Université, INSERM, CNRS, Université d'Angers, 44000 Nantes, France; Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Kristine Schauer
- Institut Gustave Roussy, Université Paris-Saclay, INSERM, CNRS, 94800 Villejuif, France
| | - Nicolas Bidère
- Team SOAP, CRCI2NA, Nantes Université, INSERM, CNRS, Université d'Angers, 44000 Nantes, France; Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Julie Gavard
- Team SOAP, CRCI2NA, Nantes Université, INSERM, CNRS, Université d'Angers, 44000 Nantes, France; Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France; Institut de Cancérologie de l'Ouest (ICO), 44800 Saint-Herblain, France.
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10
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Murigneux E, Softic L, Aubé C, Grandi C, Judith D, Bruce J, Le Gall M, Guillonneau F, Schmitt A, Parissi V, Berlioz-Torrent C, Meertens L, Hansen MMK, Gallois-Montbrun S. Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly. Nat Commun 2024; 15:640. [PMID: 38245532 PMCID: PMC10799903 DOI: 10.1038/s41467-024-44958-0] [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: 12/13/2022] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
Considerable progress has been made in understanding the molecular host-virus battlefield during SARS-CoV-2 infection. Nevertheless, the assembly and egress of newly formed virions are less understood. To identify host proteins involved in viral morphogenesis, we characterize the proteome of SARS-CoV-2 virions produced from A549-ACE2 and Calu-3 cells, isolated via ultracentrifugation on sucrose cushion or by ACE-2 affinity capture. Bioinformatic analysis unveils 92 SARS-CoV-2 virion-associated host factors, providing a valuable resource to better understand the molecular environment of virion production. We reveal that G3BP1 and G3BP2 (G3BP1/2), two major stress granule nucleators, are embedded within virions and unexpectedly favor virion production. Furthermore, we show that G3BP1/2 participate in the formation of cytoplasmic membrane vesicles, that are likely virion assembly sites, consistent with a proviral role of G3BP1/2 in SARS-CoV-2 dissemination. Altogether, these findings provide new insights into host factors required for SARS-CoV-2 assembly with potential implications for future therapeutic targeting.
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Affiliation(s)
- Emilie Murigneux
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Laurent Softic
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Corentin Aubé
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Carmen Grandi
- Institute for Molecules and Materials, Radboud University, 6525, AJ, Nijmegen, the Netherlands
| | - Delphine Judith
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Johanna Bruce
- Proteom'IC facility, Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Morgane Le Gall
- Proteom'IC facility, Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - François Guillonneau
- Proteom'IC facility, Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
- Institut de Cancérologie de l'Ouest (ICO), CRCi2NA-Inserm UMR 1307, CNRS UMR 6075, Nantes Université, Angers, France
| | - Alain Schmitt
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Vincent Parissi
- Microbiologie Fondamentale et Pathogénicité Laboratory (MFP), UMR 5234, « Mobility of pathogenic genomes and chromatin dynamics » team (MobilVIR), CNRS-University of Bordeaux, DyNAVIR network, Bordeaux, France
| | | | - Laurent Meertens
- Université Paris Cité, Inserm U944, CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Paris, France
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, 6525, AJ, Nijmegen, the Netherlands
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11
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Weiner AK, Radaoui AB, Tsang M, Martinez D, Sidoli S, Conkrite KL, Delaidelli A, Modi A, Rokita JL, Patel K, Lane MV, Zhang B, Zhong C, Ennis B, Miller DP, Brown MA, Rathi KS, Raman P, Pogoriler J, Bhatti T, Pawel B, Glisovic-Aplenc T, Teicher B, Erickson SW, Earley EJ, Bosse KR, Sorensen PH, Krytska K, Mosse YP, Havenith KE, Zammarchi F, van Berkel PH, Smith MA, Garcia BA, Maris JM, Diskin SJ. A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.06.570390. [PMID: 38106022 PMCID: PMC10723418 DOI: 10.1101/2023.12.06.570390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cancer immunotherapies have produced remarkable results in B-cell malignancies; however, optimal cell surface targets for many solid cancers remain elusive. Here, we present an integrative proteomic, transcriptomic, and epigenomic analysis of tumor specimens along with normal tissues to identify biologically relevant cell surface proteins that can serve as immunotherapeutic targets for neuroblastoma, an often-fatal childhood cancer of the developing nervous system. We apply this approach to human-derived cell lines (N=9) and cell/patient-derived xenograft (N=12) models of neuroblastoma. Plasma membrane-enriched mass spectrometry identified 1,461 cell surface proteins in cell lines and 1,401 in xenograft models, respectively. Additional proteogenomic analyses revealed 60 high-confidence candidate immunotherapeutic targets and we prioritized Delta-like canonical notch ligand 1 (DLK1) for further study. High expression of DLK1 directly correlated with the presence of a super-enhancer spanning the DLK1 locus. Robust cell surface expression of DLK1 was validated by immunofluorescence, flow cytometry, and immunohistochemistry. Short hairpin RNA mediated silencing of DLK1 in neuroblastoma cells resulted in increased cellular differentiation. ADCT-701, a DLK1-targeting antibody-drug conjugate (ADC), showed potent and specific cytotoxicity in DLK1-expressing neuroblastoma xenograft models. Moreover, DLK1 is highly expressed in several adult cancer types, including adrenocortical carcinoma (ACC), pheochromocytoma/paraganglioma (PCPG), hepatoblastoma, and small cell lung cancer (SCLC), suggesting potential clinical benefit beyond neuroblastoma. Taken together, our study demonstrates the utility of comprehensive cancer surfaceome characterization and credentials DLK1 as an immunotherapeutic target. Highlights Plasma membrane enriched proteomics defines surfaceome of neuroblastomaMulti-omic data integration prioritizes DLK1 as a candidate immunotherapeutic target in neuroblastoma and other cancersDLK1 expression is driven by a super-enhancer DLK1 silencing in neuroblastoma cells results in cellular differentiation ADCT-701, a DLK1-targeting antibody-drug conjugate, shows potent and specific cytotoxicity in DLK1-expressing neuroblastoma preclinical models.
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12
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Teraiya M, Krokhin O, Chen VC, Perreault H. Cytoplasmic Shotgun Proteomic Points to Key Proteins and Pathways in Temozolomide-Resistant Glioblastoma Multiforme. J Proteome Res 2024; 23:465-482. [PMID: 38147655 DOI: 10.1021/acs.jproteome.3c00669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Temozolomide (TMZ) is the first line of chemotherapy to treat primary brain tumors of the type glioblastoma multiforme (GBM). TMZ resistance (TMZR) is one of the main barriers to successful treatment and is a principal factor in relapse, resulting in a poor median survival of 15 months. The present paper focuses on proteomic analyses of cytosolic fractions from TMZ-resistant (TMZR) LN-18 cells. The experimental workflow includes an easy, cost-effective, and reproducible method to isolate subcellular fraction of cytosolic (CYTO) proteins, mitochondria, and plasma membrane proteins for proteomic studies. For this study, enriched cytoplasmic fractions were analyzed in replicates by nanoflow liquid chromatography tandem high-resolution mass spectrometry (nLC-MS/MS), and proteins identified were quantified using a label-free approach (LFQ). Statistical analysis of control (CTRL) and temozolomide-resistant (TMZR) proteomes revealed proteins that appear to be differentially controlled in the cytoplasm. The functions of these proteins are discussed as well as their roles in other cancers and TMZ resistance in GBM. Key proteins are also described through biological processes related to gene ontology (GO), molecular functions, and cellular components. For protein-protein interactions (PPI), network and pathway involvement analyses have been performed, highlighting the roles of key proteins in the TMZ resistance phenotypes. This study provides a detailed insight into methods of subcellular fractionation for proteomic analysis of TMZ-resistant GBM cells and the potential to apply this approach to future large-scale studies. Several key proteins, protein-protein interactions (PPI), and pathways have been identified, underlying the TMZ resistance phenotype and highlighting the proteins' biological functions.
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Affiliation(s)
- Milan Teraiya
- Chemistry Department, University of Manitoba, Winnipeg, Manitoba R3T3C7, Canada
| | - Oleg Krokhin
- Chemistry Department, University of Manitoba, Winnipeg, Manitoba R3T3C7, Canada
- Manitoba Centre for Proteomics and Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E3P4, Canada
| | - Vincent C Chen
- Chemistry Department, Brandon University, Brandon, Manitoba R7A 6A9, Canada
| | - Hélène Perreault
- Chemistry Department, University of Manitoba, Winnipeg, Manitoba R3T3C7, Canada
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13
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Pratscher B, Kuropka B, Csukovich G, Doulidis PG, Spirk K, Kramer N, Freund P, Rodríguez-Rojas A, Burgener IA. Traces of Canine Inflammatory Bowel Disease Reflected by Intestinal Organoids. Int J Mol Sci 2024; 25:576. [PMID: 38203746 PMCID: PMC10778911 DOI: 10.3390/ijms25010576] [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: 10/11/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory condition that affects humans and several domestic animal species, including cats and dogs. In this study, we have analyzed duodenal organoids derived from canine IBD patients using quantitative proteomics. Our objective was to investigate whether these organoids show phenotypic traits of the disease compared with control organoids obtained from healthy donors. To this aim, IBD and control organoids were subjected to quantitative proteomics analysis via liquid chromatography-mass spectrometry. The obtained data revealed notable differences between the two groups. The IBD organoids exhibited several alterations at the levels of multiple proteins that are consistent with some known IBD alterations. The observed phenotype in the IBD organoids to some degree mirrors the corresponding intestinal condition, rendering them a compelling approach for investigating the disease and advancing drug exploration. Additionally, our study revealed similarities to some human IBD biomarkers, further emphasizing the translational and comparative value of dogs for future investigations related to the causes and treatment of IBD. Relevant proteins such as CALU, FLNA, MSN and HMGA2, which are related to intestinal diseases, were all upregulated in the IBD duodenal organoids. At the same time, other proteins such as intestinal keratins and the mucosal immunity PIGR were depleted in these IBD organoids. Based on these findings, we propose that these organoids could serve as a valuable tool for evaluating the efficacy of therapeutic interventions against canine IBD.
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Affiliation(s)
- Barbara Pratscher
- Clinic for Small Animals, Division for Small Animal Internal Medicine, Department for Small Animal and Horses, University of Veterinary Medicine, 1210 Vienna, Austria; (B.P.); (G.C.); (P.G.D.); (K.S.); (P.F.)
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany;
| | - Georg Csukovich
- Clinic for Small Animals, Division for Small Animal Internal Medicine, Department for Small Animal and Horses, University of Veterinary Medicine, 1210 Vienna, Austria; (B.P.); (G.C.); (P.G.D.); (K.S.); (P.F.)
| | - Pavlos G. Doulidis
- Clinic for Small Animals, Division for Small Animal Internal Medicine, Department for Small Animal and Horses, University of Veterinary Medicine, 1210 Vienna, Austria; (B.P.); (G.C.); (P.G.D.); (K.S.); (P.F.)
| | - Katrin Spirk
- Clinic for Small Animals, Division for Small Animal Internal Medicine, Department for Small Animal and Horses, University of Veterinary Medicine, 1210 Vienna, Austria; (B.P.); (G.C.); (P.G.D.); (K.S.); (P.F.)
| | - Nina Kramer
- Clinic for Small Animals, Division for Small Animal Internal Medicine, Department for Small Animal and Horses, University of Veterinary Medicine, 1210 Vienna, Austria; (B.P.); (G.C.); (P.G.D.); (K.S.); (P.F.)
| | - Patricia Freund
- Clinic for Small Animals, Division for Small Animal Internal Medicine, Department for Small Animal and Horses, University of Veterinary Medicine, 1210 Vienna, Austria; (B.P.); (G.C.); (P.G.D.); (K.S.); (P.F.)
| | - Alexandro Rodríguez-Rojas
- Clinic for Small Animals, Division for Small Animal Internal Medicine, Department for Small Animal and Horses, University of Veterinary Medicine, 1210 Vienna, Austria; (B.P.); (G.C.); (P.G.D.); (K.S.); (P.F.)
| | - Iwan A. Burgener
- Clinic for Small Animals, Division for Small Animal Internal Medicine, Department for Small Animal and Horses, University of Veterinary Medicine, 1210 Vienna, Austria; (B.P.); (G.C.); (P.G.D.); (K.S.); (P.F.)
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14
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Carvalho LB, Teigas-Campos PAD, Jorge S, Protti M, Mercolini L, Dhir R, Wiśniewski JR, Lodeiro C, Santos HM, Capelo JL. Normalization methods in mass spectrometry-based analytical proteomics: A case study based on renal cell carcinoma datasets. Talanta 2024; 266:124953. [PMID: 37490822 DOI: 10.1016/j.talanta.2023.124953] [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: 05/17/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023]
Abstract
Normalization is a crucial step in proteomics data analysis as it enables data adjustment and enhances comparability between datasets by minimizing multiple sources of variability, such as sampling, sample handling, storage, treatment, and mass spectrometry measurements. In this study, we investigated different normalization methods, including Z-score normalization, median divide normalization, and quantile normalization, to evaluate their performance using a case study based on renal cell carcinoma datasets. Our results demonstrate that when comparing datasets by pairs, both the Z-score and quantile normalization methods consistently provide better results in terms of the number of proteins identified and quantified as well as in identifying statistically significant up or down-regulated proteins. However, when three or more datasets are compared at the same time the differences are found to be negligible.
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Affiliation(s)
- Luis B Carvalho
- BIOSCOPE Group, LAQV-REQUIMTE, Chemistry Department, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, 2829-516, Caparica, Portugal
| | - Pedro A D Teigas-Campos
- BIOSCOPE Group, LAQV-REQUIMTE, Chemistry Department, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, 2829-516, Caparica, Portugal
| | - Susana Jorge
- BIOSCOPE Group, LAQV-REQUIMTE, Chemistry Department, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, 2829-516, Caparica, Portugal
| | - Michele Protti
- Research Group of Pharmaco-Toxicological Analysis (PTA Lab), Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Laura Mercolini
- Research Group of Pharmaco-Toxicological Analysis (PTA Lab), Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Rajiv Dhir
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jacek R Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Carlos Lodeiro
- BIOSCOPE Group, LAQV-REQUIMTE, Chemistry Department, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, 2829-516, Caparica, Portugal
| | - Hugo M Santos
- BIOSCOPE Group, LAQV-REQUIMTE, Chemistry Department, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, 2829-516, Caparica, Portugal; Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
| | - José L Capelo
- BIOSCOPE Group, LAQV-REQUIMTE, Chemistry Department, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, 2829-516, Caparica, Portugal.
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15
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Wang L, Yang S, Xue Y, Bo T, Xu J, Wang W. Mismatch Repair Protein Msh6 Tt Is Necessary for Nuclear Division and Gametogenesis in Tetrahymena thermophila. Int J Mol Sci 2023; 24:17619. [PMID: 38139447 PMCID: PMC10743813 DOI: 10.3390/ijms242417619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023] Open
Abstract
DNA mismatch repair (MMR) improves replication accuracy by up to three orders of magnitude. The MutS protein in E. coli or its eukaryotic homolog, the MutSα (Msh2-Msh6) complex, recognizes base mismatches and initiates the mismatch repair mechanism. Msh6 is an essential protein for assembling the heterodimeric complex. However, the function of the Msh6 subunit remains elusive. Tetrahymena undergoes multiple DNA replication and nuclear division processes, including mitosis, amitosis, and meiosis. Here, we found that Msh6Tt localized in the macronucleus (MAC) and the micronucleus (MIC) during the vegetative growth stage and starvation. During the conjugation stage, Msh6Tt only localized in MICs and newly developing MACs. MSH6Tt knockout led to aberrant nuclear division during vegetative growth. The MSH6TtKO mutants were resistant to treatment with the DNA alkylating agent methyl methanesulfonate (MMS) compared to wild type cells. MSH6Tt knockout affected micronuclear meiosis and gametogenesis during the conjugation stage. Furthermore, Msh6Tt interacted with Msh2Tt and MMR-independent factors. Downregulation of MSH2Tt expression affected the stability of Msh6Tt. In addition, MSH6Tt knockout led to the upregulated expression of several MSH6Tt homologs at different developmental stages. Msh6Tt is involved in macronuclear amitosis, micronuclear mitosis, micronuclear meiosis, and gametogenesis in Tetrahymena.
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Affiliation(s)
- Lin Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (L.W.); (S.Y.); (Y.X.); (T.B.)
| | - Sitong Yang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (L.W.); (S.Y.); (Y.X.); (T.B.)
| | - Yuhuan Xue
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (L.W.); (S.Y.); (Y.X.); (T.B.)
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (L.W.); (S.Y.); (Y.X.); (T.B.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (L.W.); (S.Y.); (Y.X.); (T.B.)
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (L.W.); (S.Y.); (Y.X.); (T.B.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
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16
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Maus H, Gellert A, Englert OR, Chen JX, Schirmeister T, Barthels F. Designing photoaffinity tool compounds for the investigation of the DENV NS2B-NS3 protease allosteric binding pocket. RSC Med Chem 2023; 14:2365-2379. [PMID: 37974966 PMCID: PMC10650954 DOI: 10.1039/d3md00331k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
Dengue virus (DENV) infection still lacks specific antiviral therapy, making the NS2B-NS3 protease an attractive target for drug development. However, allosteric inhibitors that bind to a site other than the active site still need to be better understood. In this study, we designed and synthesised tool compounds for photoaffinity labelling (PAL) to investigate the binding site of allosteric inhibitors on the DENV protease. These tool compounds contained an affinity moiety, a photoreactive group, and a reporter tag for detection. Upon irradiation, the photoreactive group formed a covalent bond with the protease, allowing for binding site identification. SDS-PAGE-based assays confirmed the qualitative binding of the designed inhibitors to the allosteric pocket, and pull-down experiments validated the interaction. Tryptic protein digestion following liquid chromatography/mass spectrometry analysis further supported the binding of the inhibitor to the proposed pocket revealing photo-attachment to an NS3 loop close to the C-terminus. These results enhance our understanding of allosteric inhibitors and their mechanism of action against the DENV protease. The developed tool compounds and PAL are potent tools for future drug discovery efforts and investigations targeting the DENV protease.
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Affiliation(s)
- Hannah Maus
- IPBS, Johannes Gutenberg-University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Andrea Gellert
- IPBS, Johannes Gutenberg-University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Olivia R Englert
- IPBS, Johannes Gutenberg-University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Jia-Xuan Chen
- IMB, Johannes Gutenberg-University Mainz Ackermannweg 4 55128 Mainz Germany
| | - Tanja Schirmeister
- IPBS, Johannes Gutenberg-University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Fabian Barthels
- IPBS, Johannes Gutenberg-University Mainz Staudingerweg 5 55128 Mainz Germany
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17
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Mei J, Li Z, Zhou S, Chen XL, Wilson RA, Liu W. Effector secretion and stability in the maize anthracnose pathogen Colletotrichum graminicola requires N-linked protein glycosylation and the ER chaperone pathway. THE NEW PHYTOLOGIST 2023; 240:1449-1466. [PMID: 37598305 DOI: 10.1111/nph.19213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/01/2023] [Indexed: 08/21/2023]
Abstract
N-linked protein glycosylation is a conserved and essential modification mediating protein processing and quality control in the endoplasmic reticulum (ER), but how this contributes to the infection cycle of phytopathogenic fungi is largely unknown. In this study, we discovered that inhibition of protein N-glycosylation severely affected vegetative growth, hyphal tip development, conidial germination, appressorium formation, and, ultimately, the ability of the maize (Zea mays) anthracnose pathogen Colletotrichum graminicola to infect its host. Quantitative proteomics analysis showed that N-glycosylation can coordinate protein O-glycosylation, glycosylphosphatidylinositol anchor modification, and endoplasmic reticulum quality control (ERQC) by directly targeting the proteins from the corresponding pathway in the ER. We performed a functional study of the N-glycosylation pathway-related protein CgALG3 and of the ERQC pathway-related protein CgCNX1, which demonstrated that N-glycosylation of ER chaperone proteins is essential for effector stability, secretion, and pathogenicity of C. graminicola. Our study provides concrete evidence for the regulation of effector protein stability and secretion by N-glycosylation.
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Affiliation(s)
- Jie Mei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shaoqun Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xiao-Lin Chen
- State Key Laboratory of Agricultural Microbiology and Provincial Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Richard A Wilson
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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18
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Sushkin ME, Koehler C, Lemke EA. Remodeling the cellular stress response for enhanced genetic code expansion in mammalian cells. Nat Commun 2023; 14:6931. [PMID: 37903771 PMCID: PMC10616097 DOI: 10.1038/s41467-023-42689-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/18/2023] [Indexed: 11/01/2023] Open
Abstract
Genetic code expansion (GCE) reprograms the translational machinery to site-specifically incorporate noncanonical amino acids (ncAAs) into a selected protein. The efficiency of GCE in mammalian cells might be compromised by cellular stress responses, among which, the protein kinase R(PKR)-dependent eIF2α phosphorylation pathway can reduce translation rates. Here we test several strategies to engineer the eIF2α pathway and boost the rate of translation and show that such interventions increase GCE efficiency in mammalian cells. In particular, addition of the N-terminal PKR fragment (1-174) provides a substantial enhancement in cytoplasmic GCE and also in GCE realized by OTOs (orthogonally translating designer organelles), which built on the principle of 2D phase separation to enable mRNA-selective ncAA incorporation. Our study demonstrates an approach for improving the efficiency of GCE and provides a means by which the power of designer organelles can be further optimized to tune protein translation.
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Affiliation(s)
- Mikhail E Sushkin
- Biocenter, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
- International PhD Programme of the Institute of Molecular Biology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Christine Koehler
- Biocenter, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
- VERAXA Biotech GmbH, Carl-Friedrich-Gauß-Ring 5, 69124, Heidelberg, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
- Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128, Mainz, Germany.
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19
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Mylopotamitaki D, Harking FS, Taurozzi AJ, Fagernäs Z, Godinho RM, Smith GM, Weiss M, Schüler T, McPherron SP, Meller H, Cascalheira J, Bicho N, Olsen JV, Hublin JJ, Welker F. Comparing extraction method efficiency for high-throughput palaeoproteomic bone species identification. Sci Rep 2023; 13:18345. [PMID: 37884544 PMCID: PMC10603084 DOI: 10.1038/s41598-023-44885-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
High-throughput proteomic analysis of archaeological skeletal remains provides information about past fauna community compositions and species dispersals in time and space. Archaeological skeletal remains are a finite resource, however, and therefore it becomes relevant to optimize methods of skeletal proteome extraction. Ancient proteins in bone specimens can be highly degraded and consequently, extraction methods for well-preserved or modern bone might be unsuitable for the processing of highly degraded skeletal proteomes. In this study, we compared six proteomic extraction methods on Late Pleistocene remains with variable levels of proteome preservation. We tested the accuracy of species identification, protein sequence coverage, deamidation, and the number of post-translational modifications per method. We find striking differences in obtained proteome complexity and sequence coverage, highlighting that simple acid-insoluble proteome extraction methods perform better in highly degraded contexts. For well-preserved specimens, the approach using EDTA demineralization and protease-mix proteolysis yielded a higher number of identified peptides. The protocols presented here allowed protein extraction from ancient bone with a minimum number of working steps and equipment and yielded protein extracts within three working days. We expect further development along this route to benefit large-scale screening applications of relevance to archaeological and human evolution research.
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Affiliation(s)
- Dorothea Mylopotamitaki
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France.
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Florian S Harking
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Zandra Fagernäs
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ricardo M Godinho
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, University of Algarve, Faro, Portugal
| | - Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Anthropology and Conservation, University of Kent, Kent, UK
| | - Marcel Weiss
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institut für Ur- und Frühgeschichte, Friedrich-Alexander-Universität, Erlangen, Germany
| | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Shannon P McPherron
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Meller
- State Office for Heritage Management and Archaeology, Saxony-Anhalt-State Museum of Prehistory, Halle (Saale), Germany
| | - João Cascalheira
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, University of Algarve, Faro, Portugal
| | - Nuno Bicho
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, University of Algarve, Faro, Portugal
| | - Jesper V Olsen
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jean-Jacques Hublin
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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20
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Dedigama-Arachchige PM, Acharige NPN, Zhang X, Bremer HJ, Yi Z, Pflum MKH. Identification of PP1c-PPP1R12A Substrates Using Kinase-Catalyzed Biotinylation to Identify Phosphatase Substrates. ACS OMEGA 2023; 8:35628-35637. [PMID: 37810667 PMCID: PMC10552495 DOI: 10.1021/acsomega.3c01944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/21/2023] [Indexed: 10/10/2023]
Abstract
Protein phosphatase 1 regulatory subunit 12A (PPP1R12A) interacts with the catalytic subunit of protein phosphatase 1 (PP1c) to form the myosin phosphatase complex. In addition to a well-documented role in muscle contraction, the PP1c-PPP1R12A complex is associated with cytoskeleton organization, cell migration and adhesion, and insulin signaling. Despite the variety of biological functions, only a few substrates of the PP1c-PPP1R12A complex are characterized, which limit a full understanding of PP1c-PPP1R12A activities in muscle contraction and cytoskeleton regulation. Here, the chemoproteomics method Kinase-catalyzed Biotinylation to Identify Phosphatase Substrates (K-BIPS) was used to identify substrates of the PP1c-PPP1R12A complex in L6 skeletal muscle cells. K-BIPS enriched 136 candidate substrates with 14 high confidence hits. One high confidence hit, AKT1 kinase, was validated as a novel PP1c-PPP1R12A substrate. Given the previously documented role of AKT1 in PPP1R12A phosphorylation and cytoskeleton organization, the data suggest that PP1c-PPP1R12A regulates its own phosphatase activity through an AKT1-dependent feedback mechanism to influence cytoskeletal arrangement in muscle cells.
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Affiliation(s)
| | - Nuwan P N Acharige
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit 48202-3489, Michigan, United States
| | - Xiangmin Zhang
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Ave, Detroit 48201, Michigan, United States
| | - Hannah J Bremer
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit 48202-3489, Michigan, United States
| | - Zhengping Yi
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Ave, Detroit 48201, Michigan, United States
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit 48202-3489, Michigan, United States
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21
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Dai H, He M, Hu G, Li Z, Al-Romaima A, Wu Z, Liu X, Qiu M. Discovery of ACE Inhibitory Peptides Derived from Green Coffee Using In Silico and In Vitro Methods. Foods 2023; 12:3480. [PMID: 37761189 PMCID: PMC10529643 DOI: 10.3390/foods12183480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/04/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
Inhibition of angiotensin-I converting enzyme (ACE) is an important means of treating hypertension since it plays an important regulatory function in the renin-angiotensin system. The aim of this study was to investigate the ACE inhibitory effect of bioactive peptides from green coffee beans using in silico and in vitro methods. Alcalase and thermolysin were employed to hydrolyze protein extract from coffee beans. Bioactive peptides were identified by LC-MS/MS analysis coupled with database searching. The potential bioactivities of peptides were predicted by in silico screening, among which five novel peptides may have ACE inhibitory activity. In vitro assay was carried out to determine the ACE inhibitory degree. Two peptides (IIPNEVY, ITPPVMLPP) were obtained with IC50 values of 57.54 and 40.37 μM, respectively. Furthermore, it was found that two inhibitors bound to the receptor protein on similar sites near the S1 active pocket of ACE to form stable enzyme-peptide complexes through molecular docking, and the Lineweaver-Burk plot showed that IIPNEVY was a noncompetitive inhibitor, and ITPPVMLPP was suggested to be a mixed-type inhibitor. Our study demonstrated that two peptides isolated from coffee have potential applications as antihypertensive agents.
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Affiliation(s)
- Haopeng Dai
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (H.D.); (M.H.); (G.H.); (Z.L.); (A.A.-R.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min He
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (H.D.); (M.H.); (G.H.); (Z.L.); (A.A.-R.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guilin Hu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (H.D.); (M.H.); (G.H.); (Z.L.); (A.A.-R.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongrong Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (H.D.); (M.H.); (G.H.); (Z.L.); (A.A.-R.); (Z.W.)
| | - Abdulbaset Al-Romaima
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (H.D.); (M.H.); (G.H.); (Z.L.); (A.A.-R.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhouwei Wu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (H.D.); (M.H.); (G.H.); (Z.L.); (A.A.-R.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaocui Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (H.D.); (M.H.); (G.H.); (Z.L.); (A.A.-R.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minghua Qiu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (H.D.); (M.H.); (G.H.); (Z.L.); (A.A.-R.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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22
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Tartaglia M, Scarano P, Prigioniero A, Zuzolo D, Postiglione A, Falzarano A, Amoresano A, Illiano A, Pinto G, Schicchi R, Geraci A, Sciarrillo R, Guarino C. Multi-omic characterisation as a tool to improve knowledge, valorisation and conservation of wild fruit genetic resources: the case of Arbutus unedo L. FRONTIERS IN PLANT SCIENCE 2023; 14:1195673. [PMID: 37745992 PMCID: PMC10514896 DOI: 10.3389/fpls.2023.1195673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/11/2023] [Indexed: 09/26/2023]
Abstract
The valorisation and conservation of plant genetic resources (PGRs) and wild fruit PGRs are critical to ensure the maintenance of genetic and cultural heritage and to promote new perspectives on resource use. New strategies to characterize PGRs are needed, and the omics approach can provide information that is still largely unknown. The Strawberry tree (Arbutus unedo L.) is an underutilized, drought and fire-resistant species distributed in the Mediterranean area and its berries have large ethnobotanical use. Although their phenolic profile and antioxidant capacity are known, they are not well characterised, particularly from a proteomic perspective. The aim of this work is the characterisation of two ecotypes of A. unedo (Campania and Sicily) from a molecular viewpoint to valorise and encourage the preservation of this wild fruit. Samples were collected from two different geographical areas to assess whether different geographical conditions could influence the characteristics of leaves and fruits at the three stages of ripening (green, veraison, red). Proteomic analysis identified 904 proteins, of which 122 showed significance along the ripening. Some of these differentially abundant proteins, such as chalcone synthase, show a marked increase during ripening. The protein functional classes with the highest representation are involved in protein and amino acid metabolism, glycolysis and in secondary metabolism. From a proteomic perspective, there are no differences between the fruits from the two regions compared by the ripening stage. However, the pedoclimatic metabolic imprinting allowed the observation of good diversity in the metabolomic profiles between the two ecotypes, especially for anthocyanins, 4 times more abundant in the Sicilian veraisoned fruit than in the Campania one, and catechins, with double the abundance in the Campania ecotype compared to the Sicilian ecotype in the green phase, but more abundant (3x) in the Sicilian veraisoned fruit. Phenolic compounds show a 20% greater abundance in the Campania green arbutus fruit than in the Sicilian one, values that then equalise as ripening progresses. Multi-omic characterisation enhanced the knowledge on a wild fruit plant species which shows specific adaptations and responses to the environment to be considered when addressing the issue of local agrobiodiversity.
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Affiliation(s)
- Maria Tartaglia
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Pierpaolo Scarano
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | | | - Daniela Zuzolo
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Alessia Postiglione
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | | | - Angela Amoresano
- Department of Chemical Science, University of Naples Federico II, Naples, Italy
- INBB - Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Rome, Italy
| | - Anna Illiano
- Department of Chemical Science, University of Naples Federico II, Naples, Italy
- INBB - Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Rome, Italy
| | - Gabriella Pinto
- Department of Chemical Science, University of Naples Federico II, Naples, Italy
- INBB - Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Rome, Italy
| | - Rosario Schicchi
- Department of Agricultural, Food and Forest Sciences (SAAF), Università degli Studi di Palermo, Palermo, Italy
| | - Anna Geraci
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Rosaria Sciarrillo
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Carmine Guarino
- Department of Science and Technology, University of Sannio, Benevento, Italy
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23
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Brambilla S, Guiotto M, Torretta E, Armenia I, Moretti M, Gelfi C, Palombella S, di Summa PG. Human platelet lysate stimulates neurotrophic properties of human adipose-derived stem cells better than Schwann cell-like cells. Stem Cell Res Ther 2023; 14:179. [PMID: 37480149 PMCID: PMC10362751 DOI: 10.1186/s13287-023-03407-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Trauma-associated peripheral nerve injury is a widespread clinical problem causing sensory and motor disabilities. Schwann cells (SCs) contribute to nerve regeneration, mainly by secreting nerve growth factor (NGF) and brain-derived neurotrophic factor. In the last years, adipose-derived stem cells (ASCs) differentiated into SCs (SC-ASCs) were considered as promising cell therapy. However, the cell trans-differentiation process has not been effectively showed and presents several drawbacks, thus an alternative approach for increasing ASCs neurotrophic properties is highly demanded. In the context of human cell-based therapies, Good Manufacturing Practice directions indicate that FBS should be substituted with a xenogeneic-free supplement, such as Human Platelet Lysate (HPL). Previously, we demonstrated that neurotrophic properties of HPL-cultured ASCs were superior compared to undifferentiated FBS-cultured ASCs. Therefore, as following step, here we compared the neurotrophic properties of differentiated SC-like ASCs and HPL-cultured ASCs. METHODS Both cell groups were investigated for gene expression level of neurotrophic factors, their receptors and neuronal markers. Moreover, the expression of nestin was quantitatively evaluated by flow cytometry. The commitment toward the SC phenotype was assessed with immunofluorescence pictures. Proteomics analysis was performed on both cells and their conditioned media to compare the differential protein profile. Finally, neurotrophic abilities of both groups were evaluated with a functional co-culture assay, assessing dorsal root ganglia survival and neurite outgrowth. RESULTS HPL-cultured ASCs demonstrated higher gene expression of NGF and lower expression of S100B. Moreover, nestin was present in almost all HPL-cultured ASCs and only in one quarter of SC-ASCs. Immunofluorescence confirmed that S100B was not present in HPL-cultured ASCs. Proteomics analysis validated the higher expression of nestin and the increase in cytoskeletal and ECM proteins involved in neural regeneration processes. The co-culture assay highlighted that neurite outgrowth was higher in the presence of HPL-ASCs or their conditioned medium compared to SC-ASCs. CONCLUSIONS All together, our results show that HPL-ASCs were more neurotrophic than SC-ASCs. We highlighted that the HPL triggers an immature neuro-induction state of ASCs, while keeping their stem properties, paving the way for innovative therapies for nerve regeneration.
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Affiliation(s)
- Stefania Brambilla
- Cell and Tissue Engineering Laboratory, IRCCS Istituto Ortopedico Galeazzi, Via C. Belgioioso 173, 20157, Milan, Italy
| | - Martino Guiotto
- Department of Plastic and Hand Surgery, Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Enrica Torretta
- Laboratory of Proteomics and Lipidomics, IRCCS Istituto Ortopedico Galeazzi, Via C. Belgioioso 173, 20157, Milan, Italy
| | - Ilaria Armenia
- Instituto de Nanociencia y Materiales de Aragón, CSIC-University of Zaragoza, C/ Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Matteo Moretti
- Cell and Tissue Engineering Laboratory, IRCCS Istituto Ortopedico Galeazzi, Via C. Belgioioso 173, 20157, Milan, Italy
- Regenerative Medicine Technologies Laboratory, Laboratories for Translational Research (LRT), Ente Ospedaliero Cantonale (EOC), Via F. Chiesa 5, 6500, Bellinzona, Switzerland
- Service of Orthopaedics and Traumatology, Department of Surgery, EOC, Lugano, Switzerland
- Euler Institute, Faculty of Biomedical Sciences, USI, Lugano, Switzerland
| | - Cecilia Gelfi
- Laboratory of Proteomics and Lipidomics, IRCCS Istituto Ortopedico Galeazzi, Via C. Belgioioso 173, 20157, Milan, Italy
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Silvia Palombella
- Cell and Tissue Engineering Laboratory, IRCCS Istituto Ortopedico Galeazzi, Via C. Belgioioso 173, 20157, Milan, Italy.
| | - Pietro G di Summa
- Department of Plastic and Hand Surgery, Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland
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24
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Oppenheim T, Radzinski M, Braitbard M, Brielle ES, Yogev O, Goldberger E, Yesharim Y, Ravid T, Schneidman-Duhovny D, Reichmann D. The Cdc48 N-terminal domain has a molecular switch that mediates the Npl4-Ufd1-Cdc48 complex formation. Structure 2023; 31:764-779.e8. [PMID: 37311459 DOI: 10.1016/j.str.2023.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 02/28/2023] [Accepted: 05/18/2023] [Indexed: 06/15/2023]
Abstract
Cdc48 (VCP/p97) is a major AAA-ATPase involved in protein quality control, along with its canonical cofactors Ufd1 and Npl4 (UN). Here, we present novel structural insights into the interactions within the Cdc48-Npl4-Ufd1 ternary complex. Using integrative modeling, we combine subunit structures with crosslinking mass spectrometry (XL-MS) to map the interaction between Npl4 and Ufd1, alone and in complex with Cdc48. We describe the stabilization of the UN assembly upon binding with the N-terminal-domain (NTD) of Cdc48 and identify a highly conserved cysteine, C115, at the Cdc48-Npl4-binding interface which is central to the stability of the Cdc48-Npl4-Ufd1 complex. Mutation of Cys115 to serine disrupts the interaction between Cdc48-NTD and Npl4-Ufd1 and leads to a moderate decrease in cellular growth and protein quality control in yeast. Our results provide structural insight into the architecture of the Cdc48-Npl4-Ufd1 complex as well as its in vivo implications.
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Affiliation(s)
- Tal Oppenheim
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Meytal Radzinski
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Merav Braitbard
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Esther S Brielle
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ohad Yogev
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eliya Goldberger
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yarden Yesharim
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, the Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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25
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Wang L, Xue Y, Yang S, Bo T, Xu J, Wang W. Mismatch Repair Protein Msh2 Is Necessary for Macronuclear Stability and Micronuclear Division in Tetrahymena thermophila. Int J Mol Sci 2023; 24:10559. [PMID: 37445734 DOI: 10.3390/ijms241310559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Mismatch repair (MMR) is a conserved mechanism that is primarily responsible for the repair of DNA mismatches during DNA replication. Msh2 forms MutS heterodimer complexes that initiate the MMR in eukaryotes. The function of Msh2 is less clear under different chromatin structures. Tetrahymena thermophila contains a transcriptionally active macronucleus (MAC) and a transcriptionally silent micronucleus (MIC) in the same cytoplasm. Msh2 is localized in the MAC and MIC during vegetative growth. Msh2 is localized in the perinuclear region around the MIC and forms a spindle-like structure as the MIC divides. During the early conjugation stage, Msh2 is localized in the MIC and disappears from the parental MAC. Msh2 is localized in the new MAC and new MIC during the late conjugation stage. Msh2 also forms a spindle-like structure with a meiotic MIC and mitotic gametic nucleus. MSH2 knockdown inhibits the division of MAC and MIC during vegetative growth and affects cellular proliferation. MSH2 knockdown mutants are sensitive to cisplatin treatment. MSH2 knockdown also affects micronuclear meiosis and gametogenesis during sexual development. Furthermore, Msh2 interacts with MMR-dependent and MMR-independent factors. Therefore, Msh2 is necessary for macronuclear stability, as well as micronuclear mitosis and meiosis in Tetrahymena.
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Affiliation(s)
- Lin Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Yuhuan Xue
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Sitong Yang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
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26
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Makwana P, Rahul K, Ito K, Subhadra B. Diversity of Antimicrobial Peptides in Silkworm. Life (Basel) 2023; 13:life13051161. [PMID: 37240807 DOI: 10.3390/life13051161] [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: 03/14/2023] [Revised: 05/01/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Antimicrobial resistance is a phenomenon that the present-day world is witnessing that poses a serious threat to global health. The decline in the development of novel therapeutics over the last couple of decades has exacerbated the situation further. In this scenario, the pursuit of new alternative therapeutics to commonly used antibiotics has gained predominance amongst researchers across the world. Antimicrobial peptides (AMPs) from natural sources have drawn significant interest in the recent years as promising pharmacological substitutes over the conventional antibiotics. The most notable advantage of AMPs is that microorganisms cannot develop resistance to them. Insects represent one of the potential sources of AMPs, which are synthesized as part of an innate immune defence against invading pathogens. AMPs from different insects have been extensively studied, and silkworm is one of them. Diverse classes of AMPs (including attacins, cecropins, defensins, enbocins, gloverins, lebocins and moricins) were identified from silkworm that exhibit antimicrobial property against bacteria, fungi and viruses, indicating their potential therapeutic benefits. This review briefs about the immune responses of silkworm to invading pathogens, the isolation of AMPs from silkworms, AMPs reported in silkworms and their activity against various microorganisms.
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Affiliation(s)
- Pooja Makwana
- Central Sericultural Research & Training Institute, Central Silk Board, Ministry of Textiles, Government of India, Berhampore, Murshidabad 742101, West Bengal, India
| | - Kamidi Rahul
- Central Sericultural Research & Training Institute, Central Silk Board, Ministry of Textiles, Government of India, Berhampore, Murshidabad 742101, West Bengal, India
| | - Katsuhiko Ito
- Laboratory of Sericultural Science, Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi 183-8509, Tokyo, Japan
| | - Bindu Subhadra
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, New York, NY 11548, USA
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Carvalho LB, Martínez JLC, Lodeiro C, Bento R, Dhir R, Morrissey JJ, Pinheiro LC, Medeiros M, Santos HM. Biochemical network analysis of protein-protein interactions to follow-up T1 bladder cancer patients. J Proteomics 2023; 278:104865. [PMID: 36870676 DOI: 10.1016/j.jprot.2023.104865] [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: 11/30/2022] [Revised: 02/03/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Bladder cancer (BCa) is a prevalent disease with a high risk of aggressive recurrence in T1-stage patients. Despite the efforts to anticipate recurrence, a reliable method has yet to be developed. In this work, we employed high-resolution mass spectrometry to compare the urinary proteome of T1-stage BCa patients with recurring versus non-recurring disease to uncover actionable clinical information predicting recurrence. All patients were diagnosed with T1-stage bladder cancer between the ages of 51 and 91, and urine samples were collected before medical intervention. Our results suggest that the urinary myeloperoxidase to cubilin ratio could be used as a new tool for predicting recurrence and that dysregulation of the inflammatory and immune systems may be a key driver of disease worsening. Furthermore, we identified neutrophil degranulation and neutrophil extracellular traps (NETs) as key pathways in the progression of T1-stage BCa. We propose that proteomics follow-up of the inflammatory and immune systems may be useful for monitoring the effectiveness of therapy. SIGNIFICANCE: This article describes how proteomics can be used to characterize tumor aggressiveness in patients with the same diagnosis of bladder cancer (BCa). LC-MS/MS in combination with label free quantification (LFQ) were used to explore potential protein and pathway level changes related to the aggressiveness of the disease in 13 and 17 recurring and non-recurring T1 stage BCa patients. We have shown that the MPO/CUBN protein ratio is a candidate for a urine prognosis tool in BCa. Furthermore, we identify dysregulation of inflammation process as a driver for BCa recurrence and progression. Moreover, we propose using proteomics to track the effectiveness of therapy in the inflammatory and immune systems.
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Affiliation(s)
- Luís B Carvalho
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica 2829-516, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, Caparica 2825-182, Portugal
| | - José Luis Capelo Martínez
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica 2829-516, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, Caparica 2825-182, Portugal
| | - Carlos Lodeiro
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica 2829-516, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, Caparica 2825-182, Portugal
| | - Rafael Bento
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica 2829-516, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, Caparica 2825-182, Portugal
| | - Rajiv Dhir
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jeremiah J Morrissey
- Department of Anesthesiology, Division of Clinical and Translational Research, School of Medicine and Siteman Cancer Center, Washington University, St. Louis, MO, USA
| | - Luis Campos Pinheiro
- Urology Department, Central Lisbon Hospital Center, Lisbon, Portugal.; NOVA Medical School, NOVA University of Lisbon, Lisbon, Portugal
| | - Mariana Medeiros
- Urology Department, Central Lisbon Hospital Center, Lisbon, Portugal.; NOVA Medical School, NOVA University of Lisbon, Lisbon, Portugal
| | - Hugo M Santos
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica 2829-516, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, Caparica 2825-182, Portugal; Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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Juan H, Huang H. Quantitative analysis of high‐throughput biological data. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Hsueh‐Fen Juan
- Department of Life Science, Institute of Biomedical Electronics and Bioinformatics, and Center for Systems Biology National Taiwan University Taipei Taiwan
- Taiwan AI Labs Taipei Taiwan
| | - Hsuan‐Cheng Huang
- Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei Taiwan
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Pathway-guided monitoring of the disease course in bladder cancer with longitudinal urine proteomics. COMMUNICATIONS MEDICINE 2023; 3:8. [PMID: 36646893 PMCID: PMC9842762 DOI: 10.1038/s43856-023-00238-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 01/06/2023] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Monitoring bladder cancer over time requires invasive and costly procedures. Less invasive approaches are required using readily available biological samples such as urine. In this study, we demonstrate a method for longitudinal analysis of the urine proteome to monitor the disease course in patients with bladder cancer. METHODS We compared the urine proteomes of patients who experienced recurrence and/or progression (n = 13) with those who did not (n = 17). We identified differentially expressed proteins within various pathways related to the hallmarks of cancer. The variation of such pathways during the disease course was determined using our differential personal pathway index (dPPi) calculation, which could indicate disease progression and the need for medical intervention. RESULTS Seven hallmark pathways are used to develop the dPPi. We demonstrate that we can successfully longitudinally monitor the disease course in bladder cancer patients through a combination of urine proteomic analysis and the dPPi calculation, over a period of 62 months. CONCLUSIONS Using the information contained in the patient's urinary proteome, the dPPi reflects the individual's course of bladder cancer, and helps to optimise the use of more invasive procedures such as cystoscopy.
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Yedji RS, Sohm B, Salnot V, Guillonneau F, Cossu-Leguille C, Battaglia E. First Identification of a Large Set of Serine Hydrolases by Activity-Based Protein Profiling in Dibutyl Phthalate-Exposed Zebrafish Larvae. Int J Mol Sci 2022; 23:ijms232416060. [PMID: 36555700 PMCID: PMC9786740 DOI: 10.3390/ijms232416060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Despite the involvement of several serine hydrolases (SHs) in the metabolism of xenobiotics such as dibutyl phthalate (DBP), no study has focused on mapping this enzyme class in zebrafish, a model organism frequently used in ecotoxicology. Here, we survey and identify active SHs in zebrafish larvae and search for biological markers of SH type after exposure to DBP. Zebrafish were exposed to 0, 5, and 100 µg/L DBP from 4 to 120 h post-fertilization. A significant decrease in vitellogenin expression level of about 2-fold compared to the control was found in larvae exposed to 100 µg/L DBP for 120 h. The first comprehensive profiling of active SHs in zebrafish proteome was achieved with an activity-based protein profiling (ABPP) approach. Among 49 SHs identified with high confidence, one was the carboxypeptidase ctsa overexpressed in larvae exposed to 100 µg/L DBP for 120 h. To the best of our knowledge, this is the first time that a carboxypeptidase has been identified as deregulated following exposure to DBP. The overall results indicate that targeted proteomics approaches, such as ABPP, can, therefore, be an asset for understanding the mechanism of action related to xenobiotics in ecotoxicology.
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Affiliation(s)
- Rodrigue S. Yedji
- LIEC, UMR7360, Campus Bridoux, Université de Lorraine, 57070 Metz, France
| | - Bénédicte Sohm
- LIEC, UMR7360, Campus Bridoux, Université de Lorraine, 57070 Metz, France
| | - Virginie Salnot
- Plateforme Protéomique 3P5, Inserm U1016-Institut Cochin, MICUSPC, Université Paris Descartes, 75006 Paris, France
| | - François Guillonneau
- Plateforme Protéomique 3P5, Inserm U1016-Institut Cochin, MICUSPC, Université Paris Descartes, 75006 Paris, France
- Unité Protéomique Clinique, Institut de Cancérologie de l’Ouest, CRCI2NA-UMR INSERM 1307/CNRS 6075, team03, 15, rue André Boquel, 49055 Angers, France
| | | | - Eric Battaglia
- LIEC, UMR7360, Campus Bridoux, Université de Lorraine, 57070 Metz, France
- Correspondence:
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Caulier A, Jankovsky N, Gautier EF, El Nemer W, Guitton C, Ouled-Haddou H, Guillonneau F, Mayeux P, Salnot V, Bruce J, Picard V, Garçon L. Red blood cell proteomics reveal remnant protein biosynthesis and folding pathways in PIEZO1-related hereditary xerocytosis. Front Physiol 2022; 13:960291. [PMID: 36531183 PMCID: PMC9751340 DOI: 10.3389/fphys.2022.960291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/21/2022] [Indexed: 11/25/2023] Open
Abstract
Hereditary xerocytosis is a dominant red cell membrane disorder characterized by an increased leak of potassium from the inside to outside the red blood cell membrane, associated with loss of water leading to red cell dehydration and chronic hemolysis. 90% of cases are related to heterozygous gain of function mutations in PIEZO1, encoding a mechanotransductor that translates a mechanical stimulus into a biological signaling. Data are still required to understand better PIEZO1-HX pathophysiology. Recent studies identified proteomics as an accurate and high-input tool to study erythroid progenitors and circulating red cell physiology. Here, we isolated red blood cells from 5 controls and 5 HX patients carrying an identified and pathogenic PIEZO1 mutation and performed a comparative deep proteomic analysis. A total of 603 proteins were identified among which 56 were differentially expressed (40 over expressed and 16 under expressed) between controls and HX with a homogenous expression profile within each group. We observed relevant modifications in the protein expression profile related to PIEZO1 mutations, identifying two main "knots". The first contained both proteins of the chaperonin containing TCP1 complex involved in the assembly of unfolded proteins, and proteins involved in translation. The second contained proteins involved in ubiquitination. Deregulation of proteins involved in protein biosynthesis was also observed in in vitro-produced reticulocytes after Yoda1 exposure. Thus, our work identifies significant changes in the protein content of PIEZO1-HX erythrocytes, revealing a "PIEZO1 signature" and identifying potentially targetable pathways in this disease characterized by a heterogeneous clinical expression and contra-indication of splenectomy.
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Affiliation(s)
- Alexis Caulier
- HEMATIM, CURS, Amiens and Laboratoire d’Hématologie, CHU Amiens, UPJV, Amiens, France
| | - Nicolas Jankovsky
- HEMATIM, CURS, Amiens and Laboratoire d’Hématologie, CHU Amiens, UPJV, Amiens, France
| | - Emilie Fleur Gautier
- 3P5 Proteom’IC, Institut Cochin, INSERM, CNRS, Université Paris Cité, Paris, France
- Institut Imagine-INSERM U1163, Necker Hospital, University of Paris, Paris, France
- Laboratoire d’excellence GR-Ex, Paris, France
| | | | - Corinne Guitton
- Laboratoire d’Hématologie et Filière MCGRE, CHU Bicêtre, Le Kremlin-Bicêtre, France
| | - Hakim Ouled-Haddou
- HEMATIM, CURS, Amiens and Laboratoire d’Hématologie, CHU Amiens, UPJV, Amiens, France
| | - François Guillonneau
- 3P5 Proteom’IC, Institut Cochin, INSERM, CNRS, Université Paris Cité, Paris, France
| | - Patrick Mayeux
- 3P5 Proteom’IC, Institut Cochin, INSERM, CNRS, Université Paris Cité, Paris, France
| | - Virginie Salnot
- 3P5 Proteom’IC, Institut Cochin, INSERM, CNRS, Université Paris Cité, Paris, France
| | - Johanna Bruce
- 3P5 Proteom’IC, Institut Cochin, INSERM, CNRS, Université Paris Cité, Paris, France
| | - Véronique Picard
- Laboratoire d’Hématologie et Filière MCGRE, CHU Bicêtre, Le Kremlin-Bicêtre, France
- Laboratoire d’Hématologie, Faculté de Pharmacie, Université Paris Saclay, Amiens, France
| | - Loïc Garçon
- HEMATIM, CURS, Amiens and Laboratoire d’Hématologie, CHU Amiens, UPJV, Amiens, France
- INSERM U1134, INTS, Paris, France
- Laboratoire d’Hématologie et Filière MCGRE, CHU Bicêtre, Le Kremlin-Bicêtre, France
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Lin SY, Zhou T, Cai S, Hu ZW, Zhong J, Dong L. Proteomic characteristics of saliva in patients with different subgroups of IgG4-RD. Front Immunol 2022; 13:1026921. [PMID: 36483554 PMCID: PMC9723444 DOI: 10.3389/fimmu.2022.1026921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/25/2022] [Indexed: 11/23/2022] Open
Abstract
Background Immunoglobulin G4-related disease (IgG4-RD) is a newly defined disease entity, with great heterogeneity among IgG4-RD subgroups with different organ involvement patterns. Identification of the proteomic characteristics of IgG4-RD subgroups will be critical for the understanding of the pathogenic mechanisms of IgG4-RD. Method In this study, we performed proteomic analysis using Tandem Mass Tags (TMT) technology with "high field" mass analyzer with improved resolution and sequencing speed to investigate the proteomic profile of saliva and plasma samples from ten untreated IgG4-RD patients and five healthy controls (HCs). Differentially expressed proteins (DEPs) were identified by "t test" function in R package. Functional enrichment analysis was used to investigate pathways enriched in IgG4-RD samples. Results Most salivary DEPs identified in IgG4-RD patients compared with HCs were mainly enriched in neutrophil mediated GO bioprocess. Within the comparisons between four IgG4-RD subgroups, more DEPs were identified in the comparison of Mikulicz group and Head and neck group. Among four subgroups of IgG4-RD, Head and neck group showed the most distinctive proteomic expression pattern when compared with HCs. Moreover, "Neutrophil mediated process" related GO bioprocess was commonly identified between comparisons of Mikulicz group and Head and neck group, Head and neck group and Retroperitoneal aorta group, Head and neck group and HCs, IgG4-RD patients with saliva gland involvement and those without saliva gland involvement. Key DEPs that involved in this GO bioprocess were identified. Besides, we performed proteomic analysis for plasma samples between ten IgG4-RD and five HCs and there were several DEPs identified overlapped in saliva and plasma. Conclusion We identified multiple processes/factors and several signaling pathways in saliva that may be involved in the IgG4-RD pathogenesis.
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Affiliation(s)
| | | | | | | | - Jixin Zhong
- Department of Rheumatology and Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lingli Dong
- Department of Rheumatology and Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave. Commun Biol 2022; 5:1262. [DOI: 10.1038/s42003-022-04190-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
AbstractRecent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.
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Ciccosanti F, Antonioli M, Sacchi A, Notari S, Farina A, Beccacece A, Fusto M, Vergori A, D'Offizi G, Taglietti F, Antinori A, Nicastri E, Marchioni L, Palmieri F, Ippolito G, Piacentini M, Agrati C, Fimia GM. Proteomic analysis identifies a signature of disease severity in the plasma of COVID-19 pneumonia patients associated to neutrophil, platelet and complement activation. Clin Proteomics 2022; 19:38. [PMID: 36348270 PMCID: PMC9641302 DOI: 10.1186/s12014-022-09377-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Most patients infected with SARS-CoV-2 display mild symptoms with good prognosis, while 20% of patients suffer from severe viral pneumonia and up to 5% may require intensive care unit (ICU) admission due to severe acute respiratory syndrome, which could be accompanied by multiorgan failure.Plasma proteomics provide valuable and unbiased information about disease progression and therapeutic candidates. Recent proteomic studies have identified molecular changes in plasma of COVID-19 patients that implied significant dysregulation of several aspects of the inflammatory response accompanied by a general metabolic suppression. However, which of these plasma alterations are associated with disease severity remains only partly characterized.A known limitation of proteomic studies of plasma samples is the large difference in the macromolecule abundance, with concentration spanning at least 10 orders of magnitude. To improve the coverage of plasma contents, we performed a deep proteomic analysis of plasma from 10 COVID-19 patients with severe/fatal pneumonia compared to 10 COVID-19 patients with pneumonia who did not require ICU admission (non-ICU). To this aim, plasma samples were first depleted of the most abundant proteins, trypsin digested and peptides subjected to a high pH reversed-phase peptide fractionation before LC-MS analysis.These results highlighted an increase of proteins involved in neutrophil and platelet activity and acute phase response, which is significantly higher in severe/fatal COVID-19 patients when compared to non-ICU ones. Importantly, these changes are associated with a selective induction of complement cascade factors in severe/fatal COVID-19 patients. Data are available via ProteomeXchange with identifier PXD036491. Among these alterations, we confirmed by ELISA that higher levels of the neutrophil granule proteins DEFA3 and LCN2 are present in COVID-19 patients requiring ICU admission when compared to non-ICU and healthy donors.Altogether, our study provided an in-depth view of plasma proteome changes that occur in COVID-19 patients in relation to disease severity, which can be helpful to identify therapeutic strategies to improve the disease outcome.
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Affiliation(s)
- Fabiola Ciccosanti
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Manuela Antonioli
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Alessandra Sacchi
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Stefania Notari
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Anna Farina
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Alessia Beccacece
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Marisa Fusto
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Alessandra Vergori
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Gianpiero D'Offizi
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Fabrizio Taglietti
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Andrea Antinori
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Emanuele Nicastri
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Luisa Marchioni
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Fabrizio Palmieri
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Giuseppe Ippolito
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
- General Directorate for Research and Health Innovation, Italian Ministry of Health, Rome, Italy
| | - Mauro Piacentini
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Chiara Agrati
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy.
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, IRCCS, Rome, Italy.
| | - Gian Maria Fimia
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy.
- Department of Molecular Medicine, University of Rome "Sapienza", Rome, Italy.
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Spatial analysis of the glioblastoma proteome reveals specific molecular signatures and markers of survival. Nat Commun 2022; 13:6665. [PMID: 36333286 PMCID: PMC9636229 DOI: 10.1038/s41467-022-34208-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Molecular heterogeneity is a key feature of glioblastoma that impedes patient stratification and leads to large discrepancies in mean patient survival. Here, we analyze a cohort of 96 glioblastoma patients with survival ranging from a few months to over 4 years. 46 tumors are analyzed by mass spectrometry-based spatially-resolved proteomics guided by mass spectrometry imaging. Integration of protein expression and clinical information highlights three molecular groups associated with immune, neurogenesis, and tumorigenesis signatures with high intra-tumoral heterogeneity. Furthermore, a set of proteins originating from reference and alternative ORFs is found to be statistically significant based on patient survival times. Among these proteins, a 5-protein signature is associated with survival. The expression of these 5 proteins is validated by immunofluorescence on an additional cohort of 50 patients. Overall, our work characterizes distinct molecular regions within glioblastoma tissues based on protein expression, which may help guide glioblastoma prognosis and improve current glioblastoma classification.
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Biswas D, Kumari N, Lachén-Montes M, Dutta S, Agrawal I, Samanta D, Shenoy SV, Halder A, Fernández-Irigoyen J, Padhye AR, Santamaría E, Srivastava S. Deep Phosphoproteome Landscape of Interhemispheric Functionality of Neuroanatomical Regions of the Human Brain. J Proteome Res 2022; 22:1043-1055. [PMID: 36317652 DOI: 10.1021/acs.jproteome.2c00244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Post-translational modifications (PTMs) are one of the compulsive and predominant biological processes that regulate the diverse molecular mechanism, modulate the onset of disease, and are the reason behind the functional diversity of proteins. Despite the widespread research findings in neuroproteomics, one of the key drawbacks has been the lack of proteome-level knowledge of hemispheric lateralization. We have investigated the proteome level expression in different neuroanatomical regions under the Human Brain Proteome Project (HBPP) and developed the global interhemispheric brain proteome map (Brainprot) earlier. Furthermore, this study has extended to decipher the phosphoproteome map of human brain interhemispheric regions through high-resolution mass spectrometry. The phosphoproteomics examination of 12 unique interhemispheric neurological brain regions using Orbitrap fusion liquid chromatography with tandem mass spectrometry provided comprehensive coverage of 996 phosphoproteins, 2010 phosphopeptides, and 3567 phosphosites. Moreover, interhemispheric phosphoproteome profiling has been categorized according to synaptic ontologies and interhemispheric expression to understand the functionality. Finally, we have integrated the phosphosites data under the PhosphoMap section in the Inter-Hemispheric Brain Proteome Map Portal (https://www.brainprot.org/) for the advancement and support of the ongoing neuroproteomics research worldwide. Data is available via ProteomeXchange with the identifier PXD031188.
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Affiliation(s)
- Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Neha Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Sampurna Dutta
- School of Biological Sciences, Indian Association for the Cultivation of Science, 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Ishita Agrawal
- Department of Molecular and Human Genetics, Banaras Hindu University, Varanasi221005, India
| | - Debabrata Samanta
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal721302, India
| | - Sanjyot Vinayak Shenoy
- Department of Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Advait Rahul Padhye
- Department of Computer Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
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Overhoff M, Tellkamp F, Hess S, Tolve M, Tutas J, Faerfers M, Ickert L, Mohammadi M, De Bruyckere E, Kallergi E, Delle Vedove A, Nikoletopoulou V, Wirth B, Isensee J, Hucho T, Puchkov D, Isbrandt D, Krueger M, Kloppenburg P, Kononenko NL. Autophagy regulates neuronal excitability by controlling cAMP/protein kinase A signaling at the synapse. EMBO J 2022; 41:e110963. [PMID: 36217825 PMCID: PMC9670194 DOI: 10.15252/embj.2022110963] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 09/10/2022] [Accepted: 09/14/2022] [Indexed: 01/13/2023] Open
Abstract
Autophagy provides nutrients during starvation and eliminates detrimental cellular components. However, accumulating evidence indicates that autophagy is not merely a housekeeping process. Here, by combining mouse models of neuron-specific ATG5 deficiency in either excitatory or inhibitory neurons with quantitative proteomics, high-content microscopy, and live-imaging approaches, we show that autophagy protein ATG5 functions in neurons to regulate cAMP-dependent protein kinase A (PKA)-mediated phosphorylation of a synapse-confined proteome. This function of ATG5 is independent of bulk turnover of synaptic proteins and requires the targeting of PKA inhibitory R1 subunits to autophagosomes. Neuronal loss of ATG5 causes synaptic accumulation of PKA-R1, which sequesters the PKA catalytic subunit and diminishes cAMP/PKA-dependent phosphorylation of postsynaptic cytoskeletal proteins that mediate AMPAR trafficking. Furthermore, ATG5 deletion in glutamatergic neurons augments AMPAR-dependent excitatory neurotransmission and causes the appearance of spontaneous recurrent seizures in mice. Our findings identify a novel role of autophagy in regulating PKA signaling at glutamatergic synapses and suggest the PKA as a target for restoration of synaptic function in neurodegenerative conditions with autophagy dysfunction.
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Affiliation(s)
- Melina Overhoff
- Cologne Excellence Cluster Cellular Stress Response in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Frederik Tellkamp
- Cologne Excellence Cluster Cellular Stress Response in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany,Faculty of Mathematics and Natural Sciences, Institute of GeneticsUniversity of CologneCologneGermany
| | - Simon Hess
- Cologne Excellence Cluster Cellular Stress Response in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany,Faculty of Mathematics and Natural Sciences, Institute of ZoologyUniversity of CologneCologneGermany
| | - Marianna Tolve
- Cologne Excellence Cluster Cellular Stress Response in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany,Center for Physiology and Pathophysiology, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Janine Tutas
- Cologne Excellence Cluster Cellular Stress Response in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Marcel Faerfers
- Cologne Excellence Cluster Cellular Stress Response in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Lotte Ickert
- Cologne Excellence Cluster Cellular Stress Response in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany,Center for Physiology and Pathophysiology, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Milad Mohammadi
- Cologne Excellence Cluster Cellular Stress Response in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Elodie De Bruyckere
- Cologne Excellence Cluster Cellular Stress Response in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Emmanouela Kallergi
- Département des Neurosciences FondamentalesUniversity of LausanneLausanneSwitzerland
| | - Andrea Delle Vedove
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Center for Rare Diseases Cologne, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | | | - Brunhilde Wirth
- Faculty of Mathematics and Natural Sciences, Institute of GeneticsUniversity of CologneCologneGermany,Institute of Human Genetics, Center for Molecular Medicine Cologne, Center for Rare Diseases Cologne, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Joerg Isensee
- Translational Pain Research, Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Tim Hucho
- Translational Pain Research, Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Dmytro Puchkov
- Leibniz Institute for Molecular Pharmacology (FMP)BerlinGermany
| | - Dirk Isbrandt
- Institute for Molecular and Behavioral Neuroscience, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany,Experimental NeurophysiologyGerman Center for Neurodegenerative DiseasesBonnGermany
| | - Marcus Krueger
- Cologne Excellence Cluster Cellular Stress Response in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany,Faculty of Mathematics and Natural Sciences, Institute of GeneticsUniversity of CologneCologneGermany
| | - Peter Kloppenburg
- Cologne Excellence Cluster Cellular Stress Response in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany,Faculty of Mathematics and Natural Sciences, Institute of ZoologyUniversity of CologneCologneGermany
| | - Natalia L Kononenko
- Cologne Excellence Cluster Cellular Stress Response in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany,Center for Physiology and Pathophysiology, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
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Quantitative Proteomic Analysis Reveals Yeast Cell Wall Products Influence the Serum Proteome Composition of Broiler Chickens. Int J Mol Sci 2022; 23:ijms231911844. [PMID: 36233150 PMCID: PMC9569515 DOI: 10.3390/ijms231911844] [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: 08/26/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022] Open
Abstract
With an ever-growing market and continual financial pressures associated with the prohibition of antibiotic growth promoters, the poultry industry has had to rapidly develop non-antibiotic alternatives to increase production yields. A possible alternative is yeast and its derivatives, such as the yeast cell wall (YCW), which have been proposed to confer selected beneficial effects on the host animal. Here, the effect of YCW supplementation on the broiler chicken was investigated using a quantitative proteomic strategy, whereby serum was obtained from three groups of broilers fed with distinct YCW-based Gut Health Products (GHP) or a control basal diet. Development of a novel reagent enabled application of ProteoMiner™ technology for sample preparation and subsequent comparative quantitative proteomic analysis revealed proteins which showed a significant change in abundance (n = 167 individual proteins; p < 0.05); as well as proteins which were uniquely identified (n = 52) in, or absent (n = 37) from, GHP-fed treatment groups versus controls. An average of 7.1% of proteins showed changes in abundance with GHP supplementation. Several effects of these GHPs including immunostimulation (via elevated complement protein detection), potential alterations in the oxidative status of the animal (e.g., glutathione peroxidase and catalase), stimulation of metabolic processes (e.g., differential abundance of glyceraldehyde-3-phosphate dehydrogenase), as well as evidence of a possible hepatoprotective effect (attenuated levels of serum α-glutathione s-transferase) by one GHP feed supplement, were observed. It is proposed that specific protein detection may be indicative of GHP efficacy to stimulate broiler immune status, i.e., may be biomarkers of GHP efficacy. In summary, this work has developed a novel technology for the preparation of high dynamic range proteomic samples for LC-MS/MS analysis, is part of the growing area of livestock proteomics and, importantly, provides evidential support for beneficial effects that GHP supplementation has on the broiler chicken.
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Bishola Tshitenge T, Clayton C. The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns. RNA (NEW YORK, N.Y.) 2022; 28:1239-1262. [PMID: 35793904 PMCID: PMC9380746 DOI: 10.1261/rna.079258.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The parasite Trypanosoma brucei grows as bloodstream forms in mammals, and as procyclic forms in tsetse flies. Transcription is polycistronic, all mRNAs are trans spliced, and polyadenylation sites are defined by downstream splicing signals. Expression regulation therefore depends heavily on post-transcriptional mechanisms. The RNA-binding protein DRBD18 was previously implicated in the export of some mRNAs from the nucleus in procyclic forms. It copurifies the outer ring of the nuclear pore, mRNA export factors and exon-junction-complex proteins. We show that for more than 200 mRNAs, DRBD18 depletion caused preferential accumulation of versions with shortened 3'-untranslated regions, arising from use of polyadenylation sites that were either undetectable or rarely seen in nondepleted cells. The shortened mRNAs were often, but not always, more abundant in depleted cells than the corresponding longer versions in normal cells. Their appearance was linked to the appearance of trans-spliced, polyadenylated RNAs containing only downstream 3'-untranslated region-derived sequences. Experiments with one mRNA suggested that nuclear retention alone, through depletion of MEX67, did not affect mRNA length, suggesting a specific effect of DRBD18 on processing. DRBD18-bound mRNAs were enriched in polypyrimidine tract motifs, and DRBD18 was found in both the nucleus and the cytoplasm. We therefore suggest that in the nucleus, DRBD18 might bind to polypyrimidine tracts in 3'-UTRs of mRNA precursors. Such binding might both prevent recognition of mRNA-internal polypyrimidine tracts by splicing factors, and promote export of the processed bound mRNAs to the cytosol.
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Affiliation(s)
| | - Christine Clayton
- Heidelberg University Center for Molecular Biology (ZMBH), D69120 Heidelberg, Germany
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NPvis: An Interactive Visualizer of Peptidic Natural Product–MS/MS Matches. Metabolites 2022; 12:metabo12080706. [PMID: 36005578 PMCID: PMC9415073 DOI: 10.3390/metabo12080706] [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: 06/16/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
Peptidic natural products (PNPs) represent a medically important class of secondary metabolites that includes antibiotics, anti-inflammatory and antitumor agents. Advances in tandem mass spectra (MS/MS) acquisition and in silico database search methods have enabled high-throughput PNP discovery. However, the resulting spectra annotations are often error-prone and their validation remains a bottleneck. Here, we present NPvis, a visualizer suitable for the evaluation of PNP–MS/MS matches. The tool interactively maps annotated spectrum peaks to the corresponding PNP fragments and allows researchers to assess the match correctness. NPvis accounts for the wide chemical diversity of PNPs that prevents the use of the existing proteomics visualizers. Moreover, NPvis works even if the exact chemical structure of the matching PNP is unknown. The tool is available online and as a standalone application. We hope that it will benefit the community by streamlining PNP data analysis and validation.
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41
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Choublier N, Taghi M, Menet MC, Le Gall M, Bruce J, Chafey P, Guillonneau F, Moreau A, Denizot C, Parmentier Y, Nakib S, Borderie D, Bouzinba-Segard H, Couraud PO, Bourdoulous S, Declèves X. Exposure of human cerebral microvascular endothelial cells hCMEC/D3 to laminar shear stress induces vascular protective responses. Fluids Barriers CNS 2022; 19:41. [PMID: 35658915 PMCID: PMC9164338 DOI: 10.1186/s12987-022-00344-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/23/2022] [Indexed: 01/01/2023] Open
Abstract
Endothelial cells (ECs) are constantly submitted in vivo to hemodynamical forces derived from the blood circulation, including shear stress (SS). ECs are able to detect SS and consequently adapt their phenotype, thus affecting many endothelial functions. If a plethora of shear stress-regulated molecular networks have been described in peripheral ECs, less is known about the molecular responses of microvascular brain ECs which constitute the blood-brain barrier (BBB). In this work, we investigated the response of human cerebral microvascular ECs to laminar physiological shear stress using the well characterized hCMEC/D3 cell line. Interestingly, we showed that hCMEC/D3 cells responded to shear stress by aligning perpendicularly to the flow direction, contrary to peripheral endothelial cells which aligned in the flow direction. Whole proteomic profiles were compared between hCMEC/D3 cells cultured either in static condition or under 5 or 10 dyn.cm-2 SS for 3 days. 3592 proteins were identified and expression levels were significantly affected for 3% of them upon both SS conditions. Pathway analyses were performed which revealed that most proteins overexpressed by SS refer to the antioxidant defense, probably mediated by activation of the NRF2 transcriptional factor. Regarding down-regulated proteins, most of them participate to the pro-inflammatory response, cell motility and proliferation. These findings confirm the induction of EC quiescence by laminar physiological SS and reveal a strong protective effect of SS on hCMEC/D3 cells, suggesting a similar effect on the BBB. Our results also showed that SS did not significantly increase expression levels nor did it affect the localization of junctional proteins and did not afect either the functional activity of several ABC transporters (P-glycoprotein and MRPs). This work provides new insights on the response of microvascular brain ECs to SS and on the importance of SS for optimizing in vitro BBB models.
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Affiliation(s)
- Nina Choublier
- INSERM, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, 75006, Paris, France.
| | - Meryam Taghi
- INSERM, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, 75006, Paris, France
| | - Marie-Claude Menet
- Institut de Chimie Physique, CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Morgane Le Gall
- 3P5 Proteom'IC Facility, Institut Cochin, INSERM, CNRS, Université de Paris, F-75014, Paris, France
| | - Johanna Bruce
- 3P5 Proteom'IC Facility, Institut Cochin, INSERM, CNRS, Université de Paris, F-75014, Paris, France
| | - Philippe Chafey
- 3P5 Proteom'IC Facility, Institut Cochin, INSERM, CNRS, Université de Paris, F-75014, Paris, France
| | - François Guillonneau
- 3P5 Proteom'IC Facility, Institut Cochin, INSERM, CNRS, Université de Paris, F-75014, Paris, France
| | | | | | | | - Samir Nakib
- Service de Biochimie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, 75014, Paris, France
| | - Didier Borderie
- Service de Biochimie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, 75014, Paris, France
| | - Haniaa Bouzinba-Segard
- CNRS, INSERM, Institut Cochin, Inserm, CNRS, Université Paris Cité, 75014, Paris, France
| | - Pierre-Olivier Couraud
- CNRS, INSERM, Institut Cochin, Inserm, CNRS, Université Paris Cité, 75014, Paris, France
| | - Sandrine Bourdoulous
- CNRS, INSERM, Institut Cochin, Inserm, CNRS, Université Paris Cité, 75014, Paris, France
| | - Xavier Declèves
- INSERM, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, 75006, Paris, France.
- Biologie du Médicament Et Toxicologie, AP-HP, Hôpital Cochin, 75014, Paris, France.
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42
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Sieksmeyer T, He S, Esparza-Mora MA, Jiang S, Petrašiūnaitė V, Kuropka B, Banasiak R, Julseth MJ, Weise C, Johnston PR, Rodríguez-Rojas A, McMahon DP. Eating in a losing cause: limited benefit of modified macronutrient consumption following infection in the oriental cockroach Blatta orientalis. BMC Ecol Evol 2022; 22:67. [PMID: 35585501 PMCID: PMC9118584 DOI: 10.1186/s12862-022-02007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Host-pathogen interactions can lead to dramatic changes in host feeding behaviour. One aspect of this includes self-medication, where infected individuals consume substances such as toxins or alter their macronutrient consumption to enhance immune competence. Another widely adopted animal response to infection is illness-induced anorexia, which is thought to assist host immunity directly or by limiting the nutritional resources available to pathogens. Here, we recorded macronutrient preferences of the global pest cockroach, Blatta orientalis to investigate how shifts in host macronutrient dietary preference and quantity of carbohydrate (C) and protein (P) interact with immunity following bacterial infection. RESULTS We find that B. orientalis avoids diets enriched for P under normal conditions, and that high P diets reduce cockroach survival in the long term. However, following bacterial challenge, cockroaches significantly reduced their overall nutrient intake, particularly of carbohydrates, and increased the relative ratio of protein (P:C) consumed. Surprisingly, these behavioural shifts had a limited effect on cockroach immunity and survival, with minor changes to immune protein abundance and antimicrobial activity between individuals placed on different diets, regardless of infection status. CONCLUSIONS We show that cockroach feeding behaviour can be modulated by a pathogen, resulting in an illness-induced anorexia-like feeding response and a shift from a C-enriched to a more P:C equal diet. However, our results also indicate that such responses do not provide significant immune protection in B. orientalis, suggesting that the host's dietary shift might also result from random rather than directed behaviour. The lack of an apparent benefit of the shift in feeding behaviour highlights a possible reduced importance of diet in immune regulation in these invasive animals, although further investigations employing pathogens with alternative infection strategies are warranted.
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Affiliation(s)
- Thorben Sieksmeyer
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195, Berlin, Germany.,Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205, Berlin, Germany.,Department of Biotechnology, German Institute of Food Technology (DIL e.V.), Prof.-von-Klitzing-Str. 7, 49610, Quakenbrück, Germany
| | - Shulin He
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195, Berlin, Germany.,Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205, Berlin, Germany
| | - M Alejandra Esparza-Mora
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195, Berlin, Germany.,Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205, Berlin, Germany
| | - Shixiong Jiang
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195, Berlin, Germany.,Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205, Berlin, Germany
| | - Vesta Petrašiūnaitė
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195, Berlin, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Ronald Banasiak
- Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205, Berlin, Germany
| | - Mara Jean Julseth
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195, Berlin, Germany
| | - Christoph Weise
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Paul R Johnston
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195, Berlin, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, 14195, Berlin, Germany
| | - Alexandro Rodríguez-Rojas
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195, Berlin, Germany.,Internal Medicine, Vetmeduni Vienna, Veterinaerplätz 1, 1210, Vienna, Austria
| | - Dino P McMahon
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195, Berlin, Germany. .,Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205, Berlin, Germany.
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The production of preconditioned freeze-dried Oenococcus oeni primes its metabolism to withstand environmental stresses encountered upon inoculation into wine. Int J Food Microbiol 2022; 369:109617. [DOI: 10.1016/j.ijfoodmicro.2022.109617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/14/2022] [Accepted: 03/06/2022] [Indexed: 11/20/2022]
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44
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Characterization of Microfragmented Adipose Tissue Architecture, Mesenchymal Stromal Cell Content and Release of Paracrine Mediators. J Clin Med 2022; 11:jcm11082231. [PMID: 35456324 PMCID: PMC9026471 DOI: 10.3390/jcm11082231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/01/2022] [Accepted: 04/13/2022] [Indexed: 12/15/2022] Open
Abstract
The use of microfragmented adipose tissue (µFAT) for the treatment of musculoskeletal disorders, especially osteoarthritis (OA), is gaining popularity, following positive results reported in recent case series and clinical trials. Although these outcomes were postulated to rely on paracrine signals, to date, a thorough fingerprint of released molecules is largely missing. The purpose of this study was to first characterize both structure and cell content of unprocessed lipoaspirate (LA) and µFAT, and further identify and frame the array of signaling factors in the context of OA disease, by means of high throughput qRT-PCR for extracellular-vesicle (EV) embedded miRNAs and proteomics for tissue and secreted factors. Cell count showed reduction of blood cells in µFAT, confirmed by histological and flow cytometry analyses, that also showed a conserved presence of structural, endothelial and stromal components and pericytes. In the secretome, 376 and 381 EV-miRNAs in LA and µFAT, respectively, were identified. In particular, most abundant and µFAT upregulated EV-miRNAs were mainly recapitulating those already reported as ASC-EVs-specific, with crucial roles in cartilage protection and M2 macrophage polarization, while only a scarce presence of those related to blood cells emerged. Furthermore, secretome proteomic analysis revealed reduction in µFAT of acute phase factors driving OA progression. Taken together, these results suggest that processing of LA into µFAT allows for removal of blood elements and maintenance of tissue structure and stromal cell populations, and possibly the increase of OA-protective molecular features. Thus, microfragmentation represents a safe and efficient method for the application of adipose tissue properties in the frame of musculoskeletal disorders.
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45
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Yang R, Ma J, Zhang S, Zheng Y, Wang L, Zhu D. mzMD: visualization-oriented MS data storage and retrieval. Bioinformatics 2022; 38:2333-2340. [PMID: 35171986 DOI: 10.1093/bioinformatics/btac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/23/2022] [Accepted: 02/14/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Drawing peaks in a data window of an MS dataset happens at all time in MS data visualization applications. This asks to retrieve from an MS dataset some selected peaks in a data window whose image in a display window reflects the visual feature of all peaks in the data window. If an algorithm for this purpose is asked to output high-quality solutions in real time, then the most fundamental dependence of it is on the storage format of the MS dataset. RESULTS We present mzMD, a new storage format of MS datasets and an algorithm to query this format of a storage system for a summary (a set of selected representative peaks) of a given data window. We propose a criterion Q-score to examine the quality of data window summaries. Experimental statistics on real MS datasets verified the high speed of mzMD in retrieving high-quality data window summaries. mzMD reported summaries of data windows whose Q-score outperforms those mzTree reported. The query speed of mzMD is the same as that of mzTree whereas its query speed stability is better than that of mzTree. AVAILABILITY AND IMPLEMENTATION The source code is freely available at https://github.com/yrm9837/mzMD-java. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Runmin Yang
- School of Computer Science and Technology, Shandong University, Qingdao 266237, China
| | - Jingjing Ma
- School of Computer Science and Technology, Shandong University, Qingdao 266237, China
| | - Shu Zhang
- School of Computer Science and Technology, Shandong University, Qingdao 266237, China
| | - Yu Zheng
- School of Computer Science and Technology, Shandong University, Qingdao 266237, China
| | - Lusheng Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.,City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Daming Zhu
- School of Computer Science and Technology, Shandong University, Qingdao 266237, China
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46
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Banerjee A, Pai MGJ, Singh A, Nissa MU, Srivastava S. Mass spectrometry and proteome analysis to identify SARS-CoV-2 protein from COVID-19 patient swab samples. STAR Protoc 2022; 3:101177. [PMID: 35233542 PMCID: PMC8808698 DOI: 10.1016/j.xpro.2022.101177] [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] [Indexed: 12/01/2022] Open
Abstract
With new emerging SARS-CoV-2 strains and their increased pathogenicity, diagnosis has become more challenging. Molecular diagnosis often involves the use of nasopharyngeal swabs and subsequent real-time PCR-based tests. Although this test is the gold standard, it has several limitations; therefore, more complementary assays are required. This protocol describes how to identify SARS-CoV-2 protein from patients' nasopharyngeal swab samples. We first introduce the approach of label-free quantitative proteomics. We then detail target verification by triple quadrupole mass spectrometry (MS)-based targeted proteomics. For complete details on the use and execution of this profile, please refer to Bankar et al. (2021). A protocol for identification of SARS-CoV-2 protein from patients' swab samples Sequential steps involved in proteomic sample preparation are elaborated Detailed procedure for MS-based targeted proteomic verification is presented A detailed presentation of workflow for label-free and targeted data analyses
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47
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Schessner JP, Voytik E, Bludau I. A practical guide to interpreting and generating bottom-up proteomics data visualizations. Proteomics 2022; 22:e2100103. [PMID: 35107884 DOI: 10.1002/pmic.202100103] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/22/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022]
Abstract
Mass-spectrometry based bottom-up proteomics is the main method to analyze proteomes comprehensively and the rapid evolution of instrumentation and data analysis has made the technology widely available. Data visualization is an integral part of the analysis process and it is crucial for the communication of results. This is a major challenge due to the immense complexity of MS data. In this review, we provide an overview of commonly used visualizations, starting with raw data of traditional and novel MS technologies, then basic peptide and protein level analyses, and finally visualization of highly complex datasets and networks. We specifically provide guidance on how to critically interpret and discuss the multitude of different proteomics data visualizations. Furthermore, we highlight Python-based libraries and other open science tools that can be applied for independent and transparent generation of customized visualizations. To further encourage programmatic data visualization, we provide the Python code used to generate all data Figures in this review on GitHub (https://github.com/MannLabs/ProteomicsVisualization). This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Julia Patricia Schessner
- Max-Planck-Institute of Biochemistry, Department of Proteomics and Signal Transduction, Planegg, Germany
| | - Eugenia Voytik
- Max-Planck-Institute of Biochemistry, Department of Proteomics and Signal Transduction, Planegg, Germany
| | - Isabell Bludau
- Max-Planck-Institute of Biochemistry, Department of Proteomics and Signal Transduction, Planegg, Germany
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Hajjaji N, Aboulouard S, Cardon T, Bertin D, Robin YM, Fournier I, Salzet M. Path to Clonal Theranostics in Luminal Breast Cancers. Front Oncol 2022; 11:802177. [PMID: 35096604 PMCID: PMC8793283 DOI: 10.3389/fonc.2021.802177] [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: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 12/18/2022] Open
Abstract
Integrating tumor heterogeneity in the drug discovery process is a key challenge to tackle breast cancer resistance. Identifying protein targets for functionally distinct tumor clones is particularly important to tailor therapy to the heterogeneous tumor subpopulations and achieve clonal theranostics. For this purpose, we performed an unsupervised, label-free, spatially resolved shotgun proteomics guided by MALDI mass spectrometry imaging (MSI) on 124 selected tumor clonal areas from early luminal breast cancers, tumor stroma, and breast cancer metastases. 2868 proteins were identified. The main protein classes found in the clonal proteome dataset were enzymes, cytoskeletal proteins, membrane-traffic, translational or scaffold proteins, or transporters. As a comparison, gene-specific transcriptional regulators, chromatin related proteins or transmembrane signal receptor were more abundant in the TCGA dataset. Moreover, 26 mutated proteins have been identified. Similarly, expanding the search to alternative proteins databases retrieved 126 alternative proteins in the clonal proteome dataset. Most of these alternative proteins were coded mainly from non-coding RNA. To fully understand the molecular information brought by our approach and its relevance to drug target discovery, the clonal proteomic dataset was further compared to the TCGA breast cancer database and two transcriptomic panels, BC360 (nanoString®) and CDx (Foundation One®). We retrieved 139 pathways in the clonal proteome dataset. Only 55% of these pathways were also present in the TCGA dataset, 68% in BC360 and 50% in CDx. Seven of these pathways have been suggested as candidate for drug targeting, 22 have been associated with breast cancer in experimental or clinical reports, the remaining 19 pathways have been understudied in breast cancer. Among the anticancer drugs, 35 drugs matched uniquely with the clonal proteome dataset, with only 7 of them already approved in breast cancer. The number of target and drug interactions with non-anticancer drugs (such as agents targeting the cardiovascular system, metabolism, the musculoskeletal or the nervous systems) was higher in the clonal proteome dataset (540 interactions) compared to TCGA (83 interactions), BC360 (419 interactions), or CDx (172 interactions). Many of the protein targets identified and drugs screened were clinically relevant to breast cancer and are in clinical trials. Thus, we described the non-redundant knowledge brought by this clone-tailored approach compared to TCGA or transcriptomic panels, the targetable proteins identified in the clonal proteome dataset, and the potential of this approach for drug discovery and repurposing through drug interactions with antineoplastic agents and non-anticancer drugs.
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Affiliation(s)
- Nawale Hajjaji
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Soulaimane Aboulouard
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Tristan Cardon
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Delphine Bertin
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Yves-Marie Robin
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Isabelle Fournier
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Institut universitaire de France, Paris, France
| | - Michel Salzet
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Institut universitaire de France, Paris, France
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Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria. Proc Natl Acad Sci U S A 2022; 119:2116022119. [PMID: 35074914 PMCID: PMC8795539 DOI: 10.1073/pnas.2116022119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 12/31/2022] Open
Abstract
Sulfoquinovose, a sulfosugar derivative of glucose, is produced by most photosynthetic organisms and contains up to half of all sulfur in the biosphere. Several pathways for its breakdown are known, though they provide access to only half of the carbon in sulfoquinovose and none of its sulfur. Here, we describe a fundamentally different pathway within the plant pathogen Agrobacterium tumefaciens that features oxidative desulfurization of sulfoquinovose to access all carbon and sulfur within the molecule. Biochemical and structural analyses of the pathway’s key proteins provided insights how the sulfosugar is recognized and degraded. Genes encoding this sulfoquinovose monooxygenase pathway are present in many plant pathogens and symbionts, alluding to a possible role for sulfoquinovose in plant host–bacteria interactions. Catabolism of sulfoquinovose (SQ; 6-deoxy-6-sulfoglucose), the ubiquitous sulfosugar produced by photosynthetic organisms, is an important component of the biogeochemical carbon and sulfur cycles. Here, we describe a pathway for SQ degradation that involves oxidative desulfurization to release sulfite and enable utilization of the entire carbon skeleton of the sugar to support the growth of the plant pathogen Agrobacterium tumefaciens. SQ or its glycoside sulfoquinovosyl glycerol are imported into the cell by an ATP-binding cassette transporter system with an associated SQ binding protein. A sulfoquinovosidase hydrolyzes the SQ glycoside and the liberated SQ is acted on by a flavin mononucleotide-dependent sulfoquinovose monooxygenase, in concert with an NADH-dependent flavin reductase, to release sulfite and 6-oxo-glucose. An NAD(P)H-dependent oxidoreductase reduces the 6-oxo-glucose to glucose, enabling entry into primary metabolic pathways. Structural and biochemical studies provide detailed insights into the recognition of key metabolites by proteins in this pathway. Bioinformatic analyses reveal that the sulfoquinovose monooxygenase pathway is distributed across Alpha- and Betaproteobacteria and is especially prevalent within the Rhizobiales order. This strategy for SQ catabolism is distinct from previously described pathways because it enables the complete utilization of all carbons within SQ by a single organism with concomitant production of inorganic sulfite.
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Morimoto K, Stegmann M, Kaschani F, Mohammed S, van der Hoorn RAL. Cysteine Reactivity Profiling to Unveil Redox Regulation in Phytopathogens. Methods Mol Biol 2022; 2447:105-117. [PMID: 35583776 DOI: 10.1007/978-1-0716-2079-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Reactivity-based chemical proteomics is a powerful technology based on the use of tagged chemicals that covalently react with surface-exposed residues on proteins in native proteomes. Reactivity profiling involves the purification, identification, and quantification of labeled peptides by LC-MS/MS. Here, we have detailed a protocol for reactivity profiling of Cys residues using iodoacetamide probes, displaying >1000 reactive Cys residues in the proteome of phytopathogen Pseudomonas syringae pv. tomato DC3000 (PtoDC3000). Comparative reactivity profiling of PtoDC3000 treated with or without hydrogen peroxide (H2O2) identified ~200 H2O2-sensitive Cys residues in antioxidant enzymes, metabolic enzymes, and transcription regulators. Interestingly, half of these H2O2-sensitive Cys residues are more reactive in response to H2O2 and several proteins have multiple Cys residues with opposite reactivities in response to H2O2 exposure.
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Affiliation(s)
- Kyoko Morimoto
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Monika Stegmann
- Advanced Proteomics Centre, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Farnusch Kaschani
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Shabaz Mohammed
- Department of Chemistry, Chemistry Research Laboratory, Oxford, UK
- Department of Biochemistry, New Biochemistry Building, Oxford, UK
- The Rosalind Franklin Institute, Oxfordshire, UK
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