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Serum extracellular vesicles contain SPARC and LRG1 as biomarkers of colon cancer and differ by tumour primary location. EBioMedicine 2019; 50:211-223. [PMID: 31753726 PMCID: PMC6921233 DOI: 10.1016/j.ebiom.2019.11.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Recently, the distinction between left- and right-sided colon cancer (LCC and RCC) has been brought into focus. RCC is associated with an inferior overall survival and progression-free survival. We aimed to perform a detailed analysis of the diversity of extracellular vesicles (EV) between LCC and RCC using quantitative proteomics and to identify for new diagnostic and prognostic biomarkers. METHODS We isolated EVs from patients with LCC, RCC and healthy volunteers, and treated colorectal cancer cell line with serum-derived EVs. We then performed a quantitative proteomics analysis of the serum-derived EVs and cell line treated with EVs. Proteomic data are available via ProteomeXchange with the identifiers PXD012283 and PXD012304. In addition, we assessed the performance of EV SPARC and LRG1 as diagnosis and prognosis biomarkers in colon cancer. FINDINGS The expression profile of the serum EV proteome in patients with RCC was different from that of patients with LCC. Serum-derived EVs in RCC promoted cellular mobility more significantly than EVs derived from LCC. EV SPARC and LRG1 expression levels demonstrated area under the receiver-operating characteristic curve values of 0.95 and 0.93 for discriminating patients with colon cancer from healthy controls. Moreover, the expression levels of SPARC and LRG1 correlated with tumour sidedness and were predictive of tumour recurrence. INTERPRETATION We identified differences in EV protein profiles between LCC and RCC. Serum-derived EVs of RCC may promote metastasis via upregulation of extracellular matrix (ECM)-related proteins, especially SPARC and LRG1, which may serve as diagnosis and prognosis biomarkers in colon cancer.
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452
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Mancio J, Barros AS, Conceicao G, Pessoa-Amorim G, Santa C, Bartosch C, Ferreira W, Carvalho M, Ferreira N, Vouga L, Miranda IM, Vitorino R, Manadas B, Falcao-Pires I, Ribeiro VG, Leite-Moreira A, Bettencourt N. Epicardial adipose tissue volume and annexin A2/fetuin-A signalling are linked to coronary calcification in advanced coronary artery disease: Computed tomography and proteomic biomarkers from the EPICHEART study. Atherosclerosis 2019; 292:75-83. [PMID: 31783201 DOI: 10.1016/j.atherosclerosis.2019.11.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 10/27/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS The role of epicardial adipose tissue (EAT) in the pathophysiology of late stage-coronary artery disease (CAD) has not been investigated. We explored the association of EAT volume and its proteome with advanced coronary atherosclerosis. METHODS The EPICHEART Study prospectively enrolled 574 severe aortic stenosis patients referred to cardiac surgery. Before surgery, EAT volume was quantified by computed tomography (CT). During surgery, epicardial, mediastinal (MAT) and subcutaneous (SAT) adipose tissue samples were collected to explore fat phenotype by analyzing the proteomic profile using SWATH-mass spectrometry; pericardial fluid and peripheral venous blood were also collected. CAD presence was defined as coronary artery stenosis ≥50% in invasive angiography and by CT-derived Agatston coronary calcium score (CCS). RESULTS EAT volume adjusted for body fat was associated with higher CCS, but not with the presence of coronary stenosis. In comparison with mediastinal and subcutaneous fat depots, EAT exhibited a pro-calcifying proteomic profile in patients with CAD characterized by upregulation of annexin-A2 and downregulation of fetuin-A; annexin-A2 protein levels in EAT samples were also positively correlated with CCS. We confirmed that the annexin-A2 gene was overexpressed in EAT samples of CAD patients and positively correlated with CCS. Fetuin-A gene was not detected in EAT samples, but systemic fetuin-A was higher in CAD than in non-CAD patients, suggesting that fetuin-A was locally downregulated. CONCLUSIONS In an elderly cohort of stable patients, CCS was associated with EAT volume and annexin-A2/fetuin-A signaling, suggesting that EAT might orchestrate pro-calcifying conditions in the late phases of CAD.
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Affiliation(s)
- Jennifer Mancio
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal; Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal.
| | - Antonio S Barros
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Gloria Conceicao
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Guilherme Pessoa-Amorim
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Catia Santa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; III: Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Portugal
| | - Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Wilson Ferreira
- Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Monica Carvalho
- Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Nuno Ferreira
- Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Luis Vouga
- Department of Cardiothoracic Surgery, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Isabel M Miranda
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Rui Vitorino
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ines Falcao-Pires
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Vasco Gama Ribeiro
- Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Adelino Leite-Moreira
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal; Department of Cardiothoracic Surgery, Centro Hospitalar de Sao Joao, Portugal
| | - Nuno Bettencourt
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
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453
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Proteomic profiling of the thrombin-activated canine platelet secretome (CAPS). PLoS One 2019; 14:e0224891. [PMID: 31721811 PMCID: PMC6853320 DOI: 10.1371/journal.pone.0224891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/23/2019] [Indexed: 11/27/2022] Open
Abstract
Domestic dogs share the same environment as humans, and they represent a valuable animal model to study naturally-occurring human disease. Platelet proteomics holds promise for the discovery of biomarkers that capture the contribution of platelets to the pathophysiology of many disease states, however, canine platelet proteomic studies are lacking. Our study objectives were to establish a protocol for proteomic identification and quantification of the thrombin-activated canine platelet secretome (CAPS), and to compare the CAPS proteins to human and murine platelet proteomic data. Washed platelets were isolated from healthy dogs, and stimulated with saline (control) or gamma-thrombin (releasate). Proteins were separated by SDS-page, trypsin-digested and analyzed by liquid chromatography and tandem mass spectrometry (MS). CAPS proteins were defined as those with a MS1-abundance ratio of two or more for releasate vs. unstimulated saline control. A total of 1,918 proteins were identified, with 908 proteins common to all dogs and 693 characterized as CAPS proteins. CAPS proteins were similar to human and murine platelet secretomes and were highly represented in hemostatic pathways. Differences unique to CAPS included replacement of platelet factor 4 with other cleavage products of platelet basic protein (e.g. interleukin-8), novel proteins (e.g. C-C motif chemokine 14), and proteins in relatively high (e.g. protease nexin-1) or low (e.g. von Willebrand factor) abundance. This study establishes the first in-depth platelet releasate proteome from healthy dogs with a reference database of 693 CAPS proteins. Similarities between CAPS and the human secretome confirm the utility of dogs as translational models of human disease, but we also identify differences unique to canine platelets. Our findings provide a resource for further investigations into disease-related CAPS profiles, and for comparative pathway analyses of platelet activation among species.
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454
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Wang X, Williams D, Müller I, Lemieux M, Dukart R, Maia IBL, Wang H, Woerman AL, Schmitt-Ulms G. Tau interactome analyses in CRISPR-Cas9 engineered neuronal cells reveal ATPase-dependent binding of wild-type but not P301L Tau to non-muscle myosins. Sci Rep 2019; 9:16238. [PMID: 31700063 PMCID: PMC6838314 DOI: 10.1038/s41598-019-52543-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 10/03/2019] [Indexed: 11/09/2022] Open
Abstract
Protein interactions of Tau are of interest in efforts to decipher pathogenesis in Alzheimer's disease, a subset of frontotemporal dementias, and other tauopathies. We CRISPR-Cas9 edited two human cell lines to generate broadly adaptable models for neurodegeneration research. We applied the system to inducibly express balanced levels of 3-repeat and 4-repeat wild-type or P301L mutant Tau. Following 12-h induction, quantitative mass spectrometry revealed the Parkinson's disease-causing protein DJ-1 and non-muscle myosins as Tau interactors whose binding to Tau was profoundly influenced by the presence or absence of the P301L mutation. The presence of wild-type Tau stabilized non-muscle myosins at higher steady-state levels. Strikingly, in human differentiated co-cultures of neuronal and glial cells, the preferential interaction of non-muscle myosins to wild-type Tau depended on myosin ATPase activity. Consistently, transgenic P301L Tau mice exhibited reduced phosphorylation of regulatory myosin light chains known to activate this ATPase. The direct link of Tau to non-muscle myosins corroborates independently proposed roles of Tau in maintaining dendritic spines and mitochondrial fission biology, two subcellular niches affected early in tauopathies.
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Affiliation(s)
- Xinzhu Wang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, M5T 2S8, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Ontario, M5S 1A8, Canada
| | - Declan Williams
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, M5T 2S8, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Ontario, M5S 1A8, Canada
| | - Iris Müller
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, M5T 2S8, Canada
| | - Mackenzie Lemieux
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, M5T 2S8, Canada
| | - Ramona Dukart
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Ontario, M5S 1A8, Canada
| | - Isabella B L Maia
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, M5T 2S8, Canada
| | - Hansen Wang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, M5T 2S8, Canada
| | - Amanda L Woerman
- Department of Neurology, University of California San Francisco, California, 94158, USA
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, M5T 2S8, Canada. .,Department of Laboratory Medicine & Pathobiology, University of Toronto, Ontario, M5S 1A8, Canada.
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455
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Schmitt K, Valerius O. yRACK1/Asc1 proxiOMICs-Towards Illuminating Ships Passing in the Night. Cells 2019; 8:cells8111384. [PMID: 31689955 PMCID: PMC6912217 DOI: 10.3390/cells8111384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 02/01/2023] Open
Abstract
Diverse signals and stress factors regulate the activity and homeostasis of ribosomes in all cells. The Saccharomyces cerevisiae protein Asc1/yRACK1 occupies an exposed site at the head region of the 40S ribosomal subunit (hr40S) and represents a central hub for signaling pathways. Asc1 strongly affects protein phosphorylation and is involved in quality control pathways induced by translation elongation arrest. Therefore, it is important to understand the dynamics of protein formations in the Asc1 microenvironment at the hr40S. We made use of the in vivo protein-proximity labeling technique Biotin IDentification (BioID). Unbiased proxiOMICs from two adjacent perspectives identified nucleocytoplasmic shuttling mRNA-binding proteins, the deubiquitinase complex Ubp3-Bre5, as well as the ubiquitin E3 ligase Hel2 as neighbors of Asc1. We observed Asc1-dependency of hr40S localization of mRNA-binding proteins and the Ubp3 co-factor Bre5. Hel2 and Ubp3-Bre5 are described to balance the mono-ubiquitination of Rps3 (uS3) during ribosome quality control. Here, we show that the absence of Asc1 resulted in massive exposure and accessibility of the C-terminal tail of its ribosomal neighbor Rps3 (uS3). Asc1 and some of its direct neighbors together might form a ribosomal decision tree that is tightly connected to close-by signaling modules.
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Affiliation(s)
- Kerstin Schmitt
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077 Göttingen, Germany.
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077 Göttingen, Germany.
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456
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Loss of FBXO9 Enhances Proteasome Activity and Promotes Aggressiveness in Acute Myeloid Leukemia. Cancers (Basel) 2019; 11:cancers11111717. [PMID: 31684170 PMCID: PMC6895989 DOI: 10.3390/cancers11111717] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 12/11/2022] Open
Abstract
The hematopoietic system is maintained throughout life by stem cells that are capable of differentiating into all hematopoietic lineages. An intimate balance between self-renewal, differentiation, and quiescence is required to maintain hematopoiesis and disruption of this balance can result in malignant transformation. FBXO9, the substrate recognition component from the SCF E3 ubiquitin ligase family, is downregulated in patients with acute myeloid leukemia (AML) compared to healthy bone marrow, and this downregulation is particularly evident in patients with inv(16) AML. To study FBXO9 in malignant hematopoiesis, we generated a conditional knockout mouse model using a novel CRISPR/Cas9 strategy. Deletion of Fbxo9 in the murine hematopoietic system showed no adverse effects on stem and progenitor cell function but in AML lead to markedly accelerated and aggressive leukemia development in mice with inv(16). Not only did Fbxo9 play a role in leukemia initiation but it also functioned to maintain AML activity and promote disease progression. Quantitative mass spectrometry from primary tumors reveals tumors lacking Fbxo9 highly express proteins associated with metastasis and invasion as well as components of the ubiquitin proteasome system. We confirmed that the loss of FBXO9 leads to increased proteasome activity and tumors cells were more sensitive to in vitro proteasome inhibition with bortezomib, suggesting that FBXO9 expression may predict patients’ response to bortezomib.
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457
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Anjos L, Pinto PIS, Tsironi T, Dimopoulos G, Santos S, Santa C, Manadas B, Canario A, Taoukis P, Power DM. Experimental data from flesh quality assessment and shelf life monitoring of high pressure processed European sea bass ( Dicentrarchus labrax) fillets. Data Brief 2019; 26:104451. [PMID: 31667223 PMCID: PMC6811897 DOI: 10.1016/j.dib.2019.104451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/07/2019] [Accepted: 08/21/2019] [Indexed: 11/27/2022] Open
Abstract
Fresh fish are highly perishable food products and their short shelf-life limits their commercial exploitation and leads to waste, which has a negative impact on aquaculture sustainability. New non-thermal food processing methods, such as high pressure (HP) processing, prolong shelf-life while assuring high food quality. The effect of HP processing (600MPa, 25 °C, 5min) on European sea bass (Dicentrarchus labrax) fillet quality and shelf life was investigated. The data presented comprises microbiome and proteome profiles of control and HP-processed sea bass fillets from 1 to 67 days of isothermal storage at 2 °C. Bacterial diversity was analysed by Illumina high-throughput sequencing of the 16S rRNA gene in pooled DNAs from control or HP-processed fillets after 1, 11 or 67 days and the raw reads were deposited in the NCBI-SRA database with accession number PRJNA517618. Yeast and fungi diversity were analysed by high-throughput sequencing of the internal transcribed spacer (ITS) region for control and HP-processed fillets at the end of storage (11 or 67 days, respectively) and have the SRA accession number PRJNA517779. Quantitative label-free proteomics profiles were analysed by SWATH-MS (Sequential Windowed data independent Acquisition of the Total High-resolution-Mass Spectra) in myofibrillar or sarcoplasmic enriched protein extracts pooled for control or HP-processed fillets after 1, 11 and 67 days of storage. Proteome data was deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD012737. These data support the findings reported in the associated manuscript “High pressure processing of European sea bass (Dicentrarchus labrax) fillets and tools for flesh quality and shelf life monitoring”, Tsironi et al., 2019, JFE 262:83–91, doi.org/10.1016/j.jfoodeng.2019.05.010.
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Affiliation(s)
- Liliana Anjos
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve, Faro, Portugal
| | - Patricia I S Pinto
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve, Faro, Portugal
| | - Theofania Tsironi
- Laboratory of Food Chemistry and Technology, School of Chemical Engineering, National Technical University of Athens (NTUA), Greece
| | - George Dimopoulos
- Laboratory of Food Chemistry and Technology, School of Chemical Engineering, National Technical University of Athens (NTUA), Greece
| | - Soraia Santos
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve, Faro, Portugal
| | - Cátia Santa
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Portugal
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Portugal
| | - Adelino Canario
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve, Faro, Portugal
| | - Petros Taoukis
- Laboratory of Food Chemistry and Technology, School of Chemical Engineering, National Technical University of Athens (NTUA), Greece
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve, Faro, Portugal
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458
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Pino L, Lin A, Bittremieux W. 2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample. J Proteome Res 2019; 18:3936-3943. [PMID: 31556620 PMCID: PMC6824964 DOI: 10.1021/acs.jproteome.9b00384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For the 2018 YPIC Challenge, contestants were invited to try to decipher two unknown English questions encoded by a synthetic protein expressed in Escherichia coli. In addition to deciphering the sentence, contestants were asked to determine the three-dimensional structure and detect any post-translation modifications left by the host organism. We present our experimental and computational strategy to characterize this sample by identifying the unknown protein sequence and detecting the presence of post-translational modifications. The sample was acquired with dynamic exclusion disabled to increase the signal-to-noise ratio of the measured molecules, after which spectral clustering was used to generate high-quality consensus spectra. De novo spectrum identification was used to determine the synthetic protein sequence, and any post-translational modifications introduced by E. coli on the synthetic protein were analyzed via spectral networking. This workflow resulted in a de novo sequence coverage of 70%, on par with sequence database searching performance. Additionally, the spectral networking analysis indicated that no systematic modifications were introduced on the synthetic protein by E. coli. The strategy presented here can be directly used to analyze samples for which no protein sequence information is available or when the identity of the sample is unknown. All software and code to perform the bioinformatics analysis is available as open source, and self-contained Jupyter notebooks are provided to fully recreate the analysis.
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Affiliation(s)
- Lindsay Pino
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Andy Lin
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Wout Bittremieux
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
- Department of Mathematics and Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Biomedical Informatics Network Antwerpen (biomina), 2020 Antwerp, Belgium
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459
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Weng SSH, Demir F, Ergin EK, Dirnberger S, Uzozie A, Tuscher D, Nierves L, Tsui J, Huesgen PF, Lange PF. Sensitive Determination of Proteolytic Proteoforms in Limited Microscale Proteome Samples. Mol Cell Proteomics 2019; 18:2335-2347. [PMID: 31471496 PMCID: PMC6823850 DOI: 10.1074/mcp.tir119.001560] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/09/2019] [Indexed: 12/15/2022] Open
Abstract
Protein N termini unambiguously identify truncated, alternatively translated or modified proteoforms with distinct functions and reveal perturbations in disease. Selective enrichment of N-terminal peptides is necessary to achieve proteome-wide coverage for unbiased identification of site-specific regulatory proteolytic processing and protease substrates. However, many proteolytic processes are strictly confined in time and space and therefore can only be analyzed in minute samples that provide insufficient starting material for current enrichment protocols. Here we present High-efficiency Undecanal-based N Termini EnRichment (HUNTER), a robust, sensitive and scalable method for the analysis of previously inaccessible microscale samples. HUNTER achieved identification of >1000 N termini from as little as 2 μg raw HeLa cell lysate. Broad applicability is demonstrated by the first N-terminome analysis of sorted human primary immune cells and enriched mitochondrial fractions from pediatric cancer patients, as well as protease substrate identification from individual Arabidopsis thaliana wild type and Vacuolar Processing Enzyme-deficient mutant seedlings. We further implemented the workflow on a liquid handling system and demonstrate the feasibility of clinical degradomics by automated processing of liquid biopsies from pediatric cancer patients.
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Affiliation(s)
- Samuel S H Weng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Enes K Ergin
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Sabrina Dirnberger
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Anuli Uzozie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Domenic Tuscher
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Lorenz Nierves
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Janice Tsui
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany.
| | - Philipp F Lange
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada.
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460
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Katsogiannou M, Boyer JB, Valdeolivas A, Remy E, Calzone L, Audebert S, Rocchi P, Camoin L, Baudot A. Integrative proteomic and phosphoproteomic profiling of prostate cell lines. PLoS One 2019; 14:e0224148. [PMID: 31675377 PMCID: PMC6824562 DOI: 10.1371/journal.pone.0224148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/06/2019] [Indexed: 12/15/2022] Open
Abstract
Background Prostate cancer is a major public health issue, mainly because patients relapse after androgen deprivation therapy. Proteomic strategies, aiming to reflect the functional activity of cells, are nowadays among the leading approaches to tackle the challenges not only of better diagnosis, but also of unraveling mechanistic details related to disease etiology and progression. Methods We conducted here a large SILAC-based Mass Spectrometry experiment to map the proteomes and phosphoproteomes of four widely used prostate cell lines, namely PNT1A, LNCaP, DU145 and PC3, representative of different cancerous and hormonal status. Results We identified more than 3000 proteins and phosphosites, from which we quantified more than 1000 proteins and 500 phosphosites after stringent filtering. Extensive exploration of this proteomics and phosphoproteomics dataset allowed characterizing housekeeping as well as cell-line specific proteins, phosphosites and functional features of each cell line. In addition, by comparing the sensitive and resistant cell lines, we identified protein and phosphosites differentially expressed in the resistance context. Further data integration in a molecular network highlighted the differentially expressed pathways, in particular migration and invasion, RNA splicing, DNA damage repair response and transcription regulation. Conclusions Overall, this study proposes a valuable resource toward the characterization of proteome and phosphoproteome of four widely used prostate cell lines and reveals candidates to be involved in prostate cancer progression for further experimental validation.
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Affiliation(s)
- Maria Katsogiannou
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
- Obstetrics and Gynecology department, Hôpital Saint Joseph, Marseille, France
| | - Jean-Baptiste Boyer
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Alberto Valdeolivas
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- ProGeLife, Marseille, France
| | - Elisabeth Remy
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - Laurence Calzone
- Mines Paris Tech, Institut Curie, PSL Research University, Paris, France
| | - Stéphane Audebert
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Palma Rocchi
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
- * E-mail: (PR); (LC); (AB)
| | - Luc Camoin
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
- * E-mail: (PR); (LC); (AB)
| | - Anaïs Baudot
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- * E-mail: (PR); (LC); (AB)
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461
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Metaxas A, Thygesen C, Kempf SJ, Anzalone M, Vaitheeswaran R, Petersen S, Landau AM, Audrain H, Teeling JL, Darvesh S, Brooks DJ, Larsen MR, Finsen B. Ageing and amyloidosis underlie the molecular and pathological alterations of tau in a mouse model of familial Alzheimer's disease. Sci Rep 2019; 9:15758. [PMID: 31673052 PMCID: PMC6823454 DOI: 10.1038/s41598-019-52357-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 10/13/2019] [Indexed: 02/07/2023] Open
Abstract
Despite compelling evidence that the accumulation of amyloid-beta (Aβ) promotes neocortical MAPT (tau) aggregation in familial and idiopathic Alzheimer's disease (AD), murine models of cerebral amyloidosis are not considered to develop tau-associated pathology. In the present study, we show that tau can accumulate spontaneously in aged transgenic APPswe/PS1ΔE9 mice. Tau pathology is abundant around Aβ deposits, and further characterized by accumulation of Gallyas and thioflavin-S-positive inclusions, which were detected in the APPswe/PS1ΔE9 brain at 18 months of age. Age-dependent increases in argyrophilia correlated positively with binding levels of the paired helical filament (PHF) tracer [18F]Flortaucipir, in all brain areas examined. Sarkosyl-insoluble PHFs were visualized by electron microscopy. Quantitative proteomics identified sequences of hyperphosphorylated and three-repeat tau in transgenic mice, along with signs of RNA missplicing, ribosomal dysregulation and disturbed energy metabolism. Tissue from the frontal gyrus of human subjects was used to validate these findings, revealing primarily quantitative differences between the tau pathology observed in AD patient vs. transgenic mouse tissue. As physiological levels of endogenous, 'wild-type' tau aggregate secondarily to Aβ in APPswe/PS1ΔE9 mice, this study suggests that amyloidosis is both necessary and sufficient to drive tauopathy in experimental models of familial AD.
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Affiliation(s)
- Athanasios Metaxas
- Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark.
| | - Camilla Thygesen
- Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark.,Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Stefan J Kempf
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Marco Anzalone
- Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark
| | | | - Sussanne Petersen
- Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark
| | - Anne M Landau
- Department of Nuclear Medicine and PET-Centre, Aarhus University, Aarhus, Denmark.,Translational Neuropsychiatry Unit, Aarhus University, Aarhus, Denmark
| | - Hélène Audrain
- Department of Nuclear Medicine and PET-Centre, Aarhus University, Aarhus, Denmark
| | - Jessica L Teeling
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Sultan Darvesh
- Department of Medical Neuroscience, Dalhousie University, Halifax, NS, Canada.,Department of Medicine (Neurology and Geriatric Medicine), Dalhousie University, Halifax, NS, Canada
| | - David J Brooks
- Department of Nuclear Medicine and PET-Centre, Aarhus University, Aarhus, Denmark.,Division of Neuroscience, Faculty of Medical Science, University of Newcastle upon Tyne, Newcastle upon Tyne, UK
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Bente Finsen
- Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark
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462
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Deutsch EW, Lane L, Overall CM, Bandeira N, Baker MS, Pineau C, Moritz RL, Corrales F, Orchard S, Van Eyk JE, Paik YK, Weintraub ST, Vandenbrouck Y, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. J Proteome Res 2019; 18:4108-4116. [PMID: 31599596 DOI: 10.1021/acs.jproteome.9b00542] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Human Proteome Organization's (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guidelines address several major and minor identified gaps. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems, and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well, and this timely update to version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ∼20 000 human proteins encoded by the human genome.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva , CMU, Michel Servet 1 , 1211 Geneva 4 , Switzerland
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry , The University of British Columbia , Vancouver , BC V6T 1Z4 , Canada
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Science , Macquarie University , Macquarie Park , NSW 2109 , Australia
| | - Charles Pineau
- Univ. Rennes , Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085 , F-35042 Rennes cedex , France
| | - Robert L Moritz
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología , Spanish Research Council , ProteoRed-.ISCIII , Madrid 117 , Spain
| | - Sandra Orchard
- European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus , Hinxton , Cambridge CB10 1SD , U.K
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Department of Medicine , Cedars Sinai Medical Center , Los Angeles , California 90048 , United States
| | - Young-Ki Paik
- Yonsei Proteome Research Center , Yonsei University , 50 Yonsei-ro , Sudaemoon-ku , Seoul 03720 , Korea
| | - Susan T Weintraub
- The University of Texas Health Science Center at San Antonio , San Antonio , Texas 78229 , United States
| | - Yves Vandenbrouck
- Univ. Grenoble Alpes , CEA, INSERM, IRIG-BGE, U1038 , F-38000 Grenoble , France
| | - Gilbert S Omenn
- Institute for Systems Biology , Seattle , Washington 98109 , United States.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health , University of Michigan , Ann Arbor , Michigan 48109-2218 , United States
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463
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Ignjatovic V, Geyer PE, Palaniappan KK, Chaaban JE, Omenn GS, Baker MS, Deutsch EW, Schwenk JM. Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data. J Proteome Res 2019; 18:4085-4097. [PMID: 31573204 DOI: 10.1021/acs.jproteome.9b00503] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The proteomic analysis of human blood and blood-derived products (e.g., plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing proteomics assays with plasma is challenging. Plasma proteomics has regained interest due to recent technological advances, but challenges imposed by both complications inherent to studying human biology (e.g., interindividual variability) and analysis of biospecimens (e.g., sample variability), as well as technological limitations remain. As part of the Human Proteome Project (HPP), the Human Plasma Proteome Project (HPPP) brings together key aspects of the plasma proteomics pipeline. Here, we provide considerations and recommendations concerning study design, plasma collection, quality metrics, plasma processing workflows, mass spectrometry (MS) data acquisition, data processing, and bioinformatic analysis. With exciting opportunities in studying human health and disease though this plasma proteomics pipeline, a more informed analysis of human plasma will accelerate interest while enhancing possibilities for the incorporation of proteomics-scaled assays into clinical practice.
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Affiliation(s)
- Vera Ignjatovic
- Haematology Research , Murdoch Children's Research Institute , Parkville , VIC 3052 , Australia.,Department of Paediatrics , The University of Melbourne , Parkville , VIC 3052 , Australia
| | - Philipp E Geyer
- NNF Center for Protein Research, Faculty of Health Sciences , University of Copenhagen , 2200 Copenhagen , Denmark.,Department of Proteomics and Signal Transduction , Max Planck Institute of Biochemistry , 82152 Martinsried , Germany
| | - Krishnan K Palaniappan
- Freenome , 259 East Grand Avenue , South San Francisco , California 94080 , United States
| | - Jessica E Chaaban
- Haematology Research , Murdoch Children's Research Institute , Parkville , VIC 3052 , Australia
| | - Gilbert S Omenn
- Departments of Computational Medicine & Bioinformatics, Human Genetics, and Internal Medicine and School of Public Health , University of Michigan , 100 Washtenaw Avenue , Ann Arbor , Michigan 48109-2218 , United States
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , 75 Talavera Road , North Ryde , NSW 2109 , Australia
| | - Eric W Deutsch
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab , KTH Royal Institute of Technology , 171 65 Stockholm , Sweden
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464
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Bittremieux W, Laukens K, Noble WS. Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units. J Proteome Res 2019; 18:3792-3799. [PMID: 31448616 PMCID: PMC6886738 DOI: 10.1021/acs.jproteome.9b00291] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Open modification searching (OMS) is a powerful search strategy to identify peptides with any type of modification. OMS works by using a very wide precursor mass window to allow modified spectra to match against their unmodified variants, after which the modification types can be inferred from the corresponding precursor mass differences. A disadvantage of this strategy, however, is the large computational cost, because each query spectrum has to be compared against a multitude of candidate peptides. We have previously introduced the ANN-SoLo tool for fast and accurate open spectral library searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up OMS by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. Here we demonstrate how this candidate selection procedure can be further optimized using graphics processing units. Additionally, we introduce a feature hashing scheme to convert high-resolution spectra to low-dimensional vectors. On the basis of these algorithmic advances, along with low-level code optimizations, the new version of ANN-SoLo is up to an order of magnitude faster than its initial version. This makes it possible to efficiently perform open searches on a large scale to gain a deeper understanding about the protein modification landscape. We demonstrate the computational efficiency and identification performance of ANN-SoLo based on a large data set of the draft human proteome. ANN-SoLo is implemented in Python and C++. It is freely available under the Apache 2.0 license at https://github.com/bittremieux/ANN-SoLo .
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Affiliation(s)
- Wout Bittremieux
- Department of Mathematics and Computer Science , University of Antwerp , 2020 Antwerp , Belgium
- Biomedical Informatics Network Antwerpen (biomina) , 2020 Antwerp , Belgium
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Kris Laukens
- Department of Mathematics and Computer Science , University of Antwerp , 2020 Antwerp , Belgium
- Biomedical Informatics Network Antwerpen (biomina) , 2020 Antwerp , Belgium
| | - William Stafford Noble
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
- Department of Computer Science and Engineering , University of Washington , Seattle , Washington 98195 , United States
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465
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LeSassier DS, Schulte KQ, Manley TE, Smith AR, Powals ML, Albright NC, Ludolph BC, Weber KL, Woerner AE, Gardner MW, Hewitt FC. Artificial fingerprints for cross-comparison of forensic DNA and protein recovery methods. PLoS One 2019; 14:e0223170. [PMID: 31581206 PMCID: PMC6776342 DOI: 10.1371/journal.pone.0223170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/20/2019] [Indexed: 11/18/2022] Open
Abstract
Quantitative genomic and proteomic evaluation of human latent fingerprint depositions represents a challenge within the forensic field, due to the high variability in the amount of DNA and protein initially deposited. To better assess recovery techniques for touch depositions, we present a method to produce simple and customizable artificial fingerprints. These artificial fingerprint samples include the primary components of a typical latent fingerprint, specifically sebaceous fluid, eccrine perspiration, extracellular DNA, and proteinaceous epidermal skin material (i.e., shed skin cells). A commercially available emulsion of sebaceous and eccrine perspiration material provides a chemically-relevant suspension solution for fingerprint deposition, simplifying artificial fingerprint production. Extracted human genomic DNA is added to accurately mimic the extracellular DNA content of a typical latent print and comparable DNA yields are recovered from the artificial prints relative to human prints across surface types. Capitalizing on recent advancements in the use of protein sequence identification for human forensic analysis, these samples also contain a representative quantity of protein, originating from epidermal skin cells collected from the fingers and palms of volunteers. Proteomic sequencing by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis indicates a high level of protein overlap between artificial and latent prints. Data are available via ProteomeXchange with identifier PXD015445. By including known quantities of DNA and protein into each artificial print, this method enables total DNA and protein recovery to be quantitatively assessed across different sample collection and extraction methods to better evaluate extraction efficiency. Collectively, these artificial fingerprint samples are simple to make, highly versatile and customizable, and accurately represent the biochemical composition and biological signatures of human fingerprints.
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Affiliation(s)
| | | | - Tara E. Manley
- Signature Science, LLC, Austin, Texas, United States of America
| | - Alan R. Smith
- Signature Science, LLC, Austin, Texas, United States of America
| | - Megan L. Powals
- Signature Science, LLC, Austin, Texas, United States of America
| | | | | | | | - August E. Woerner
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
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466
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Pillar array columns for peptide separations in nanoscale reversed-phase chromatography. J Chromatogr A 2019; 1603:426-432. [DOI: 10.1016/j.chroma.2019.06.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 06/13/2019] [Accepted: 06/30/2019] [Indexed: 12/21/2022]
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467
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Cadmium tolerance pathway in Anopheles gambiae senso stricto. Acta Trop 2019; 198:105033. [PMID: 31121147 DOI: 10.1016/j.actatropica.2019.05.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/16/2019] [Accepted: 05/18/2019] [Indexed: 02/05/2023]
Abstract
Cadmium is one of the widely used heavy metals (HM) in commercial and industrial products and contributes to environmental contamination in an urban setting. In our previous studies, we established that An. gambiae sensu stricto, a vector of malaria, had adapted to HM pollutants in nature despite their proclivity for unpolluted aquatic habitats. We further demonstrated that heavy metal tolerance adaptation process impacts a biological cost to the fitness of the mosquito and potentially involves the induction of specific HM-responsive transcripts and proteins. Here we interrogated differential proteomic profiles of the cadmium tolerant vs. naïve strains of An. gambiae to shed light on proteomic processes that underpinned biological cost to fitness. We identified a total of 1067 larval proteins and observed significant down-regulation of proteins involved in larval immune responses, energy metabolism, antioxidant enzymes, protein synthesis, and proton transport. Our results suggest that mosquitoes can adjust their biological program through proteome changes to counter HM pollution. Since our study was done in controlled laboratory settings, we acknowledge this may not wholly represent the conditions HM polluted environments. Nevertheless, mosquitoes deploying this strategy have the potential of creating an urban enclave for breeding and thrive and become agents of sporadic malaria epidemics.
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468
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Piano D, Cocco E, Guadalupi G, Kalaji HM, Kirkpatrick J, Farci D. Characterization under quasi-native conditions of the capsanthin/capsorubin synthase from Capsicum annuum L. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:165-175. [PMID: 31505449 DOI: 10.1016/j.plaphy.2019.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Chromoplasts are typical plastids of fruits and flowers, deriving from chloroplasts through complex processes of re-organization and recycling. Since this transition leads to the production of reactive species, chromoplasts are characteristic sites for biosynthesis and accumulation of carotenoids and other antioxidants. Here, we have analysed the chromoplast membranes from Capsicum annuum L. fruits, finding a significant expression of the capsanthin/capsorubin synthase. This enzyme was isolated by a very mild procedure allowing its analyses under quasi-native conditions. The isolated complex appeared as a red coloured homo-trimer, suggesting the retention of at least one of the typical carotenoids from C. annuum. Moreover, the protein complex was co-purified with a non-proteinaceous fraction of carotenoid aggregates carrying a high molecular weight and separable only by Size Exclusion Chromatography. This last finding suggested a relationship between the carotenoids synthesis on chromoplast membranes, the presence, and storage of organised carotenoids aggregates typical for chromoplasts. Further MS analyses also provided important hints on the interactome network associated to the capsanthin/capsorubin synthase, confirming its functional relevance during ripening. Results are discussed in the frame of the primary role played by carotenoids in quenching the growing oxidative stress during fruits ripening.
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Affiliation(s)
- Dario Piano
- Department of Life and Environmental Sciences, Laboratory of Photobiology and Plant Physiology, University of Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy; Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Nowoursynowska Str. 159, 02776, Warsaw, Poland
| | - Emma Cocco
- Department of Life and Environmental Sciences, Laboratory of Photobiology and Plant Physiology, University of Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy
| | - Giulia Guadalupi
- Department of Life and Environmental Sciences, Laboratory of Photobiology and Plant Physiology, University of Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy
| | - Hazem M Kalaji
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Nowoursynowska Str. 159, 02776, Warsaw, Poland; White Hill Company, Ciołkowskiego 161, 15-545, Białystok, Poland
| | - Joanna Kirkpatrick
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstraβe 11, 07745, Jena, Germany
| | - Domenica Farci
- White Hill Company, Ciołkowskiego 161, 15-545, Białystok, Poland.
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469
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Djuric U, Lam KHB, Kao J, Batruch I, Jevtic S, Papaioannou MD, Diamandis P. Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry. Mol Cell Proteomics 2019; 18:2029-2043. [PMID: 31353322 PMCID: PMC6773564 DOI: 10.1074/mcp.ra119.001521] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/09/2019] [Indexed: 12/18/2022] Open
Abstract
Molecular characterization of diffuse gliomas has thus far largely focused on genomic and transcriptomic interrogations. Here, we utilized mass spectrometry and overlay protein-level information onto genomically defined cohorts of diffuse gliomas to improve our downstream molecular understanding of these lethal malignancies. Bulk and macrodissected tissues were utilized to quantitate 5,496 unique proteins over three glioma cohorts subclassified largely based on their IDH and 1p19q codeletion status (IDH wild type (IDHwt), n = 7; IDH mutated (IDHmt), 1p19q non-codeleted, n = 7; IDH mutated, 1p19q-codeleted, n = 10). Clustering analysis highlighted proteome and systems-level pathway differences in gliomas according to IDH and 1p19q-codeletion status, including 287 differentially abundant proteins in macrodissection-enriched tumor specimens. IDHwt tumors were enriched for proteins involved in invasiveness and epithelial to mesenchymal transition (EMT), while IDHmt gliomas had increased abundances of proteins involved in mRNA splicing. Finally, these abundance changes were compared with IDH-matched GBM stem-like cells (GSCs) to better pinpoint protein patterns enriched in putative cellular drivers of gliomas. Using this integrative approach, we outline specific proteins involved in chloride transport (e.g. chloride intracellular channel 1, CLIC1) and EMT (e.g. procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3, PLOD3, and serpin peptidase inhibitor clade H member 1, SERPINH1) that showed concordant IDH-status-dependent abundance differences in both primary tissue and purified GSC cultures. Given the downstream position proteins occupy in driving biology and phenotype, understanding the proteomic patterns operational in distinct glioma subtypes could help propose more specific, personalized, and effective targets for the management of patients with these aggressive malignancies.
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Affiliation(s)
- Ugljesa Djuric
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, Ontario, M5G 2C4, Canada
| | - K H Brian Lam
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Jennifer Kao
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ihor Batruch
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Stefan Jevtic
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada
| | - Michail-Dimitrios Papaioannou
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, Ontario, M5G 2C4, Canada
| | - Phedias Diamandis
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, Ontario, M5G 2C4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.
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470
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Dataset of Nematostella vectensis Hsp70 isoform interactomes upon heat shock. Data Brief 2019; 27:104580. [PMID: 31673583 PMCID: PMC6817661 DOI: 10.1016/j.dib.2019.104580] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/12/2019] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Nematostella vectensis is an estuarine sea anemone that has emerged as a model species to characterize molecular responses to physiological stressors due to its exposure to diverse, extreme abiotic conditions. In marine cnidarians, Hsp70 proteins can be effective biomarkers to determine mechanisms of physiological acclimation and evolutionary adaptations to environmental stress: a pressing issue as concerns about climate change grow. Here we show the results of affinity purification mass spectrometry of three Nematostella vectensis Hsp70 isoforms, NvHsp70A, B and D when expressed in untreated and heat shocked yeast cells lacking their native Hsp70s. We identified a total of 1031 interactors for the three NvHsp70 isoforms, 549 or which were shared. NvHsp70 isoform interactions altered substantially under heat stress with 17% of NvHsp70A, 51% of NvHsp70B and 20% of NvHsp70D interactions increasing after exposure to 39 °C for 2 hours. For further interpretation of the data presented in this article, please see the research article “Dynamic remodeling of the interactomes of Nematostella vectensis Hsp70 isoforms under heat shock”.
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471
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Ayala-Nunez NV, Follain G, Delalande F, Hirschler A, Partiot E, Hale GL, Bollweg BC, Roels J, Chazal M, Bakoa F, Carocci M, Bourdoulous S, Faklaris O, Zaki SR, Eckly A, Uring-Lambert B, Doussau F, Cianferani S, Carapito C, Jacobs FMJ, Jouvenet N, Goetz JG, Gaudin R. Zika virus enhances monocyte adhesion and transmigration favoring viral dissemination to neural cells. Nat Commun 2019; 10:4430. [PMID: 31562326 PMCID: PMC6764950 DOI: 10.1038/s41467-019-12408-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 09/04/2019] [Indexed: 02/06/2023] Open
Abstract
Zika virus (ZIKV) invades and persists in the central nervous system (CNS), causing severe neurological diseases. However the virus journey, from the bloodstream to tissues through a mature endothelium, remains unclear. Here, we show that ZIKV-infected monocytes represent suitable carriers for viral dissemination to the CNS using human primary monocytes, cerebral organoids derived from embryonic stem cells, organotypic mouse cerebellar slices, a xenotypic human-zebrafish model, and human fetus brain samples. We find that ZIKV-exposed monocytes exhibit higher expression of adhesion molecules, and higher abilities to attach onto the vessel wall and transmigrate across endothelia. This phenotype is associated to enhanced monocyte-mediated ZIKV dissemination to neural cells. Together, our data show that ZIKV manipulates the monocyte adhesive properties and enhances monocyte transmigration and viral dissemination to neural cells. Monocyte transmigration may represent an important mechanism required for viral tissue invasion and persistence that could be specifically targeted for therapeutic intervention. Zika virus (ZIKV) can infect the central nervous system, but it is not clear how it reaches the brain. Here, Ayala-Nunez et al. show in ex vivo and in vivo models that ZIKV can hitch a ride in monocytes in a Trojan Horse manner to cross the endothelium and disseminate the virus.
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Affiliation(s)
- Nilda Vanesa Ayala-Nunez
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, Université de Montpellier, 34293, Montpellier, France.,Université de Strasbourg, INSERM, 67000, Strasbourg, France
| | | | - François Delalande
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, UMR 7178, CNRS-Université de Strasbourg, ECPM, 67087, Strasbourg, France
| | - Aurélie Hirschler
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, UMR 7178, CNRS-Université de Strasbourg, ECPM, 67087, Strasbourg, France
| | - Emma Partiot
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, Université de Montpellier, 34293, Montpellier, France
| | - Gillian L Hale
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention, 1600 Clifton Rd NE, MS: G32, Atlanta, GA, 30329-4027, USA
| | - Brigid C Bollweg
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention, 1600 Clifton Rd NE, MS: G32, Atlanta, GA, 30329-4027, USA
| | - Judith Roels
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Maxime Chazal
- Viral Genomics and Vaccination Unit, UMR3569 CNRS, Virology Department, Institut Pasteur, 75015, Paris, France
| | - Florian Bakoa
- Viral Genomics and Vaccination Unit, UMR3569 CNRS, Virology Department, Institut Pasteur, 75015, Paris, France
| | - Margot Carocci
- Université de Strasbourg, INSERM, EFS Grand Est, BPPS UMR-S1255, FMTS, 67000, Strasbourg, France
| | - Sandrine Bourdoulous
- INSERM U1016, Institut Cochin, CNRS UMR8104, Université Paris Descartes, Paris, France
| | - Orestis Faklaris
- MRI Core facility, Biocampus, CNRS UMS 3426, 34293, Montpellier, France
| | - Sherif R Zaki
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention, 1600 Clifton Rd NE, MS: G32, Atlanta, GA, 30329-4027, USA
| | - Anita Eckly
- Université de Strasbourg, INSERM, EFS Grand Est, BPPS UMR-S1255, FMTS, 67000, Strasbourg, France
| | - Béatrice Uring-Lambert
- Hôpitaux universitaires de Strasbourg, laboratoire central d'immunologie, 67000, Strasbourg, France
| | - Frédéric Doussau
- Institut des Neurosciences Cellulaires et Intégratives, CNRS, Université de Strasbourg, 67000, Strasbourg, France
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, UMR 7178, CNRS-Université de Strasbourg, ECPM, 67087, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, UMR 7178, CNRS-Université de Strasbourg, ECPM, 67087, Strasbourg, France
| | - Frank M J Jacobs
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Nolwenn Jouvenet
- Viral Genomics and Vaccination Unit, UMR3569 CNRS, Virology Department, Institut Pasteur, 75015, Paris, France
| | | | - Raphael Gaudin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, Université de Montpellier, 34293, Montpellier, France. .,Université de Strasbourg, INSERM, 67000, Strasbourg, France.
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472
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Castro-Severyn J, Pardo-Esté C, Sulbaran Y, Cabezas C, Gariazzo V, Briones A, Morales N, Séveno M, Decourcelle M, Salvetat N, Remonsellez F, Castro-Nallar E, Molina F, Molina L, Saavedra CP. Arsenic Response of Three Altiplanic Exiguobacterium Strains With Different Tolerance Levels Against the Metalloid Species: A Proteomics Study. Front Microbiol 2019; 10:2161. [PMID: 31611848 PMCID: PMC6775490 DOI: 10.3389/fmicb.2019.02161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/03/2019] [Indexed: 12/23/2022] Open
Abstract
Exiguobacterium is a polyextremophile bacterial genus with a physiology that allows it to develop in different adverse environments. The Salar de Huasco is one of these environments due to its altitude, atmospheric pressure, solar radiation, temperature variations, pH, salinity, and the presence of toxic compounds such as arsenic. However, the physiological and/or molecular mechanisms that enable them to prosper in these environments have not yet been described. Our research group has isolated several strains of Exiguobacterium genus from different sites of Salar de Huasco, which show different resistance levels to As(III) and As(V). In this work, we compare the protein expression patterns of the three strains in response to arsenic by a proteomic approach; strains were grown in absence of the metalloid and in presence of As(III) and As(V) sublethal concentrations and the protein separation was carried out in 2D electrophoresis gels (2D-GE). In total, 999 spots were detected, between 77 and 173 of which showed significant changes for As(III) among the three strains, and between 90 and 143 for As(V), respectively, compared to the corresponding control condition. Twenty-seven of those were identified by mass spectrometry (MS). Among these identified proteins, the ArsA [ATPase from the As(III) efflux pump] was found to be up-regulated in response to both arsenic conditions in the three strains, as well as the Co-enzyme A disulfide reductase (Cdr) in the two more resistant strains. Interestingly, in this genus the gene that codifies for Cdr is found within the genic context of the ars operon. We suggest that this protein could be restoring antioxidants molecules, necessary for the As(V) reduction. Additionally, among the proteins that change their expression against As, we found several with functions relevant to stress response, e.g., Hpf, LuxS, GLpX, GlnE, and Fur. This study allowed us to shed light into the physiology necessary for these bacteria to be able to tolerate the toxicity and stress generated by the presence of arsenic in their niche.
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Affiliation(s)
- Juan Castro-Severyn
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Yoelvis Sulbaran
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Carolina Cabezas
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Valentina Gariazzo
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Alan Briones
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Naiyulin Morales
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Martial Séveno
- BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Mathilde Decourcelle
- BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | | | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile.,Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Franck Molina
- Sys2Diag, UMR9005 CNRS ALCEDIAG, Montpellier, France
| | | | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
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473
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Barshop WD, Kim HJ, Fan X, Sha J, Rayatpisheh S, Wohlschlegel JA. Chemical Derivatization of Affinity Matrices Provides Protection from Tryptic Proteolysis. J Proteome Res 2019; 18:3586-3596. [PMID: 31498634 DOI: 10.1021/acs.jproteome.9b00254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enrichment of biotinylated proteins using immobilized streptavidin has become a staple methodology for affinity purification-based proteomics. Many of these workflows rely upon tryptic digestion to elute streptavidin-captured moieties from the beads. The concurrent release of high amounts of streptavidin-derived peptides into the digested sample, however, can significantly hamper the effectiveness of downstream proteomic analyses by increasing the complexity and dynamic range of the mixture. Here, we describe a strategy for the chemical derivatization of streptavidin that renders it largely resistant to proteolysis by trypsin and thereby dramatically reduces the amount of streptavidin contamination in the sample. This rapid and robust approach improves the effectiveness of mass spectrometry-based characterization of streptavidin-purified samples making it broadly useful for a wide variety of applications. In addition, we show that this chemical protection strategy can also be applied to other affinity matrices including immobilized antibodies against HA epitopes.
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Affiliation(s)
- William D Barshop
- Department of Biological Chemistry, David Geffen School of Medicine , University of California-Los Angeles , Los Angeles , California 951737 , United States
| | - Hee Jong Kim
- Department of Biological Chemistry, David Geffen School of Medicine , University of California-Los Angeles , Los Angeles , California 951737 , United States
| | - Xiaorui Fan
- Department of Biological Chemistry, David Geffen School of Medicine , University of California-Los Angeles , Los Angeles , California 951737 , United States
| | - Jihui Sha
- Department of Biological Chemistry, David Geffen School of Medicine , University of California-Los Angeles , Los Angeles , California 951737 , United States
| | - Shima Rayatpisheh
- Department of Biological Chemistry, David Geffen School of Medicine , University of California-Los Angeles , Los Angeles , California 951737 , United States
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine , University of California-Los Angeles , Los Angeles , California 951737 , United States
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474
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Hickl O, Heintz-Buschart A, Trautwein-Schult A, Hercog R, Bork P, Wilmes P, Becher D. Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome. Microorganisms 2019; 7:microorganisms7090367. [PMID: 31546776 PMCID: PMC6780314 DOI: 10.3390/microorganisms7090367] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 12/27/2022] Open
Abstract
With the technological advances of the last decade, it is now feasible to analyze microbiome samples, such as human stool specimens, using multi-omic techniques. Given the inherent sample complexity, there exists a need for sample methods which preserve as much information as possible about the biological system at the time of sampling. Here, we analyzed human stool samples preserved and stored using different methods, applying metagenomics as well as metaproteomics. Our results demonstrate that sample preservation and storage have a significant effect on the taxonomic composition of identified proteins. The overall identification rates, as well as the proportion of proteins from Actinobacteria were much higher when samples were flash frozen. Preservation in RNAlater overall led to fewer protein identifications and a considerable increase in the share of Bacteroidetes, as well as Proteobacteria. Additionally, a decrease in the share of metabolism-related proteins and an increase of the relative amount of proteins involved in the processing of genetic information was observed for RNAlater-stored samples. This suggests that great care should be taken in choosing methods for the preservation and storage of microbiome samples, as well as in comparing the results of analyses using different sampling and storage methods. Flash freezing and subsequent storage at −80 °C should be chosen wherever possible.
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Affiliation(s)
- Oskar Hickl
- Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany.
| | - Anna Heintz-Buschart
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, D-04103 Leipzig, Germany.
- Helmholtz Centre for Environmental Research GmbH - UFZ, D-06120 Halle, Germany.
- Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg.
| | | | - Rajna Hercog
- European Molecular Biology Laboratory Heidelberg, D-69117 Heidelberg, Germany.
| | - Peer Bork
- European Molecular Biology Laboratory Heidelberg, D-69117 Heidelberg, Germany.
- Max Delbrück Centre for Molecular Medicine, D-13125 Berlin, Germany.
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory and University Hospital Heidelberg, D-69120 Heidelberg, Germany.
- Faculty of Biology, University of Würzburg, D-97074 Würzburg, Germany.
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg.
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany.
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475
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Bakail M, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard MC, Courbeyrette R, Mann C, Thuret JY, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du MH, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1. Cell Chem Biol 2019; 26:1573-1585.e10. [PMID: 31543461 DOI: 10.1016/j.chembiol.2019.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 06/12/2019] [Accepted: 09/03/2019] [Indexed: 12/16/2022]
Abstract
Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.
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Affiliation(s)
- May Bakail
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Albane Gaubert
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Jessica Andreani
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Gwenaëlle Moal
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Guillaume Pinna
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Ekaterina Boyarchuk
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS, UMR3664, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, 75005 Paris, France
| | - Marie-Cécile Gaillard
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Regis Courbeyrette
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Carl Mann
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Jean-Yves Thuret
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Bérengère Guichard
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Brice Murciano
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Nicolas Richet
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Adeline Poitou
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Claire Frederic
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Marie-Hélène Le Du
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Morgane Agez
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Caroline Roelants
- Institut National de la Santé et de la Recherche Médicale, Unité 1036, 38000 Grenoble, France; Commissariat à l'Energie Atomique, Institut de Recherche Interdisciplinaire de Grenoble, Biologie du Cancer et de l'Infection, 38000 Grenoble, France; Université Grenoble Alpes, Unité Mixte de Recherche-S1036, 38000 Grenoble, France
| | - Zachary A Gurard-Levin
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS, UMR3664, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, 75005 Paris, France
| | - Geneviève Almouzni
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS, UMR3664, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, 75005 Paris, France
| | - Nadia Cherradi
- Institut National de la Santé et de la Recherche Médicale, Unité 1036, 38000 Grenoble, France; Commissariat à l'Energie Atomique, Institut de Recherche Interdisciplinaire de Grenoble, Biologie du Cancer et de l'Infection, 38000 Grenoble, France; Université Grenoble Alpes, Unité Mixte de Recherche-S1036, 38000 Grenoble, France
| | - Raphael Guerois
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
| | - Françoise Ochsenbein
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
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476
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Herreros-Cabello A, Callejas-Hernández F, Fresno M, Gironès N. Comparative proteomic analysis of trypomastigotes from Trypanosoma cruzi strains with different pathogenicity. INFECTION GENETICS AND EVOLUTION 2019; 76:104041. [PMID: 31536808 DOI: 10.1016/j.meegid.2019.104041] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/05/2019] [Accepted: 09/14/2019] [Indexed: 02/02/2023]
Abstract
Chagas disease, caused by the parasite Trypanosoma cruzi, is one of the most neglected diseases in Latin America, being currently a global health problem. Its immunopathogenesis is still quite unknown. Moreover, there are important differences in pathogenicity between some different T. cruzi strains. For example, in mice, Y strain produces a high acute lethality while VFRA remains in the host mostly in a chronic manner. Comparative proteomic studies between T. cruzi strains represent a complement for transcriptomics and may allow the detection of relevant factors or distinctive functions. Here for the first time, we compared the proteome of trypomastigotes from 2 strains, Y and VFRA, analyzed by mass spectrometry. Gene ontology analysis were used to display similarities or differences in cellular components, biological processes and molecular functions. Also, we performed metabolic pathways enrichment analysis to detect the most relevant pathways in each strain. Although in general they have similar profiles in the different ontology groups, there were some particular interesting differences. Moreover, there were around 10% of different proteins between Y and VFRA strains, that were shared by other T. cruzi strains or protozoan species. They displayed many common enriched metabolic pathways but some others were uniquely enriched in one strain. Thus, we detected enriched antioxidant defenses in VFRA that could correlate with its ability to induce a chronic infection in mice controlling ROS production, while the Y strain revealed a great enrichment of pathways related with nucleotides and protein production, that could fit with its high parasite replication and lethality. In summary, Y and VFRA strains displayed comparable proteomes with some particular distinctions that could contribute to understand their different biological behaviors.
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Affiliation(s)
- Alfonso Herreros-Cabello
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Francisco Callejas-Hernández
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Manuel Fresno
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain; Instituto Sanitario de Investigación la Princesa, Madrid, Spain.
| | - Núria Gironès
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain; Instituto Sanitario de Investigación la Princesa, Madrid, Spain.
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477
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Nassa G, Giurato G, Salvati A, Gigantino V, Pecoraro G, Lamberti J, Rizzo F, Nyman TA, Tarallo R, Weisz A. The RNA-mediated estrogen receptor α interactome of hormone-dependent human breast cancer cell nuclei. Sci Data 2019; 6:173. [PMID: 31527615 PMCID: PMC6746822 DOI: 10.1038/s41597-019-0179-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/25/2019] [Indexed: 01/11/2023] Open
Abstract
Estrogen Receptor alpha (ERα) is a ligand-inducible transcription factor that mediates estrogen signaling in hormone-responsive cells, where it controls key cellular functions by assembling in gene-regulatory multiprotein complexes. For this reason, interaction proteomics has been shown to represent a useful tool to investigate the molecular mechanisms underlying ERα action in target cells. RNAs have emerged as bridging molecules, involved in both assembly and activity of transcription regulatory protein complexes. By applying Tandem Affinity Purification (TAP) coupled to mass spectrometry (MS) before and after RNase digestion in vitro, we generated a dataset of nuclear ERα molecular partners whose association with the receptor involves RNAs. These data provide a useful resource to elucidate the combined role of nuclear RNAs and the proteins identified here in ERα signaling to the genome in breast cancer and other cell types.
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Affiliation(s)
- Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Valerio Gigantino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Giovanni Pecoraro
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Jessica Lamberti
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, 0372, Oslo, Norway
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy.
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy.
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478
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Esteves P, Dard L, Brillac A, Hubert C, Sarlak S, Rousseau B, Dumon E, Izotte J, Bonneu M, Lacombe D, Dupuy JW, Amoedo N, Rossignol R. Nuclear control of lung cancer cells migration, invasion and bioenergetics by eukaryotic translation initiation factor 3F. Oncogene 2019; 39:617-636. [PMID: 31527668 PMCID: PMC6962096 DOI: 10.1038/s41388-019-1009-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 08/07/2019] [Accepted: 08/20/2019] [Indexed: 02/07/2023]
Abstract
The basic understanding of the biological effects of eukaryotic translation initiation factors (EIFs) remains incomplete, notably for their roles independent of protein translation. Different EIFs exhibit nuclear localization and DNA-related functions have been proposed, but the understanding of EIFs novel functions beyond protein translation lacks of integrative analyses between the genomic and the proteomic levels. Here, the noncanonical function of EIF3F was studied in human lung adenocarcinoma by combining methods that revealed both the protein-protein and the protein-DNA interactions of this factor. We discovered that EIF3F promotes cell metastasis in vivo. The underpinning molecular mechanisms involved the regulation of a cluster of 34 metastasis-promoting genes including Snail2, as revealed by proteomics combined with immuno-affinity purification of EIF3F and ChIP-seq/Q-PCR analyses. The interaction between EIF3F and signal transducer and activator of transcription 3 (STAT3) controlled the EIF3F-mediated increase in Snail2 expression and cellular invasion, which were specifically abrogated using the STAT3 inhibitor Nifuroxazide or knockdown approaches. Furthermore, EIF3F overexpression reprogrammed energy metabolism through the activation of AMP-activated protein kinase and the stimulation of oxidative phosphorylation. Our findings demonstrate the role of EIF3F in the molecular control of cell migration, invasion, bioenergetics, and metastasis. The discovery of a role for EIF3F-STAT3 interaction in the genetic control of cell migration and metastasis in human lung adenocarcinoma could lead to the development of diagnosis and therapeutic strategies.
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Affiliation(s)
- Pauline Esteves
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Laetitia Dard
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Aurélia Brillac
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Christophe Hubert
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Saharnaz Sarlak
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Benoît Rousseau
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,Transgenic Animal Facility A2, University of Bordeaux, 33000, Bordeaux, France
| | - Elodie Dumon
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Julien Izotte
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,Transgenic Animal Facility A2, University of Bordeaux, 33000, Bordeaux, France
| | - Marc Bonneu
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,Functional Genomics Center (CGFB), Proteomics Facility, 146 Rue Léo Saignat, 33076, Bordeaux, France.,Bordeaux-INP, Avenue des Facultés, 33405, Talence Cedex, France
| | - Didier Lacombe
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Jean-William Dupuy
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,Functional Genomics Center (CGFB), Proteomics Facility, 146 Rue Léo Saignat, 33076, Bordeaux, France
| | - Nivea Amoedo
- CELLOMET, Functional Genomics Center (CGFB), 146 rue Léo Saignat, 33000, Bordeaux, France
| | - Rodrigue Rossignol
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France. .,INSERM U1211, 33000, Bordeaux, France. .,CELLOMET, Functional Genomics Center (CGFB), 146 rue Léo Saignat, 33000, Bordeaux, France.
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479
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Li Z, Zhang X, Xue W, Zhang Y, Li C, Song Y, Mei M, Lu L, Wang Y, Zhou Z, Jin M, Bian Y, Zhang L, Wang X, Li L, Li X, Fu X, Sun Z, Wu J, Nan F, Chang Y, Yan J, Yu H, Feng X, Wang G, Zhang D, Fu X, Zhang Y, Young KH, Li W, Zhang M. Recurrent GNAQ mutation encoding T96S in natural killer/T cell lymphoma. Nat Commun 2019; 10:4209. [PMID: 31527657 PMCID: PMC6746819 DOI: 10.1038/s41467-019-12032-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 08/16/2019] [Indexed: 01/04/2023] Open
Abstract
Natural killer/T cell lymphoma (NKTCL) is a rare and aggressive malignancy with a higher prevalence in Asia and South America. However, the molecular genetic mechanisms underlying NKTCL remain unclear. Here, we identify somatic mutations of GNAQ (encoding the T96S alteration of Gαq protein) in 8.7% (11/127) of NKTCL patients, through whole-exome/targeted deep sequencing. Using conditional knockout mice (Ncr1-Cre-Gnaqfl/fl), we demonstrate that Gαq deficiency leads to enhanced NK cell survival. We also find that Gαq suppresses tumor growth of NKTCL via inhibition of the AKT and MAPK signaling pathways. Moreover, the Gαq T96S mutant may act in a dominant negative manner to promote tumor growth in NKTCL. Clinically, patients with GNAQ T96S mutations have inferior survival. Taken together, we identify recurrent somatic GNAQ T96S mutations that may contribute to the pathogenesis of NKTCL. Our work thus has implications for refining our understanding of the genetic mechanisms of NKTCL and for the development of therapies.
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Affiliation(s)
- Zhaoming Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Xudong Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Weili Xue
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Yanjie Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Chaoping Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Yue Song
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Mei Mei
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Lisha Lu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Yingjun Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Zhiyuan Zhou
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Mengyuan Jin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Yangyang Bian
- Medical Research Centre, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Lei Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Xinhua Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Ling Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Xin Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Xiaorui Fu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Zhenchang Sun
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Jingjing Wu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Feifei Nan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Yu Chang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Jiaqin Yan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Hui Yu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Xiaoyan Feng
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China
| | - Guannan Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Dandan Zhang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Xuefei Fu
- Novogene Bioinformatics Technology Co, Ltd, 38 Xueqing Road, 100083, Beijing, China
| | - Yuan Zhang
- The Academy of Medical Science of Zhengzhou University, 450052, Zhengzhou, China
| | - Ken H Young
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wencai Li
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
| | - Mingzhi Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
- Lymphoma Diagnosis and Treatment Center of Henan Province, 450000, Zhengzhou, China.
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480
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Xu Z, Zhang H, Zhang X, Jiang H, Liu C, Wu F, Qian L, Hao B, Czajkowsky DM, Guo S, Xu Z, Bi L, Wang S, Li H, Tan M, Yan W, Feng L, Hou J, Tao S. Interplay between the bacterial protein deacetylase CobB and the second messenger c-di-GMP. EMBO J 2019; 38:e100948. [PMID: 31418899 PMCID: PMC6745502 DOI: 10.15252/embj.2018100948] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 07/05/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
As a ubiquitous bacterial secondary messenger, c-di-GMP plays key regulatory roles in processes such as bacterial motility and transcription regulation. CobB is the Sir2 family protein deacetylase that controls energy metabolism, chemotaxis, and DNA supercoiling in many bacteria. Using an Escherichia coli proteome microarray, we found that c-di-GMP strongly binds to CobB. Further, protein deacetylation assays showed that c-di-GMP inhibits the activity of CobB and thereby modulates the biogenesis of acetyl-CoA. Interestingly, we also found that one of the key enzymes directly involved in c-di-GMP production, DgcZ, is a substrate of CobB. Deacetylation of DgcZ by CobB enhances its activity and thus the production of c-di-GMP. Our work establishes a novel negative feedback loop linking c-di-GMP biogenesis and CobB-mediated protein deacetylation.
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Affiliation(s)
- Zhaowei Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Hainan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Xingrun Zhang
- MOE Key Laboratory of Protein SciencesCenter for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
- Department of Basic Medical SciencesSchool of MedicineTsinghua UniversityBeijingChina
| | - Hewei Jiang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Chengxi Liu
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Fanlin Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Lili Qian
- The Chemical Proteomics Center and State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Bingbing Hao
- The Chemical Proteomics Center and State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | | | - Shujuan Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Zhijing Xu
- College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Lijun Bi
- National Key Laboratory of BiomacromoleculesKey Laboratory of Non‐Coding RNA and Key Laboratory of Protein and Peptide PharmaceuticalsInstitute of BiophysicsChinese Academy of SciencesBeijingChina
- School of Stomatology and MedicineFoshan UniversityFoshanChina
| | - Shihua Wang
- School of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Haitao Li
- MOE Key Laboratory of Protein SciencesCenter for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
- Department of Basic Medical SciencesSchool of MedicineTsinghua UniversityBeijingChina
| | - Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Wei Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Lei Feng
- Instrumental Analysis CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Jingli Hou
- Instrumental Analysis CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Sheng‐ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Oncogenes and Related GenesShanghaiChina
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481
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Zhao T, Huan Q, Sun J, Liu C, Hou X, Yu X, Silverman IM, Zhang Y, Gregory BD, Liu CM, Qian W, Cao X. Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency. Genome Biol 2019; 20:189. [PMID: 31481099 PMCID: PMC6724284 DOI: 10.1186/s13059-019-1799-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 08/22/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. RESULTS We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. CONCLUSIONS Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression.
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Affiliation(s)
- Taolan Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Huan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiuli Hou
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiang Yu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ian M Silverman
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yi Zhang
- Laboratory for Genome Regulation and Human Health and Center for Genome Analysis, ABLife Inc, Wuhan, 430075, Hubei, China
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Chun-Ming Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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482
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Ribeiro D, Planchon S, Leclercq C, Raundrup K, Alves S, Bessa R, Renaut J, Almeida A. The muscular, hepatic and adipose tissues proteomes in muskox (Ovibos moschatus): Differences between males and females. J Proteomics 2019; 208:103480. [DOI: 10.1016/j.jprot.2019.103480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/28/2019] [Accepted: 08/02/2019] [Indexed: 02/07/2023]
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483
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Kampstra ASB, van Heemst J, Janssen GM, de Ru AH, van Lummel M, van Veelen PA, Toes REM. Ligandomes obtained from different HLA-class II-molecules are homologous for N- and C-terminal residues outside the peptide-binding cleft. Immunogenetics 2019; 71:519-530. [PMID: 31520135 PMCID: PMC6790208 DOI: 10.1007/s00251-019-01129-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/23/2019] [Indexed: 12/31/2022]
Abstract
Human CD4+ T lymphocytes play an important role in inducing potent immune responses. T cells are activated and stimulated by peptides presented in human leucocyte antigen (HLA)-class II molecules. These HLA-class II molecules typically present peptides of between 12 and 20 amino acids in length. The region that interacts with the HLA molecule, designated as the peptide-binding core, is highly conserved in the residues which anchor the peptide to the molecule. In addition, as these peptides are the product of proteolytic cleavages, certain conserved residues may be expected at the N- and C-termini outside the binding core. To study whether similar conserved residues are present in different cell types, potentially harbouring different proteolytic enzymes, the ligandomes of HLA-DRB1*03:01/HLA-DRB > 1 derived from two different cell types (dendritic cells and EBV-transformed B cells) were identified with mass spectrometry and the binding core and N- and C-terminal residues of a total of 16,568 peptides were analysed using the frequencies of the amino acids in the human proteome. Similar binding motifs were found as well as comparable conservations in the N- and C-terminal residues. Furthermore, the terminal conservations of these ligandomes were compared to the N- and C-terminal conservations of the ligandome acquired from dendritic cells homozygous for HLA-DRB1*04:01. Again, comparable conservations were evident with only minor differences. Taken together, these data show that there are conservations in the terminal residues of peptides, presumably the result of the activity of proteases involved in antigen processing.
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Affiliation(s)
- Arieke S B Kampstra
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Jurgen van Heemst
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - George M Janssen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Menno van Lummel
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
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484
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Bilsland AE, Liu Y, Turnbull A, Sumpton D, Stevenson K, Cairney CJ, Boyd SM, Roffey J, Jenkinson D, Keith WN. A Novel Pyrazolopyrimidine Ligand of Human PGK1 and Stress Sensor DJ1 Modulates the Shelterin Complex and Telomere Length Regulation. Neoplasia 2019; 21:893-907. [PMID: 31401411 PMCID: PMC6700475 DOI: 10.1016/j.neo.2019.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 11/15/2022]
Abstract
Telomere signaling and metabolic dysfunction are hallmarks of cell aging. New agents targeting these processes might provide therapeutic opportunities, including chemoprevention strategies against cancer predisposition. We report identification and characterization of a pyrazolopyrimidine compound series identified from screens focused on cell immortality and whose targets are glycolytic kinase PGK1 and oxidative stress sensor DJ1. We performed structure-activity studies on the series to develop a photoaffinity probe to deconvolute the cellular targets. In vitro binding and structural analyses confirmed these targets, suggesting that PGK1/DJ1 interact, which we confirmed by immunoprecipitation. Glucose homeostasis and oxidative stress are linked to telomere signaling and exemplar compound CRT0063465 blocked hypoglycemic telomere shortening. Intriguingly, PGK1 and DJ1 bind to TRF2 and telomeric DNA. Compound treatment modulates these interactions and also affects Shelterin complex composition, while conferring cellular protection from cytotoxicity due to bleomycin and desferroxamine. These results demonstrate therapeutic potential of the compound series.
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Affiliation(s)
- Alan E Bilsland
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1QH, UK
| | - Yu Liu
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1QH, UK
| | - Andrew Turnbull
- Cancer Research Technology Ltd., Wolfson Institute for Biomedical Research, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - David Sumpton
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
| | - Katrina Stevenson
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1QH, UK
| | - Claire J Cairney
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1QH, UK
| | - Susan M Boyd
- CompChem Solutions Ltd, St John's Innovation Centre, Cambridge, CB4 0WS, UK
| | - Jon Roffey
- Cancer Research Technology Ltd., Wolfson Institute for Biomedical Research, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - David Jenkinson
- Cancer Research Technology Ltd., Wolfson Institute for Biomedical Research, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - W Nicol Keith
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1QH, UK.
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485
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Burat B, Faucher Q, Čechová P, Arnion H, Di Meo F, Sauvage F, Marquet P, Essig M. Cyclosporine A inhibits MRTF-SRF signaling through Na +/K + ATPase inhibition and actin remodeling. FASEB Bioadv 2019; 1:561-578. [PMID: 32123851 PMCID: PMC6996406 DOI: 10.1096/fba.2019-00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 03/22/2019] [Accepted: 07/25/2019] [Indexed: 01/07/2023] Open
Abstract
Calcineurin inhibitors (CNI) are the pillars of immunosuppression in transplantation. However, they display a potent nephrotoxicity whose mechanisms remained widely unsolved. We used an untargeted quantitative proteomic approach (iTRAQ technology) to highlight new targets of CNI in renal proximal tubular cells (RPTCs). CNI-treated RPTCs proteome displayed an over-representation of actin-binding proteins with a CNI-specific expression profile. Cyclosporine A (CsA) induced F-actin remodeling and depolymerization, decreased F-actin-stabilizing, polymerization-promoting cofilin (CFL) oligomers, and inhibited the G-actin-regulated serum response factor (SRF) pathway. Inhibition of CFL canonical phosphorylation pathway reproduced CsA effects; however, S3-R, an analogue of the phosphorylation site of CFL prevented the effects of CsA which suggests that CsA acted independently from the canonical CFL regulation. CFL is known to be regulated by the Na+/K+-ATPase. Molecular docking calculations identified two inhibiting sites of CsA on Na+/K+-ATPase and a 23% decrease in Na+/K+-ATPase activity of RPTCs was observed with CsA. Ouabain, a specific inhibitor of Na+/K+-ATPase also reproduced CsA effects on actin organization and SRF activity. Altogether, these results described a new original pathway explaining CsA nephrotoxicity.
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Affiliation(s)
- Bastien Burat
- Centre for Biology & Health Research, UMR INSERM 1248 IPPRIT (Individual Profiling and Prevention of RIsks in Transplantation)Limoges UniversityLimogesFrance
| | - Quentin Faucher
- Centre for Biology & Health Research, UMR INSERM 1248 IPPRIT (Individual Profiling and Prevention of RIsks in Transplantation)Limoges UniversityLimogesFrance
| | - Petra Čechová
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of SciencePalacký University OlomoucOlomoucCzech Republic
- Department of Physical Chemistry, Regional Centre of Advanced Technologies and Materials, Faculty of SciencePalacký University OlomoucOlomoucCzech Republic
| | - Hélène Arnion
- Centre for Biology & Health Research, UMR INSERM 1248 IPPRIT (Individual Profiling and Prevention of RIsks in Transplantation)Limoges UniversityLimogesFrance
| | - Florent Di Meo
- Centre for Biology & Health Research, UMR INSERM 1248 IPPRIT (Individual Profiling and Prevention of RIsks in Transplantation)Limoges UniversityLimogesFrance
| | - François‐Ludovic Sauvage
- Centre for Biology & Health Research, UMR INSERM 1248 IPPRIT (Individual Profiling and Prevention of RIsks in Transplantation)Limoges UniversityLimogesFrance
| | - Pierre Marquet
- Centre for Biology & Health Research, UMR INSERM 1248 IPPRIT (Individual Profiling and Prevention of RIsks in Transplantation)Limoges UniversityLimogesFrance
- Department of Pharmacology and ToxicologyLimoges University HospitalLimogesFrance
| | - Marie Essig
- Centre for Biology & Health Research, UMR INSERM 1248 IPPRIT (Individual Profiling and Prevention of RIsks in Transplantation)Limoges UniversityLimogesFrance
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486
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Federspiel JD, Tandon P, Wilczewski CM, Wasson L, Herring LE, Venkatesh SS, Cristea IM, Conlon FL. Conservation and divergence of protein pathways in the vertebrate heart. PLoS Biol 2019; 17:e3000437. [PMID: 31490923 PMCID: PMC6750614 DOI: 10.1371/journal.pbio.3000437] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 09/18/2019] [Accepted: 08/14/2019] [Indexed: 12/18/2022] Open
Abstract
Heart disease is the leading cause of death in the western world. Attaining a mechanistic understanding of human heart development and homeostasis and the molecular basis of associated disease states relies on the use of animal models. Here, we present the cardiac proteomes of 4 model vertebrates with dual circulatory systems: the pig (Sus scrofa), the mouse (Mus musculus), and 2 frogs (Xenopus laevis and Xenopus tropicalis). Determination of which proteins and protein pathways are conserved and which have diverged within these species will aid in our ability to choose the appropriate models for determining protein function and to model human disease. We uncover mammalian- and amphibian-specific, as well as species-specific, enriched proteins and protein pathways. Among these, we find and validate an enrichment in cell-cycle-associated proteins within Xenopus laevis. To further investigate functional units within cardiac proteomes, we develop a computational approach to profile the abundance of protein complexes across species. Finally, we demonstrate the utility of these data sets for predicting appropriate model systems for studying given cardiac conditions by testing the role of Kielin/chordin-like protein (Kcp), a protein found as enriched in frog hearts compared to mammals. We establish that germ-line mutations in Kcp in Xenopus lead to valve defects and, ultimately, cardiac failure and death. Thus, integrating these findings with data on proteins responsible for cardiac disease should lead to the development of refined, species-specific models for protein function and disease states.
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Affiliation(s)
| | - Panna Tandon
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Caralynn M. Wilczewski
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lauren Wasson
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Laura E. Herring
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Ileana M. Cristea
- Princeton University, Princeton, New Jersey, United States of America
| | - Frank L. Conlon
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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487
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Goos C, Dejung M, Wehman AM, M-Natus E, Schmidt J, Sunter J, Engstler M, Butter F, Kramer S. Trypanosomes can initiate nuclear export co-transcriptionally. Nucleic Acids Res 2019; 47:266-282. [PMID: 30418648 PMCID: PMC6326799 DOI: 10.1093/nar/gky1136] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/25/2018] [Indexed: 02/03/2023] Open
Abstract
The nuclear envelope serves as important messenger RNA (mRNA) surveillance system. In yeast and human, several control systems act in parallel to prevent nuclear export of unprocessed mRNAs. Trypanosomes lack homologues to most of the involved proteins and their nuclear mRNA metabolism is non-conventional exemplified by polycistronic transcription and mRNA processing by trans-splicing. We here visualized nuclear export in trypanosomes by intra- and intermolecular multi-colour single molecule FISH. We found that, in striking contrast to other eukaryotes, the initiation of nuclear export requires neither the completion of transcription nor splicing. Nevertheless, we show that unspliced mRNAs are mostly prevented from reaching the nucleus-distant cytoplasm and instead accumulate at the nuclear periphery in cytoplasmic nuclear periphery granules (NPGs). Further characterization of NPGs by electron microscopy and proteomics revealed that the granules are located at the cytoplasmic site of the nuclear pores and contain most cytoplasmic RNA-binding proteins but none of the major translation initiation factors, consistent with a function in preventing faulty mRNAs from reaching translation. Our data indicate that trypanosomes regulate the completion of nuclear export, rather than the initiation. Nuclear export control remains poorly understood, in any organism, and the described way of control may not be restricted to trypanosomes.
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Affiliation(s)
- Carina Goos
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Mario Dejung
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Ann M Wehman
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Elisabeth M-Natus
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Johannes Schmidt
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jack Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Susanne Kramer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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488
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Chakraborty S, Randall A, Vickers TJ, Molina D, Harro CD, DeNearing B, Brubaker J, Sack DA, Bourgeois AL, Felgner PL, Liang X, Mani S, Wenzel H, Townsend RR, Gilmore PE, Darsley MJ, Rasko DA, Fleckenstein JM. Interrogation of a live-attenuated enterotoxigenic Escherichia coli vaccine highlights features unique to wild-type infection. NPJ Vaccines 2019; 4:37. [PMID: 31482013 PMCID: PMC6713706 DOI: 10.1038/s41541-019-0131-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/01/2019] [Indexed: 01/01/2023] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) infections are a common cause of severe diarrheal illness in low- and middle-income countries. The live-attenuated ACE527 ETEC vaccine, adjuvanted with double mutant heat-labile toxin (dmLT), affords clear but partial protection against ETEC challenge in human volunteers. Comparatively, initial wild-type ETEC challenge completely protects against severe diarrhea on homologous re-challenge. To investigate determinants of protection, vaccine antigen content was compared to wild-type ETEC, and proteome microarrays were used to assess immune responses following vaccination and ETEC challenge. Although molecular interrogation of the vaccine confirmed expression of targeted canonical antigens, relative to wild-type ETEC, vaccine strains were deficient in production of flagellar antigens, immotile, and lacked production of the EtpA adhesin. Similarly, vaccination ± dmLT elicited responses to targeted canonical antigens, but relative to wild-type challenge, vaccine responses to some potentially protective non-canonical antigens including EtpA and the YghJ metalloprotease were diminished or absent. These studies highlight important differences in vaccine and wild-type ETEC antigen content and call attention to distinct immunologic signatures that could inform investigation of correlates of protection, and guide vaccine antigen selection for these pathogens of global importance.
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Affiliation(s)
| | | | - Tim J. Vickers
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO USA
| | - Doug Molina
- Antigen Discovery, Inc. (ADI), Irvine, CA USA
| | - Clayton D. Harro
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | | | - Jessica Brubaker
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - David A. Sack
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | | | - Philip L. Felgner
- Antigen Discovery, Inc. (ADI), Irvine, CA USA
- Vaccine R & D Center, University of California, Irvine, Irvine, CA USA
| | | | - Sachin Mani
- Enteric Vaccine Initiative, PATH, Washington DC, USA
| | | | - R. Reid Townsend
- Department of Medicine, Divsion of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, St. Louis, USA
| | - Petra E. Gilmore
- Department of Medicine, Divsion of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, St. Louis, USA
| | | | - David A. Rasko
- The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - James M. Fleckenstein
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO USA
- Medicine Service, John Cochran VA Medical Center, St. Louis, MO USA
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489
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SILAC-Based Quantification of TGFBR2-Regulated Protein Expression in Extracellular Vesicles of Microsatellite Unstable Colorectal Cancers. Int J Mol Sci 2019; 20:ijms20174162. [PMID: 31454892 PMCID: PMC6747473 DOI: 10.3390/ijms20174162] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022] Open
Abstract
Microsatellite unstable (MSI) colorectal cancers (CRCs) are characterized by mutational inactivation of Transforming Growth Factor Beta Receptor Type 2 (TGFBR2). TGFBR2-deficient CRCs present altered target gene and protein expression. Such cellular alterations modulate the content of CRC-derived extracellular vesicles (EVs). EVs function as couriers of proteins, nucleic acids, and lipids in intercellular communication. At a qualitative level, we have previously shown that TGFBR2 deficiency causes overall alterations in the EV protein content. To deepen the basic understanding of altered protein dynamics, this work aimed to determine TGFBR2-dependent EV protein signatures in a quantitative manner. Using a stable isotope labeling with amino acids in cell culture (SILAC) approach for mass spectrometry-based quantification, 48 TGFBR2-regulated proteins were identified in MSI CRC-derived EVs. Overall, TGFBR2 deficiency caused upregulation of several EV proteins related to the extracellular matrix and nucleosome as well as downregulation of proteasome-associated proteins. The present study emphasizes the general overlap of proteins between EVs and their parental CRC cells but also highlights the impact of TGFBR2 deficiency on EV protein composition. From a clinical perspective, TGFBR2-regulated quantitative differences of protein expression in EVs might nominate novel biomarkers for liquid biopsy-based MSI typing in the future.
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490
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Ghisaura S, Melis R, Biosa G, Pagnozzi D, Slavski H, Uzzau S, Anedda R, Addis MF. Liver proteome dataset of Sparus aurata exposed to low temperatures. Data Brief 2019; 26:104419. [PMID: 31528672 PMCID: PMC6742852 DOI: 10.1016/j.dib.2019.104419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/29/2019] [Accepted: 08/12/2019] [Indexed: 11/20/2022] Open
Abstract
We report the proteomic dataset of livers from Sparus aurata exposed to low temperature during growth. Gilthead sea bream juveniles were reared in Recirculating Aquaculture Systems (RAS) and exposed to a temperature ramp made of two phases of four weeks each: a Cooling phase from 18 °C (t0) to 11 °C (t1) and a Cold Maintenance phase at 11 °C (t1-t2) in a 8 week feeding trial. At the end of the experiment, sea bream livers were collected and analyzed with a shotgun proteomics approach based on filter-aided sample preparation followed by tandem mass spectrometry, peptide identification carried out using Sequest-HT as search engine within the Proteome Discoverer informatic platform, and label-free differential analysis. The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD011059 (Vizcaíno et al., 2016; Deutsch et al., 2017; Perez-Riverol et al., 2016). The dataset described here is also related to the research article entitled “Liver proteomics of gilthead sea bream (Sparus aurata) exposed to cold stress” (Ghisaura et al., 2019).
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Affiliation(s)
- S Ghisaura
- Porto Conte Ricerche, SP 55 Porto Conte/Capo Caccia, Km 8.400, Loc. Tramariglio, 07041 Alghero, Italy
| | - R Melis
- Porto Conte Ricerche, SP 55 Porto Conte/Capo Caccia, Km 8.400, Loc. Tramariglio, 07041 Alghero, Italy
| | - G Biosa
- Porto Conte Ricerche, SP 55 Porto Conte/Capo Caccia, Km 8.400, Loc. Tramariglio, 07041 Alghero, Italy
| | - D Pagnozzi
- Porto Conte Ricerche, SP 55 Porto Conte/Capo Caccia, Km 8.400, Loc. Tramariglio, 07041 Alghero, Italy
| | - H Slavski
- Aller Aqua, Allervej 130, DK-6070, Christiansfeld, Denmark
| | - S Uzzau
- Porto Conte Ricerche, SP 55 Porto Conte/Capo Caccia, Km 8.400, Loc. Tramariglio, 07041 Alghero, Italy.,Università degli Studi di Sassari, Dipartimento di Scienze Biomediche, Viale S. Pietro 43/B, 07100 Sassari, Italy
| | - R Anedda
- Porto Conte Ricerche, SP 55 Porto Conte/Capo Caccia, Km 8.400, Loc. Tramariglio, 07041 Alghero, Italy
| | - M F Addis
- Porto Conte Ricerche, SP 55 Porto Conte/Capo Caccia, Km 8.400, Loc. Tramariglio, 07041 Alghero, Italy.,Università degli Studi di Milano, Dipartimento di Medicina Veterinaria, Via Celoria 10, 20133 Milano, Italy
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491
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Petyuk VA, Gatto L, Payne SH. Reproducibility and Transparency by Design. Mol Cell Proteomics 2019; 18:S202-S204. [PMID: 31273047 PMCID: PMC6692781 DOI: 10.1074/mcp.ip119.001567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/24/2019] [Indexed: 12/24/2022] Open
Abstract
The reproducibility of bioinformatics analyses can be elevated to equal status with biological discovery. To achieve this, reproducibility must become part of the process, not an afterthought.
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Affiliation(s)
| | - Laurent Gatto
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
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492
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Uyaniker S, van der Spek SJF, Reinders NR, Xiong H, Li KW, Bossers K, Smit AB, Verhaagen J, Kessels HW. The Effects of Sindbis Viral Vectors on Neuronal Function. Front Cell Neurosci 2019; 13:362. [PMID: 31440143 PMCID: PMC6694438 DOI: 10.3389/fncel.2019.00362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/25/2019] [Indexed: 11/16/2022] Open
Abstract
Viral vectors are attractive tools to express genes in neurons. Transduction of neurons with a recombinant, replication-deficient Sindbis viral vector is a method of choice for studying the effects of short-term protein overexpression on neuronal function. However, to which extent Sindbis by itself may affect neurons is not fully understood. We assessed effects of neuronal transduction with a Sindbis viral vector on the transcriptome and proteome in organotypic hippocampal slice cultures, and analyzed the electrophysiological properties of individual CA1 neurons, at 24 h and 72 h after viral vector injection. Whereas Sindbis caused substantial gene expression alterations, changes at the protein level were less pronounced. Alterations in transcriptome and proteome were predominantly limited to proteins involved in mediating anti-viral innate immune responses. Sindbis transduction did not affect the intrinsic electrophysiological properties of individual neurons: the membrane potential and neuronal excitability were similar between transduced and non-transduced CA1 neurons up to 72 h after Sindbis injection. Synaptic currents also remained unchanged upon Sindbis transduction, unless slices were massively infected for 72 h. We conclude that Sindbis viral vectors at low transduction rates are suitable for studying short-term effects of a protein of interest on electrophysiological properties of neurons, but not for studies on the regulation of gene expression.
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Affiliation(s)
- Seçil Uyaniker
- Laboratory for Neuroregeneration, The Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, Netherlands
| | - Sophie J F van der Spek
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
| | - Niels R Reinders
- Laboratory for Neuroregeneration, The Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, Netherlands.,Department of Cellular and Computational Neuroscience, Swammerdam Institute for Life Sciences, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, Netherlands
| | - Hui Xiong
- Laboratory for Neuroregeneration, The Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, Netherlands.,Department of Cellular and Computational Neuroscience, Swammerdam Institute for Life Sciences, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
| | - Koen Bossers
- Laboratory for Neuroregeneration, The Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
| | - Joost Verhaagen
- Laboratory for Neuroregeneration, The Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, Netherlands.,Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
| | - Helmut W Kessels
- Laboratory for Neuroregeneration, The Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, Netherlands.,Department of Cellular and Computational Neuroscience, Swammerdam Institute for Life Sciences, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, Netherlands
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493
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Resistance in marine cyanobacteria differs against specialist and generalist cyanophages. Proc Natl Acad Sci U S A 2019; 116:16899-16908. [PMID: 31383764 PMCID: PMC6708340 DOI: 10.1073/pnas.1906897116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Long-term coexistence between unicellular cyanobacteria and their lytic viruses (cyanophages) in the oceans is thought to be due to the presence of sensitive cells in which cyanophages reproduce, ultimately killing the cell, while other cyanobacteria survive due to resistance to infection. Here, we investigated resistance in marine cyanobacteria from the genera Synechococcus and Prochlorococcus and compared modes of resistance against specialist and generalist cyanophages belonging to the T7-like and T4-like cyanophage families. Resistance was extracellular in most interactions against specialist cyanophages irrespective of the phage family, preventing entry into the cell. In contrast, resistance was intracellular in practically all interactions against generalist T4-like cyanophages. The stage of intracellular arrest was interaction-specific, halting at various stages of the infection cycle. Incomplete infection cycles proceeded to various degrees of phage genome transcription and translation as well as phage genome replication in numerous interactions. In a particularly intriguing case, intracellular capsid assembly was observed, but the phage genome was not packaged. The cyanobacteria survived the encounter despite late-stage infection and partial genome degradation. We hypothesize that this is tolerated due to genome polyploidy, which we found for certain strains of both Synechococcus and Prochlorococcus Our findings unveil a heavy cost of promiscuous entry of generalist phages into nonhost cells that is rarely paid by specialist phages and suggests the presence of unknown mechanisms of intracellular resistance in the marine unicellular cyanobacteria. Furthermore, these findings indicate that the range for virus-mediated horizontal gene transfer extends beyond hosts to nonhost cyanobacterial cells.
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494
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Papaioannou MD, Djuric U, Kao J, Karimi S, Zadeh G, Aldape K, Diamandis P. Proteomic analysis of meningiomas reveals clinically distinct molecular patterns. Neuro Oncol 2019; 21:1028-1038. [PMID: 31077268 PMCID: PMC6682208 DOI: 10.1093/neuonc/noz084] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Meningiomas represent one of the most common brain tumors and exhibit a clinically heterogeneous behavior, sometimes difficult to predict with classic histopathologic features. While emerging molecular profiling efforts have linked specific genomic drivers to distinct clinical patterns, the proteomic landscape of meningiomas remains largely unexplored. METHODS We utilize liquid chromatography tandem mass spectrometry with an Orbitrap mass analyzer to quantify global protein abundances of a clinically well-annotated formalin-fixed paraffin embedded (FFPE) cohort (n = 61) of meningiomas spanning all World Health Organization (WHO) grades and various degrees of clinical aggressiveness. RESULTS In total, we quantify 3042 unique proteins comparing patterns across different clinical parameters. Unsupervised clustering analysis highlighted distinct proteomic (n = 106 proteins, Welch's t-test, P < 0.01) and pathway-level (eg, Notch and PI3K/AKT/mTOR) differences between convexity and skull base meningiomas. Supervised comparative analyses of different pathological grades revealed distinct patterns between benign (grade I) and atypical/malignant (grades II‒III) meningiomas with specific oncogenes enriched in higher grade lesions. Independent of WHO grade, clinically aggressive meningiomas that rapidly recurred (<3 y) had distinctive protein patterns converging on mRNA processing and impaired activation of the matrisome complex. Larger sized meningiomas (>3 cm maximum tumor diameter) and those with previous radiation exposure revealed perturbed pro-proliferative (eg, epidermal growth factor receptor) and metabolic as well as inflammatory response pathways (mitochondrial activity, interferon), respectively. CONCLUSIONS Our proteomic study demonstrates that meningiomas of different grades and clinical parameters present distinct proteomic profiles. These proteomic variations offer potential future utility in helping better predict patient outcome and in nominating novel therapeutic targets for personalized care.
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Affiliation(s)
- Michail-Dimitrios Papaioannou
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Ugljesa Djuric
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Jennifer Kao
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shirin Karimi
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
| | - Kenneth Aldape
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
| | - Phedias Diamandis
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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495
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Abstract
The amount of omics data in the public domain is increasing every year. Modern science has become a data-intensive discipline. Innovative solutions for data management, data sharing, and for discovering novel datasets are therefore increasingly required. In 2016, we released the first version of the Omics Discovery Index (OmicsDI) as a light-weight system to aggregate datasets across multiple public omics data resources. OmicsDI aggregates genomics, transcriptomics, proteomics, metabolomics and multiomics datasets, as well as computational models of biological processes. Here, we propose a set of novel metrics to quantify the attention and impact of biomedical datasets. A complete framework (now integrated into OmicsDI) has been implemented in order to provide and evaluate those metrics. Finally, we propose a set of recommendations for authors, journals and data resources to promote an optimal quantification of the impact of datasets. Increasing amount of public omics data are important and valuable resources for the research community. Here, the authors develop a set of metrics to quantify the attention and impact of biomedical datasets and integrate them into the framework of Omics Discovery Index (OmicsDI).
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496
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Escobar-Correas S, Mendoza-Porras O, Dellagnola FA, Colgrave ML, Vega IA. Integrative Proteomic Analysis of Digestive Tract Glycosidases from the Invasive Golden Apple Snail, Pomacea canaliculata. J Proteome Res 2019; 18:3342-3352. [PMID: 31321981 DOI: 10.1021/acs.jproteome.9b00282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The freshwater snail Pomacea canaliculata, an invasive species of global significance, possesses a well-developed digestive system and diverse feeding mechanisms enabling the intake of a wide variety of food. The identification of glycosidases in adult snails would increase the understanding of their digestive physiology and potentially generate new opportunities to eradicate and/or control this invasive species. In this study, liquid chromatography coupled to tandem mass spectrometry was applied to define the occurrence, diversity, and origin of glycoside hydrolases along the digestive tract of P. canaliculata. A range of cellulases, hemicellulases, amylases, maltases, fucosidases, and galactosidases were identified across the digestive tract. The digestive gland and the contents of the crop and style sac yield a higher diversity of glycosidase-derived peptides. Subsequently, peptides derived from 81 glycosidases (46 proteins from the public database and 35 uniquely from the transcriptome database) that were distributed among 13 glycoside hydrolase families were selected and quantified using multiple reaction monitoring mass spectrometry. This study showed a high glycosidase abundance and diversity in the gut contents of P. canaliculata which participate in extracellular digestion of complex dietary carbohydrates. Salivary and digestive glands were the main tissues involved in their synthesis and secretion.
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Affiliation(s)
- Sophia Escobar-Correas
- IHEM, CONICET , Universidad Nacional de Cuyo , Mendoza , Argentina.,Universidad Nacional de Cuyo, Facultad de Ciencias Médicas , Instituto de Fisiología , Mendoza 5500 , Argentina
| | - Omar Mendoza-Porras
- Agriculture & Food , CSIRO , 306 Carmody Road , St. Lucia , Queensland 4067 , Australia
| | - Federico A Dellagnola
- IHEM, CONICET , Universidad Nacional de Cuyo , Mendoza , Argentina.,Universidad Nacional de Cuyo, Facultad de Ciencias Médicas , Instituto de Fisiología , Mendoza 5500 , Argentina.,Universidad Nacional de Cuyo , Facultad de Ciencias Exactas y Naturales, Departamento de Biología , Mendoza 5500 , Argentina
| | - Michelle L Colgrave
- Agriculture & Food , CSIRO , 306 Carmody Road , St. Lucia , Queensland 4067 , Australia
| | - Israel A Vega
- IHEM, CONICET , Universidad Nacional de Cuyo , Mendoza , Argentina.,Universidad Nacional de Cuyo, Facultad de Ciencias Médicas , Instituto de Fisiología , Mendoza 5500 , Argentina.,Universidad Nacional de Cuyo , Facultad de Ciencias Exactas y Naturales, Departamento de Biología , Mendoza 5500 , Argentina
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497
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Loi VV, Huyen NTT, Busche T, Tung QN, Gruhlke MCH, Kalinowski J, Bernhardt J, Slusarenko AJ, Antelmann H. Staphylococcus aureus responds to allicin by global S-thioallylation - Role of the Brx/BSH/YpdA pathway and the disulfide reductase MerA to overcome allicin stress. Free Radic Biol Med 2019; 139:55-69. [PMID: 31121222 DOI: 10.1016/j.freeradbiomed.2019.05.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/08/2019] [Accepted: 05/15/2019] [Indexed: 12/12/2022]
Abstract
The prevalence of methicillin-resitant Staphylococcus aureus (MRSA) in hospitals and the community poses an increasing health burden, which requires the discovery of alternative antimicrobials. Allicin (diallyl thiosulfinate) from garlic exhibits broad-spectrum antimicrobial activity against many multidrug resistant bacteria. The thiol-reactive mode of action of allicin involves its S-thioallylations of low molecular weight (LMW) thiols and protein thiols. To investigate the mode of action and stress response caused by allicin in S. aureus, we analyzed the transcriptome signature, the targets for S-thioallylation in the proteome and the changes in the bacillithiol (BSH) redox potential (EBSH) under allicin stress. Allicin caused a strong thiol-specific oxidative and sulfur stress response and protein damage as revealed by the induction of the PerR, HypR, QsrR, MhqR, CstR, CtsR, HrcA and CymR regulons in the RNA-seq transcriptome. Allicin also interfered with metal and cell wall homeostasis and caused induction of the Zur, CsoR and GraRS regulons. Brx-roGFP2 biosensor measurements revealed a strongly increased EBSH under allicin stress. In the proteome, 57 proteins were identified with S-thioallylations under allicin treatment, including translation factors (EF-Tu, EF-Ts), metabolic and redox enzymes (AldA, GuaB, Tpx, KatA, BrxA, MsrB) as well as redox-sensitive MarR/SarA-family regulators (MgrA, SarA, SarH1, SarS). Phenotype and biochemical analyses revealed that BSH and the HypR-controlled disulfide reductase MerA are involved in allicin detoxification in S. aureus. The reversal of protein S-thioallylation was catalyzed by the Brx/BSH/YpdA pathway. Finally, the BSSB reductase YpdA was shown to use S-allylmercaptobacillithiol (BSSA) as substrate to regenerate BSH in S. aureus. In conclusion, allicin results in an oxidative shift of EBSH and protein S-thioallylation, which can be reversed by YpdA and the Brx/BSH/YpdA electron pathways in S. aureus to regenerate thiol homeostasis.
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Affiliation(s)
- Vu Van Loi
- Freie Universität Berlin, Institute for Biology-Microbiology, D-14195, Berlin, Germany
| | - Nguyen Thi Thu Huyen
- Freie Universität Berlin, Institute for Biology-Microbiology, D-14195, Berlin, Germany
| | - Tobias Busche
- Freie Universität Berlin, Institute for Biology-Microbiology, D-14195, Berlin, Germany; Center for Biotechnology, Bielefeld University, D-33594, Bielefeld, Germany
| | - Quach Ngoc Tung
- Freie Universität Berlin, Institute for Biology-Microbiology, D-14195, Berlin, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, D-33594, Bielefeld, Germany
| | - Jörg Bernhardt
- Freie Universität Berlin, Institute for Biology-Microbiology, D-14195, Berlin, Germany; Institute for Microbiology, University of Greifswald, D-17489, Greifswald, Germany
| | - Alan John Slusarenko
- Department of Plant Physiology, RWTH Aachen University, D-52056, Aachen, Germany
| | - Haike Antelmann
- Freie Universität Berlin, Institute for Biology-Microbiology, D-14195, Berlin, Germany.
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498
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Wu J, Jiang Q, Zhu H, Zhou Y, Lu D, Liu X, Chen X, Chen J, Wang Y, Liu J, Song R, Huang R, Zhou H. Uncovering kappa-opioid receptor agonist-induced PAK1/2 phosphorylation by quantitative phosphoproteomics. Biochem Biophys Res Commun 2019; 516:320-326. [DOI: 10.1016/j.bbrc.2019.06.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022]
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499
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Vamathevan J, Apweiler R, Birney E. Biomolecular Data Resources: Bioinformatics Infrastructure for Biomedical Data Science. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-072018-021321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Technological advances have continuously driven the generation of bio-molecular data and the development of bioinformatics infrastructure, which enables data reuse for scientific discovery. Several types of data management resources have arisen, such as data deposition databases, added-value databases or knowledgebases, and biology-driven portals. In this review, we provide a unique overview of the gradual evolution of these resources and discuss the goals and features that must be considered in their development. With the increasing application of genomics in the health care context and with 60 to 500 million whole genomes estimated to be sequenced by 2022, biomedical research infrastructure is transforming, too. Systems for federated access, portable tools, provision of reference data, and interpretation tools will enable researchers to derive maximal benefits from these data. Collaboration, coordination, and sustainability of data resources are key to ensure that biomedical knowledge management can scale with technology shifts and growing data volumes.
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Affiliation(s)
- Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Rolf Apweiler
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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500
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Jobin PG, Solis N, Machado Y, Bell PA, Kwon NH, Kim S, Overall CM, Butler GS. Matrix metalloproteinases inactivate the proinflammatory functions of secreted moonlighting tryptophanyl-tRNA synthetase. J Biol Chem 2019; 294:12866-12879. [PMID: 31324718 DOI: 10.1074/jbc.ra119.009584] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/11/2019] [Indexed: 01/08/2023] Open
Abstract
Tryptophanyl-tRNA synthetase (WRS) is a cytosolic aminoacyl-tRNA synthetase essential for protein synthesis. WRS is also one of a growing number of intracellular proteins that are attributed distinct noncanonical "moonlighting" functions in the extracellular milieu. Moonlighting aminoacyl-tRNA synthetases regulate processes such as inflammation, but how these multifunctional enzymes are themselves regulated remains unclear. Here, we demonstrate that WRS is secreted from human macrophages, fibroblasts, and endothelial cells in response to the proinflammatory cytokine interferon γ (IFNγ). WRS signaled primarily through Toll-like receptor 2 (TLR2) in macrophages, leading to phosphorylation of the p65 subunit of NF-κB with associated loss of NF-κB inhibitor α (IκB-α) protein. This signaling initiated secretion of tumor necrosis factor α (TNFα) and CXCL8 (IL8) from macrophages. We also demonstrated that WRS is a potent monocyte chemoattractant. Of note, WRS increased matrix metalloproteinase (MMP) activity in the conditioned medium of macrophages in a TNFα-dependent manner. Using purified recombinant proteins and LC-MS/MS to identify proteolytic cleavage sites, we demonstrated that multiple MMPs, but primarily macrophage MMP7 and neutrophil MMP8, cleave secreted WRS at several sites. Loss of the WHEP domain following cleavage at Met48 generated a WRS proteoform that also results from alternative splicing, designated Δ1-47 WRS. The MMP-cleaved WRS lacked TLR signaling and proinflammatory activities. Thus, our results suggest that moonlighting WRS promotes IFNγ proinflammatory activities, and these responses can be dampened by MMPs.
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Affiliation(s)
- Parker G Jobin
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nestor Solis
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, 2199 Wesbrook Mall, Faculty of Dentistry, Vancouver, British Columbia V6T 1Z3, Canada
| | - Yoan Machado
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, 2199 Wesbrook Mall, Faculty of Dentistry, Vancouver, British Columbia V6T 1Z3, Canada
| | - Peter A Bell
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, 2199 Wesbrook Mall, Faculty of Dentistry, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nam Hoon Kwon
- College of Pharmacy, Seoul National University, 151-742 Seoul, Republic of Korea; Medicinal Bioconvergance Research Center, Seoul National University, 151-742 Seoul, Republic of Korea
| | - Sunghoon Kim
- College of Pharmacy, Seoul National University, 151-742 Seoul, Republic of Korea; Medicinal Bioconvergance Research Center, Seoul National University, 151-742 Seoul, Republic of Korea
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, 2199 Wesbrook Mall, Faculty of Dentistry, Vancouver, British Columbia V6T 1Z3, Canada.
| | - Georgina S Butler
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, 2199 Wesbrook Mall, Faculty of Dentistry, Vancouver, British Columbia V6T 1Z3, Canada
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