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Ahmad S, Verli H. In silico identification of drug targets and vaccine candidates against Bartonella quintana: a subtractive proteomics approach. Mem Inst Oswaldo Cruz 2024; 119:e230040. [PMID: 38655925 PMCID: PMC11034861 DOI: 10.1590/0074-02760230040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 02/29/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND The availability of genes and protein sequences for parasites has provided valuable information for drug target identification and vaccine development. One such parasite is Bartonella quintana, a Gram-negative, intracellular pathogen that causes bartonellosis in mammalian hosts. OBJECTIVE Despite progress in understanding its pathogenesis, limited knowledge exists about the virulence factors and regulatory mechanisms specific to B. quintana. METHODS AND FINDINGS To explore these aspects, we have adopted a subtractive proteomics approach to analyse the proteome of B. quintana. By subtractive proteins between the host and parasite proteome, a set of proteins that are likely unique to the parasite but absent in the host were identified. This analysis revealed that out of the 1197 protein sequences of the parasite, 660 proteins are non-homologous to the human host. Further analysis using the Database of Essential Genes predicted 159 essential proteins, with 28 of these being unique to the pathogen and predicted as potential putative targets. Subcellular localisation of the predicted targets revealed 13 cytoplasmic, eight membranes, one periplasmic, and multiple location proteins. The three-dimensional structure and B cell epitopes of the six membrane antigenic protein were predicted. Four B cell epitopes in KdtA and mraY proteins, three in lpxB and BQ09550, whereas the ftsl and yidC proteins were located with eleven and six B cell epitopes, respectively. MAINS CONCLUSIONS This insight prioritises such proteins as novel putative targets for further investigations on their potential as drug and vaccine candidates.
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Affiliation(s)
- Shabir Ahmad
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Porto Alegre, RS, Brasil
| | - Hugo Verli
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Porto Alegre, RS, Brasil
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2
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Zhang X, Su Z, Zhao Y, Wu D, Wu Y, Li G. Recent advances of nanopore technique in single cell analysis. Analyst 2024; 149:1350-1363. [PMID: 38312056 DOI: 10.1039/d3an01973j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Single cells and their dynamic behavior are closely related to biological research. Monitoring their dynamic behavior is of great significance for disease prevention. How to achieve rapid and non-destructive monitoring of single cells is a major issue that needs to be solved urgently. As an emerging technology, nanopores have been proven to enable non-destructive and label-free detection of single cells. The structural properties of nanopores enable a high degree of sensitivity and accuracy during analysis. In this article, we summarize and classify the different types of solid-state nanopores that can be used for single-cell detection and illustrate their specific applications depending on the size of the analyte. In addition, their research progress in material transport and microenvironment monitoring is also highlighted. Finally, a brief summary of existing research challenges and future trends in nanopore single-cell analysis is tentatively provided.
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Affiliation(s)
- Xue Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Zhuoqun Su
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Yan Zhao
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Yongning Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
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3
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Plou J, Valera PS, García I, Vila-Liarte D, Renero-Lecuna C, Ruiz-Cabello J, Carracedo A, Liz-Marzán LM. Machine Learning-Assisted High-Throughput SERS Classification of Cell Secretomes. Small 2023; 19:e2207658. [PMID: 37046181 DOI: 10.1002/smll.202207658] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/25/2023] [Indexed: 06/19/2023]
Abstract
During the response to different stress conditions, damaged cells react in multiple ways, including the release of a diverse cocktail of metabolites. Moreover, secretomes from dying cells can contribute to the effectiveness of anticancer therapies and can be exploited as predictive biomarkers. The nature of the stress and the resulting intracellular responses are key determinants of the secretome composition, but monitoring such processes remains technically arduous. Hence, there is growing interest in developing tools for noninvasive secretome screening. In this regard, it has been previously shown that the relative concentrations of relevant metabolites can be traced by surface-enhanced Raman scattering (SERS), thereby allowing label-free biofluid interrogation. However, conventional SERS approaches are insufficient to tackle the requirements imposed by high-throughput modalities, namely fast data acquisition and automatized analysis. Therefore, machine learning methods were implemented to identify cell secretome variations while extracting standard features for cell death classification. To this end, ad hoc microfluidic chips were devised, to readily conduct SERS measurements through a prototype relying on capillary pumps made of filter paper, which eventually would function as the SERS substrates. The developed strategy may pave the way toward a faster implementation of SERS into cell secretome classification, which can be extended even to laboratories lacking highly specialized facilities.
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Affiliation(s)
- Javier Plou
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Donostia-San Sebastián, 20014, Spain
| | - Pablo S Valera
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Donostia-San Sebastián, 20014, Spain
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, 48160, Spain
- Department of Applied Chemistry, University of the Basque Country, Donostia, 20018, Spain
| | - Isabel García
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Donostia-San Sebastián, 20014, Spain
| | - David Vila-Liarte
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Donostia-San Sebastián, 20014, Spain
| | - Carlos Renero-Lecuna
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Donostia-San Sebastián, 20014, Spain
| | - Jesús Ruiz-Cabello
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48009, Spain
- Biomedical Research Networking Center in Respiratory Diseases (CIBERES), Madrid, 28029, Spain
- Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Arkaitz Carracedo
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, 48160, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48009, Spain
- Biomedical Research Networking Center in Cancer (CIBERONC), Derio, 48160, Spain
- Translational Prostate Cancer Research Lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute, Derio, 48160, Spain
| | - Luis M Liz-Marzán
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Donostia-San Sebastián, 20014, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48009, Spain
- Cinbio, Universidade de Vigo, Vigo, 36310, Spain
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4
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Knecht S, Eberl HC, Kreisz N, Ugwu UJ, Starikova T, Kuster B, Wilhelm S. An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry-Based Secretomics. Mol Cell Proteomics 2023; 22:100636. [PMID: 37597723 PMCID: PMC10518356 DOI: 10.1016/j.mcpro.2023.100636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
The active release of proteins into the extracellular space and the proteolytic cleavage of cell surface proteins are key processes that coordinate and fine-tune a multitude of physiological functions. The entirety of proteins that fulfill these extracellular tasks are referred to as the secretome and are of special interest for the investigation of biomarkers of disease states and physiological processes related to cell-cell communication. LC-MS-based proteomics approaches are a valuable tool for the comprehensive and unbiased characterization of this important subproteome. This review discusses procedures, opportunities, and limitations of mass spectrometry-based secretomics to better understand and navigate the complex analytical landscape for studying protein secretion in biomedical science.
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Affiliation(s)
- Sascha Knecht
- Omics Sciences, Genomic Sciences, GlaxoSmithKline, Heidelberg, Germany; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - H Christian Eberl
- Omics Sciences, Genomic Sciences, GlaxoSmithKline, Heidelberg, Germany
| | - Norbert Kreisz
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Ukamaka Juliet Ugwu
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Tatiana Starikova
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
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5
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Kirschner F, Arnold-Schild D, Leps C, Łącki MK, Klein M, Chen Y, Ludt A, Marini F, Kücük C, Stein L, Distler U, Sielaff M, Michna T, Riegel K, Rajalingam K, Bopp T, Tenzer S, Schild H. Modulation of cellular transcriptome and proteome composition by azidohomoalanine-implications on click chemistry-based secretome analysis. J Mol Med (Berl) 2023; 101:855-867. [PMID: 37231147 PMCID: PMC10300158 DOI: 10.1007/s00109-023-02333-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/25/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
The analysis of the secretome provides important information on proteins defining intercellular communication and the recruitment and behavior of cells in specific tissues. Especially in the context of tumors, secretome data can support decisions for diagnosis and therapy. The mass spectrometry-based analysis of cell-conditioned media is widely used for the unbiased characterization of cancer secretomes in vitro. Metabolic labeling using azide-containing amino acid analogs in combination with click chemistry facilitates this type of analysis in the presence of serum, preventing serum starvation-induced effects. The modified amino acid analogs, however, are less efficiently incorporated into newly synthesized proteins and may perturb protein folding. Combining transcriptome and proteome analysis, we elucidate in detail the effects of metabolic labeling with the methionine analog azidohomoalanine (AHA) on gene and protein expression. Our data reveal that 15-39% of the proteins detected in the secretome displayed changes in transcript and protein expression induced by AHA labeling. Gene Ontology (GO) analyses indicate that metabolic labeling using AHA leads to induction of cellular stress and apoptosis-related pathways and provide first insights on how this affects the composition of the secretome on a global scale. KEY MESSAGES: Azide-containing amino acid analogs affect gene expression profiles. Azide-containing amino acid analogs influence cellular proteome. Azidohomoalanine labeling induces cellular stress and apoptotic pathways. Secretome consists of proteins with dysregulated expression profiles.
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Affiliation(s)
- Friederike Kirschner
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Danielle Arnold-Schild
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Christian Leps
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Mateusz Krzysztof Łącki
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Matthias Klein
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Yannic Chen
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany
| | - Annekathrin Ludt
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Can Kücük
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany
| | - Lara Stein
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Malte Sielaff
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Thomas Michna
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Kristina Riegel
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tobias Bopp
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- University Cancer Center Mainz, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany.
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany.
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany.
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany.
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
- University Cancer Center Mainz, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
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Feser R, Opperman RM, Nault B, Maiti S, Chen VC, Majumder M. Breast cancer cell secretome analysis to decipher miRNA regulating the tumor microenvironment and discover potential biomarkers. Heliyon 2023; 9:e15421. [PMID: 37128318 PMCID: PMC10148110 DOI: 10.1016/j.heliyon.2023.e15421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 05/03/2023] Open
Abstract
MicroRNA (miRNA/miR) 526 b- and miR655-overexpressed tumor cell-free secretions regulate the breast cancer tumor microenvironment (TME) by promoting tumor-associated angiogenesis, oxidative stress, and hypoxic responses. Additionally, premature miRNA (pri-miR526b and pri-miR655) are established breast cancer blood biomarkers. However, the mechanisms of how these miRNAs regulate the TME has yet to be investigated. Mass spectrometry analysis of miRNA-overexpressed cell lines MCF7-miR526b, MCF7-miR655, and miRNA-low MCF7-Mock cell-free secretomes identified 34 differentially expressed proteins coded by eight genes. In both miRNA-high cell secretomes, four markers are upregulated: YWHAB, SFN, TXNDC12, and MYL6B, and four are downregulated: PEA15, PRDX4, PSMB6, and FN1. All upregulated marker transcripts are significantly high in both total cellular RNA pool and cell-free secretions of miRNA-high cell lines, validated with quantitative RT-PCR. Bioinformatics tools were used to investigate these markers' roles in breast cancer. These markers' top gene ontology functions are related to apoptosis, oxidative stress, membrane transport, and motility supporting oncogenic miR526b- and miR655-induced functions. Gene transcription factor analysis tools were used to show how these miRNAs regulate the expression of each secretory marker. Data extracted from the Human Protein Atlas showed that YWHAB, SFN, and TXNDC12 expression could distinguish early and late-stage breast cancer in various breast cancer subtypes and are associated with poor patient survival. Additionally, immunohistochemistry analysis showed the expression of each marker in breast tumors. A stronger correlation between miRNA clusters and upregulated secretory markers gene expression was found in the luminal A tumor subtype. YWHAB, SFN, and MYL6B are upregulated in breast cancer patient's blood, showing biomarker potential. Of these identified novel miRNA secretory markers, SFN and YWHAB successfully passed all validations and are the best candidates to further investigate their roles in miRNA associated TME regulation. Also, these markers show the potential to serve as blood-based breast cancer biomarkers, especially for luminal-A subtypes.
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Affiliation(s)
- Riley Feser
- Department of Biology, Brandon University, 3rd Floor, John R. Brodie Science Centre, 270 18th Street, Brandon, MB, Canada, R7A 6A9
| | - Reid M. Opperman
- Department of Biology, Brandon University, 3rd Floor, John R. Brodie Science Centre, 270 18th Street, Brandon, MB, Canada, R7A 6A9
| | - Braydon Nault
- Department of Biology, Brandon University, 3rd Floor, John R. Brodie Science Centre, 270 18th Street, Brandon, MB, Canada, R7A 6A9
| | - Sujit Maiti
- Department of Biology, Brandon University, 3rd Floor, John R. Brodie Science Centre, 270 18th Street, Brandon, MB, Canada, R7A 6A9
| | - Vincent C. Chen
- Department of Chemistry, Brandon University, 4th Floor, John R. Brodie Science Centre, 270 18th Street, Brandon, MB, Canada, R7A 6A9
| | - Mousumi Majumder
- Department of Biology, Brandon University, 3rd Floor, John R. Brodie Science Centre, 270 18th Street, Brandon, MB, Canada, R7A 6A9
- Corresponding author.
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7
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Katta M, Mathew BA, Chaturvedi P, Ludhiadch A, Munshi A. Advanced molecular therapies for neurological diseases: focus on stroke, alzheimer's disease, and parkinson's disease. Neurol Sci 2023; 44:19-36. [PMID: 36066674 DOI: 10.1007/s10072-022-06356-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/16/2022] [Indexed: 01/10/2023]
Abstract
Neurological diseases (NDs) are one of the leading causes of disability and the second leading cause of death globally. Among these stroke, Alzheimer's disease (AD), and Parkinson's disease (PD) are the most common NDs. A rise in the absolute number of individuals affected with these diseases indicates that the current treatment strategies in management and prevention of these debilitating diseases are not effective sufficiently. Therefore, novel treatment strategies are being explored to cure these diseases by addressing the causative mechanisms at the molecular level. Advanced therapies like gene therapy (gene editing and gene silencing) and stem cell therapies aim to cure diseases by gene editing, gene silencing and tissue regeneration, respectively. Gene editing results in the deletion of the aberrant gene or insertion of the corrected gene which can be executed using the CRISPR/Cas gene editing tool a promising treatment strategy being explored for many other prevalent diseases. Gene silencing using siRNA silences the gene by inhibiting protein translation, thereby silencing its expression. Stem cell therapy aims to regenerate damaged cells or tissues because of their ability to divide into any type of cell in the human body. Among these approaches, gene editing and gene silencing have currently been applied in vitro and to animal models, while stem cell therapy has reached the clinical trial stage for the treatment of NDs. The current status of these strategies suggests a promising outcome in their clinical translation.
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Padgaonkar M, Shendre S, Chatterjee P, Banerjee S. Cancer secretome: finding out hidden messages in extracellular secretions. Clin Transl Oncol 2022. [PMID: 36525229 DOI: 10.1007/s12094-022-03027-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022]
Abstract
Secretome analysis has gained popularity recently as a very well-designed proteomic approach that is being used to study various interactions and their effects on cellular activity. This analysis is especially helpful while studying the effects of the cells on their microenvironment, paracrine and autocrine processes, their therapeutic purposes, and as a new diagnostic perspective. Cancer is a condition rather than a specific type of disease and is still yet to be fully understood. Cancer secretome is a fairly new concept that is being implemented to examine the interactions taking place in the tumor microenvironment and can help to understand the phenomena like induction of tumorigenesis, stimulation of immune cells, etc. The secretome analysis helps to gain a different perspective on the existing knowledge on cancer and its effects. The recent advances in secretome studies are directed toward secreted components as drug targets, biomarkers, and companion tools for diagnostic and prognostic purposes in cancer. This review aims to find the interactors in different types of cancer and understand the existing unstructured secretome data and its application in prognosis, diagnosis, and in biomarker study.
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Zubair M, Wang J, Yu Y, Faisal M, Qi M, Shah AU, Feng Z, Shao G, Wang Y, Xiong Q. Proteomics approaches: A review regarding an importance of proteome analyses in understanding the pathogens and diseases. Front Vet Sci 2022; 9:1079359. [PMID: 36601329 PMCID: PMC9806867 DOI: 10.3389/fvets.2022.1079359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Proteomics is playing an increasingly important role in identifying pathogens, emerging and re-emerging infectious agents, understanding pathogenesis, and diagnosis of diseases. Recently, more advanced and sophisticated proteomics technologies have transformed disease diagnostics and vaccines development. The detection of pathogens is made possible by more accurate and time-constrained technologies, resulting in an early diagnosis. More detailed and comprehensive information regarding the proteome of any noxious agent is made possible by combining mass spectrometry with various gel-based or short-gun proteomics approaches recently. MALDI-ToF has been proved quite useful in identifying and distinguishing bacterial pathogens. Other quantitative approaches are doing their best to investigate bacterial virulent factors, diagnostic markers and vaccine candidates. Proteomics is also helping in the identification of secreted proteins and their virulence-related functions. This review aims to highlight the role of cutting-edge proteomics approaches in better understanding the functional genomics of pathogens. This also underlines the limitations of proteomics in bacterial secretome research.
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Affiliation(s)
- Muhammad Zubair
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jia Wang
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yanfei Yu
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China,School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Faisal
- Division of Hematology, Department of Medicine, The Ohio State University College of Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Mingpu Qi
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Abid Ullah Shah
- National Research Centre of Engineering and Technology for Veterinary Biologicals, Institute of Veterinary Immunology and Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhixin Feng
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Guoqing Shao
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China,School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yu Wang
- China Pharmaceutical University, Nanjing, China,*Correspondence: Yu Wang
| | - Qiyan Xiong
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China,School of Life Sciences, Jiangsu University, Zhenjiang, China,Qiyan Xiong
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10
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Gianazza E, Brioschi M, Eligini S, Banfi C. Mass spectrometry for the study of adipocyte cell secretome in cardiovascular diseases. Mass Spectrom Rev 2022:e21812. [PMID: 36161723 DOI: 10.1002/mas.21812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/04/2022] [Accepted: 09/03/2022] [Indexed: 06/16/2023]
Abstract
Adipose tissue is classically considered the primary site of lipid storage, but in recent years has garnered appreciation for its broad role as an endocrine organ, capable of remotely signaling to other tissues to alter their metabolic program. The adipose tissue is now recognized as a crucial regulator of cardiovascular health, mediated by the secretion of several bioactive products, with a wide range of endocrine and paracrine effects on the cardiovascular system. Thanks to the development and improvement of high-throughput mass spectrometry, the size and components of the human secretome have been characterized. In this review, we summarized the recent advances in mass spectrometry-based studies of the cell and tissue secretome for the understanding of adipose tissue biology, which may help to decipher the complex molecular mechanisms controlling the crosstalk between the adipose tissue and the cardiovascular system, and their possible clinical translation.
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Affiliation(s)
- Erica Gianazza
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
| | - Maura Brioschi
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
| | - Sonia Eligini
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
| | - Cristina Banfi
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
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Azimzadeh O, Moertl S, Ramadan R, Baselet B, Laiakis EC, Sebastian S, Beaton D, Hartikainen JM, Kaiser JC, Beheshti A, Salomaa S, Chauhan V, Hamada N. Application of radiation omics in the development of adverse outcome pathway networks: an example of radiation-induced cardiovascular disease. Int J Radiat Biol 2022; 98:1722-1751. [PMID: 35976069 DOI: 10.1080/09553002.2022.2110325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Epidemiological studies have indicated that exposure of the heart to doses of ionizing radiation as low as 0.5 Gy increases the risk of cardiac morbidity and mortality with a latency period of decades. The damaging effects of radiation to myocardial and endothelial structures and functions have been confirmed radiobiologically at high dose, but much less is known at low dose. Integration of radiation biology and epidemiology data is a recommended approach to improve the radiation risk assessment process. The adverse outcome pathway (AOP) framework offers a comprehensive tool to compile and translate mechanistic information into pathological endpoints which may be relevant for risk assessment at the different levels of a biological system. Omics technologies enable the generation of large volumes of biological data at various levels of complexity, from molecular pathways to functional organisms. Given the quality and quantity of available data across levels of biology, omics data can be attractive sources of information for use within the AOP framework. It is anticipated that radiation omics studies could improve our understanding of the molecular mechanisms behind the adverse effects of radiation on the cardiovascular system. In this review, we explored the available omics studies on radiation-induced cardiovascular disease (CVD) and their applicability to the proposed AOP for CVD. RESULTS The results of 80 omics studies published on radiation-induced CVD over the past 20 years have been discussed in the context of the AOP of CVD proposed by Chauhan et al. Most of the available omics data on radiation-induced CVD are from proteomics, transcriptomics, and metabolomics, whereas few datasets were available from epigenomics and multi-omics. The omics data presented here show great promise in providing information for several key events of the proposed AOP of CVD, particularly oxidative stress, alterations of energy metabolism, extracellular matrix and vascular remodeling. CONCLUSIONS The omics data presented here shows promise to inform the various levels of the proposed AOP of CVD. However, the data highlight the urgent need of designing omics studies to address the knowledge gap concerning different radiation scenarios, time after exposure and experimental models. This review presents the evidence to build a qualitative omics-informed AOP and provides views on the potential benefits and challenges in using omics data to assess risk-related outcomes.
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Affiliation(s)
- Omid Azimzadeh
- Federal Office for Radiation Protection (BfS), Section Radiation Biology, 85764 Neuherberg, Germany
| | - Simone Moertl
- Federal Office for Radiation Protection (BfS), Section Radiation Biology, 85764 Neuherberg, Germany
| | - Raghda Ramadan
- Institute for Environment, Health and Safety, Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Bjorn Baselet
- Institute for Environment, Health and Safety, Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Evagelia C Laiakis
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | | | | | - Jaana M Hartikainen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
| | - Jan Christian Kaiser
- Helmholtz Zentrum München, Institute of Radiation Medicine (HMGU-IRM), 85764 Neuherberg, Germany
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sisko Salomaa
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Vinita Chauhan
- Environmental Health Science Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Nobuyuki Hamada
- Biology and Environmental Chemistry Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), Komae, Tokyo 201-8511, Japan
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12
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Knecht S, Eberl HC, Bantscheff M. Interval-Based Secretomics Unravels Acute-Phase Response in Hepatocyte Model Systems. Mol Cell Proteomics 2022; 21:100241. [PMID: 35525403 PMCID: PMC9184749 DOI: 10.1016/j.mcpro.2022.100241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 11/21/2022] Open
Abstract
Mass spectrometry-based secretomics approaches frequently utilize serum-free culture conditions to circumvent serum-induced interference and to increase analytical depth. However, this can negatively affect a wide range of cellular functions and cell viability. These effects become particularly apparent when investigating transcriptionally regulated secretion events and feedback-loops in response to perturbations that require 48 h or more to fully manifest. We present an “interval-based” secretomics workflow, which determines protein secretion rates in short serum-free time windows. Relative quantification using tandem mass tags enables precise monitoring of time-dependent changes. We applied this approach to determine temporal profiles of protein secretion in the hepatocyte model cell lines HepG2 and HepaRG after stimulation of the acute-phase response (APR) by the cytokines IL1b and IL6. While the popular hepatocarcinoma cell line HepG2 showed an incomplete APR, secretion patterns derived from differentiated HepaRG cells recapitulated the expected APR more comprehensively. For several APR response proteins, substantial secretion was only observed after 72 h, a time window at which cell fitness is substantially impaired under serum-free cell culture conditions. The interval-based secretomics approach enabled the first comprehensive analysis of time-dependent secretion of liver cell models in response to these proinflammatory cytokines. The extended time range facilitated the observation of distinct chronological phases and cytokine-dependent secretion phenotypes of the APR. IL1b directed the APR toward pathogen defense over three distinct phases—chemotaxis, effector, clearance—while IL6 directed the APR toward regeneration. Protein shedding on the cell surface was pronounced upon IL1b stimulation, and small molecule inhibition of ADAM and matrix metalloproteases identified induced as well as constitutive shedding events. Inhibition of ADAM proteases with TAPI-0 resulted in reduced shedding of the sorting receptor SORT1, and an attenuated cytokine response suggesting a direct link between cell surface shedding and cytokine secretion rates. Interval-based secretomics enables extended time course analysis. Time-resolved acute phase response in liver model systems HepG2 and HepaRG. IL1b response clusters in three phases. Cell surface shedding is amplified during acute-phase response. ADAM inhibition dampens secretion of inflammatory cytokines.
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Affiliation(s)
- Sascha Knecht
- Cellzome GmbH, GlaxoSmithKline (GSK), Heidelberg, Germany
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13
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Poschmann G, Bahr J, Schrader J, Stejerean-Todoran I, Bogeski I, Stühler K. Secretomics—A Key to a Comprehensive Picture of Unconventional Protein Secretion. Front Cell Dev Biol 2022; 10:878027. [PMID: 35392176 PMCID: PMC8980719 DOI: 10.3389/fcell.2022.878027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/07/2022] [Indexed: 12/20/2022] Open
Abstract
For a long time, leaderless secreted proteins (LLSP) were neglected as artifacts derived from dying cells. It is now generally accepted that secretion of LLSP–as a part of the collective term unconventional protein secretion (UPS) - is an evolutionarily conserved process and that these LLSP are actively and selectively secreted from living cells bypassing the classical endoplasmic reticulum-Golgi pathway. However, the mechanism of UPS pathways, as well as the number of LLSP and which part of a protein is involved in the selection of LLSPs for secretion, are still enigmatic and await clarification. Secretomics-a proteomics-based approach to identify and quantify all proteins secreted by a cell-is inherently unbiased toward a particular secretion pathway and offers the opportunity to shed light on the UPS. Here, we will evaluate and present recent results of proteomic workflows allowing to obtain high-confident secretome data. Additionally, we address that cell culture conditions largely affect the composition of the secretome. This has to be kept in mind to control cell culture induced artifacts and adaptation stress in serum free conditions. Evaluation of click chemistry for secretome analysis of cells under serum-containing conditions showed a significant change in the cellular proteome with longer incubation time upon treatment with non-canonical amino acid azidohomoalanine. Finally, we showed that the number of LLSP far exceeds the number of secreted proteins annotated in Uniprot and ProteinAtlas. Thus, secretomics in combination with sophisticated microbioanalytical and sample preparation methods is well suited to provide a comprehensive picture of UPS.
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Affiliation(s)
- Gereon Poschmann
- Institute for Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Jasmin Bahr
- Department of Molecular Cardiology, University Hospital and Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Jürgen Schrader
- Department of Molecular Cardiology, University Hospital and Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Ioana Stejerean-Todoran
- Molecular Physiology, Institute for Cardiovascular Physiology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Ivan Bogeski
- Molecular Physiology, Institute for Cardiovascular Physiology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Kai Stühler
- Institute for Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Molecular Proteomics Laboratory, Biological Medical Research Center, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- *Correspondence: Kai Stühler,
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14
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Morretta E, D'Agostino A, Cassese E, Maglione B, Petrella A, Schiraldi C, Monti MC. Label-Free Quantitative Proteomics to Explore the Action Mechanism of the Pharmaceutical-Grade Triticum vulgare Extract in Speeding Up Keratinocyte Healing. Molecules 2022; 27:1108. [PMID: 35164377 DOI: 10.3390/molecules27031108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/21/2022] [Accepted: 02/01/2022] [Indexed: 02/07/2023]
Abstract
Plant extracts have shown beneficial properties in terms of skin repair, promoting wound healing through a plethora of mechanisms. In particular, the poly-/oligosaccharidic aqueous extract of Triticum vulgare (TVE), as well as TVE-based products, shows interesting biological assets, hastening wound repair. Indeed, TVE acts in the treatment of tissue regeneration mainly on decubitus and venous leg ulcers. Moreover, on scratched monolayers, TVE prompts HaCat cell migration, correctly modulating the expression of metalloproteases toward a physiological matrix remodeling. Here, using the same HaCat-based in vitro scratch model, the TVE effect has been investigated thanks to an LFQ proteomic analysis of HaCat secretomes and immunoblotting. Indeed, the unbiased TVE effect on secreted proteins has not yet been fully understood, and it could be helpful to obtain a comprehensive picture of its bio-pharmacological profile. It has emerged that TVE treatment induces significant up-regulation of several proteins in the secretome (153 to be exact) whereas only a few were down-regulated (72 to be exact). Interestingly, many of the up-regulated proteins are implicated in promoting wound-healing-related processes, such as modulating cell-cell interaction and communication, cell proliferation and differentiation, and prompting cell adhesion and migration.
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15
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Crescenzi E, Leonardi A, Pacifico F. NGAL as a Potential Target in Tumor Microenvironment. Int J Mol Sci 2021; 22:12333. [DOI: 10.3390/ijms222212333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
The signaling network between cancer and stromal cells plays a crucial role in tumor microenvironment. The fate of tumor progression mainly depends on the huge amount of information that these cell populations exchange from the onset of neoplastic transformation. Interfering with such signaling has been producing exciting results in cancer therapy: just think of anti-PD-1/anti-PD-L1/anti-CTLA-4 antibodies that, acting as immune checkpoint inhibitors, interrupt the inhibitory signaling exerted by cancer cells on immune cells or the CAR-T technology that fosters the reactivation of anti-tumoral immunity in a restricted group of leukemias and lymphomas. Nevertheless, many types of cancers, in particular solid tumors, are still refractory to these treatments, so the identification of novel molecular targets in tumor secretome would benefit from implementation of current anti-cancer therapeutical strategies. Neutrophil Gelatinase-Associated Lipocalin (NGAL) is a secreted protein abundantly expressed in the secretome of various human tumors. It represents a promising target for the multiple roles that are played inside cancer and stromal cells, and also overall in their cross-talk. The review focuses on the different roles of NGAL in tumor microenvironment and in cancer senescence-associated secretory phenotype (SASP), highlighting the most crucial functions that could be eventually targetable in cancer therapy.
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16
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Crescenzi E, Leonardi A, Pacifico F. NGAL as a Potential Target in Tumor Microenvironment. Int J Mol Sci 2021; 22:12333. [PMID: 34830212 PMCID: PMC8623964 DOI: 10.3390/ijms222212333&set/a 915137580+984946846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
The signaling network between cancer and stromal cells plays a crucial role in tumor microenvironment. The fate of tumor progression mainly depends on the huge amount of information that these cell populations exchange from the onset of neoplastic transformation. Interfering with such signaling has been producing exciting results in cancer therapy: just think of anti-PD-1/anti-PD-L1/anti-CTLA-4 antibodies that, acting as immune checkpoint inhibitors, interrupt the inhibitory signaling exerted by cancer cells on immune cells or the CAR-T technology that fosters the reactivation of anti-tumoral immunity in a restricted group of leukemias and lymphomas. Nevertheless, many types of cancers, in particular solid tumors, are still refractory to these treatments, so the identification of novel molecular targets in tumor secretome would benefit from implementation of current anti-cancer therapeutical strategies. Neutrophil Gelatinase-Associated Lipocalin (NGAL) is a secreted protein abundantly expressed in the secretome of various human tumors. It represents a promising target for the multiple roles that are played inside cancer and stromal cells, and also overall in their cross-talk. The review focuses on the different roles of NGAL in tumor microenvironment and in cancer senescence-associated secretory phenotype (SASP), highlighting the most crucial functions that could be eventually targetable in cancer therapy.
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Affiliation(s)
- Elvira Crescenzi
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale, CNR, Via S. Pansini, 5-80131 Naples, Italy;
| | - Antonio Leonardi
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, “Federico II” University of Naples, Via S. Pansini, 5-80131 Naples, Italy;
| | - Francesco Pacifico
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale, CNR, Via S. Pansini, 5-80131 Naples, Italy;
- Correspondence:
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17
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Crescenzi E, Leonardi A, Pacifico F. NGAL as a Potential Target in Tumor Microenvironment. Int J Mol Sci 2021; 22:12333. [PMID: 34830212 DOI: 10.3390/ijms222212333] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 12/29/2022] Open
Abstract
The signaling network between cancer and stromal cells plays a crucial role in tumor microenvironment. The fate of tumor progression mainly depends on the huge amount of information that these cell populations exchange from the onset of neoplastic transformation. Interfering with such signaling has been producing exciting results in cancer therapy: just think of anti-PD-1/anti-PD-L1/anti-CTLA-4 antibodies that, acting as immune checkpoint inhibitors, interrupt the inhibitory signaling exerted by cancer cells on immune cells or the CAR-T technology that fosters the reactivation of anti-tumoral immunity in a restricted group of leukemias and lymphomas. Nevertheless, many types of cancers, in particular solid tumors, are still refractory to these treatments, so the identification of novel molecular targets in tumor secretome would benefit from implementation of current anti-cancer therapeutical strategies. Neutrophil Gelatinase-Associated Lipocalin (NGAL) is a secreted protein abundantly expressed in the secretome of various human tumors. It represents a promising target for the multiple roles that are played inside cancer and stromal cells, and also overall in their cross-talk. The review focuses on the different roles of NGAL in tumor microenvironment and in cancer senescence-associated secretory phenotype (SASP), highlighting the most crucial functions that could be eventually targetable in cancer therapy.
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18
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Moreira C, Hétru J, Paiola M, Duflot A, Chan P, Vaudry D, Pinto PIS, Monsinjon T, Knigge T. Proteomic changes in the extracellular environment of sea bass thymocytes exposed to 17α-ethinylestradiol in vitro. Comp Biochem Physiol Part D Genomics Proteomics 2021; 40:100911. [PMID: 34583305 DOI: 10.1016/j.cbd.2021.100911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/14/2021] [Accepted: 08/28/2021] [Indexed: 11/28/2022]
Abstract
The thymus is an important immune organ providing the necessary microenvironment for the development of a diverse, self-tolerant T cell repertoire, which is selected to allow for the recognition of foreign antigens while avoiding self-reactivity. Thymus function and activity are known to be regulated by sex steroid hormones, such as oestrogen, leading to sexual dimorphisms in immunocompetence between males and females. The oestrogenic modulation of the thymic function provides a potential target for environmental oestrogens, such as 17α-ethynylestradiol (EE2), to interfere with the cross-talk between the endocrine and the immune system. Oestrogen receptors have been identified on thymocytes and the thymic microenvironment, but it is unclear how oestrogens regulate thymic epithelial and T cell communication including paracrine signalling. Much less is known regarding intrathymic signalling in fish. Secretomics allows for the analysis of complex mixtures of immunomodulatory signalling factors secreted by T cells. Thus, in the present study, isolated thymocytes of the European sea bass, Dicentrarchus labrax, were exposed in vitro to 30 nM EE2 for 4 h and the T cell-secretome (i.e., extracellular proteome) was analysed by quantitative label-free mass-spectrometry. Progenesis revealed a total of 111 proteins differentially displayed between EE2-treated and control thymocytes at an α-level of 5% and a 1.3-fold change cut off (n = 5-6). The EE2-treatment significantly decreased the level of 90 proteins. Gene ontology revealed the proteasome to be the most impacted pathway. In contrast, the abundance of 21 proteins was significantly increased, with cathepsins showing the highest level of induction. However, no particular molecular pathway was significantly altered for these upregulated proteins. To the best of our knowledge, this work represents the first study of the secretome of the fish thymus exposed to the environmental oestrogen EE2, highlighting the impact on putative signalling pathways linked to immune surveillance, which may be of crucial importance for fish health and defence against pathogens.
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Affiliation(s)
- Catarina Moreira
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600 Le Havre, France
| | - Julie Hétru
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600 Le Havre, France
| | - Matthieu Paiola
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600 Le Havre, France; Department of Microbiology and Immunology, University of Rochester Medical Center, 14642 Rochester, NY, United States
| | - Aurélie Duflot
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600 Le Havre, France
| | - Philippe Chan
- Normandie Univ, UNIROUEN, PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UNIROUEN, Institute for Research and Innovation in Biomedicine (IRIB), F-76183 Rouen, France
| | - David Vaudry
- Normandie Univ, UNIROUEN, PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UNIROUEN, Neuronal and Neuroendocrine Differentiation and Communication (DC2N), Inserm U1239, 76821 Mont-Saint-Aignan, France; Normandie Univ, UNIROUEN, Institute for Research and Innovation in Biomedicine (IRIB), F-76183 Rouen, France
| | - Patrícia I S Pinto
- Centro de Ciências Do Mar (CCMAR), Universidade Do Algarve, 8005-139 Faro, Portugal
| | - Tiphaine Monsinjon
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600 Le Havre, France
| | - Thomas Knigge
- Normandie Univ, UNILEHAVRE, FR CNRS 3730 SCALE, UMR-I 02 Environmental Stress and Aquatic Biomonitoring (SEBIO), F-76600 Le Havre, France.
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Etxebeste-Mitxeltorena M, Del Rincón-Loza I, Martín-Antonio B. Tumor Secretome to Adoptive Cellular Immunotherapy: Reduce Me Before I Make You My Partner. Front Immunol 2021; 12:717850. [PMID: 34447383 PMCID: PMC8382692 DOI: 10.3389/fimmu.2021.717850] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/26/2021] [Indexed: 12/11/2022] Open
Abstract
Adoptive cellular immunotherapy using chimeric antigen receptor (CAR)-modified T cells and Natural Killer (NK) cells are common immune cell sources administered to treat cancer patients. In detail, whereas CAR-T cells induce outstanding responses in a subset of hematological malignancies, responses are much more deficient in solid tumors. Moreover, NK cells have not shown remarkable results up to date. In general, immune cells present high plasticity to change their activity and phenotype depending on the stimuli they receive from molecules secreted in the tumor microenvironment (TME). Consequently, immune cells will also secrete molecules that will shape the activities of other neighboring immune and tumor cells. Specifically, NK cells can polarize to activities as diverse as angiogenic ones instead of their killer activity. In addition, tumor cell phagocytosis by macrophages, which is required to remove dying tumor cells after the attack of NK cells or CAR-T cells, can be avoided in the TME. In addition, chemotherapy or radiotherapy treatments can induce senescence in tumor cells modifying their secretome to a known as “senescence-associated secretory phenotype” (SASP) that will also impact the immune response. Whereas the SASP initially attracts immune cells to eliminate senescent tumor cells, at high numbers of senescent cells, the SASP becomes detrimental, impacting negatively in the immune response. Last, CAR-T cells are an attractive option to overcome these events. Here, we review how molecules secreted in the TME by either tumor cells or even by immune cells impact the anti-tumor activity of surrounding immune cells.
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Affiliation(s)
- Mikel Etxebeste-Mitxeltorena
- Department of Experimental Hematology, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz, UAM, Madrid, Spain
| | - Inés Del Rincón-Loza
- Department of Experimental Hematology, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz, UAM, Madrid, Spain
| | - Beatriz Martín-Antonio
- Department of Experimental Hematology, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz, UAM, Madrid, Spain
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Kim JH, Park SH, Han J, Ko PW, Kwon D, Suk K. Gliome database: a comprehensive web-based tool to access and analyze glia secretome data. Database (Oxford) 2021; 2020:5879255. [PMID: 32743661 PMCID: PMC7396318 DOI: 10.1093/database/baaa057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/12/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022]
Abstract
Glial cells are phenotypically heterogeneous non-neuronal components of the central and peripheral nervous systems. These cells are endowed with diverse functions and molecular machineries to detect and regulate neuronal or their own activities by various secreted mediators, such as proteinaceous factors. In particular, glia-secreted proteins form a basis of a complex network of glia-neuron or glia-glia interactions in health and diseases. In recent years, the analysis and profiling of glial secretomes have raised new expectations for the diagnosis and treatment of neurological disorders due to the vital role of glia in numerous physiological or pathological processes of the nervous system. However, there is no online database of glia-secreted proteins available to facilitate glial research. Here, we developed a user-friendly 'Gliome' database (available at www.gliome.org), a web-based tool to access and analyze glia-secreted proteins. The database provides a vast collection of information on 3293 proteins that are released from glia of multiple species and have been reported to have differential functions under diverse experimental conditions. It contains a web-based interface with the following four key features regarding glia-secreted proteins: (i) fundamental information, such as signal peptide, SecretomeP value, functions and Gene Ontology category; (ii) differential expression patterns under distinct experimental conditions; (iii) disease association; and (iv) interacting proteins. In conclusion, the Gliome database is a comprehensive web-based tool to access and analyze glia-secretome data obtained from diverse experimental settings, whereby it may facilitate the integration of bioinformatics into glial research.
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Affiliation(s)
- Jong-Heon Kim
- Brain Science and Engineering Institute, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Su-Hyeong Park
- Department of Pharmacology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea.,D&P BIOTECH, 807 Hoguk-ro, Buk-gu, Daegu, 41404, Republic of Korea
| | - Jin Han
- Department of Pharmacology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Pan-Woo Ko
- Department of Neurology, Kyungpook National University Chilgok Hospital, 807 Hoguk-ro, Buk-gu, Daegu, 41404, Republic of Korea
| | - Dongseop Kwon
- School of Software Convergence, Myongji University, 34 Geobukgol-ro, Seodaemun-gu, Seoul, 03674, Republic of Korea
| | - Kyoungho Suk
- Brain Science and Engineering Institute, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea.,Department of Pharmacology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
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21
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Poschmann G, Prescher N, Stühler K. Quantitative MS Workflow for a High-Quality Secretome Analysis by a Quantitative Secretome-Proteome Comparison. Methods Mol Biol 2021; 2228:293-306. [PMID: 33950499 DOI: 10.1007/978-1-0716-1024-4_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Abstract
Cells secrete proteins to communicate with their environment. Therefore, it is interesting to characterize the proteins which are released from cells under certain experimental conditions the so-called secretome. Here, often proteins from conditioned medium of cultured cells are analyzed, but these additionally might include also contaminating proteins of serum that have not been sufficiently removed or proteins from dying cells. To provide high-quality secretome data and minimize potential contaminants, we describe a quantitative comparison of conditioned medium and the cellular proteome. The described workflow comprises cell cultivation, sample preparation, and final data analysis which is based on the comparison of data from label-free mass spectrometric quantification of proteins from the conditioned medium with corresponding cellular proteomes enabling the detection of bona fide secreted proteins.
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22
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Abstract
Outbreaks and deaths related to Foodborne Diseases (FBD) occur constantly in the world, as a result of the consumption of contaminated foodstuffs with pathogens such as Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, Salmonella spp, Clostridium spp. and Campylobacter spp. The purpose of this review is to discuss the main omic techniques applied in foodborne pathogen and to demonstrate their functionalities through the food chain and to guarantee the food safety. The main techniques presented are genomic, transcriptomic, secretomic, proteomic, and metabolomic, which together, in the field of food and nutrition, are known as "Foodomics." This review had highlighted the potential of omics to integrate variables that contribute to food safety and to enable us to understand their application on foodborne diseases. The appropriate use of these techniques had driven the definition of critical parameters to achieve successful results in the improvement of consumers health, costs and to obtain safe and high-quality products.
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Affiliation(s)
| | | | | | - Emmanuel Barboza
- Health Sciences Faculty, University of Western Sao Paulo, Presidente Prudente, Sao Paulo, Brazil
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Godlewski J, Farhath M, Ricklefs FL, Passaro C, Kiel K, Nakashima H, Chiocca EA, Bronisz A. Oncolytic Virus Therapy Alters the Secretome of Targeted Glioblastoma Cells. Cancers (Basel) 2021; 13:1287. [PMID: 33799381 DOI: 10.3390/cancers13061287] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Proteins secreted by cancer cells in response to oncolytic virus anti-tumor therapy constitute the instructions for the immune cells. Yet as there are hundreds of proteins, including those encapsulated in vesicles, whose message drives the mobilization of immune cells, we aimed to decipher the instruction sent by cancer cells in response to therapy. Searching the cataloged vesicle and vesicle-free secreted proteins, we found that the proteins associated with the favorable survival of brain cancer patients were those that have the power to mobilize the immune cells. Thus, this approach established cancer-secreted contributors to the immune–therapeutic effect of the oncolytic virus. Abstract Oncolytic virus (OV) therapy, which is being tested in clinical trials for glioblastoma, targets cancer cells, while triggering immune cells. Yet OV sensitivity varies from patient to patient. As OV therapy is regarded as an anti-tumor vaccine, by making OV-infected cancer cells secrete immunogenic proteins, linking these proteins to transcriptome would provide a measuring tool to predict their sensitivity. A set of six patient-derived glioblastoma cells treated ex-vivo with herpes simplex virus type 1 (HSV1) modeled a clinical setting of OV infection. The cellular transcriptome and secreted proteome (separated into extracellular vesicles (EV) and EV-depleted fractions) were analyzed by gene microarray and mass-spectroscopy, respectively. Data validation and in silico analysis measured and correlated the secretome content with the response to infection and patient survival. Glioblastoma cells reacted to the OV infection in a seemingly dissimilar fashion, but their transcriptomes changed in the same direction. Therefore, the upregulation of transcripts encoding for secreted proteins implies a common thread in the response of cancer cells to infection. Indeed, the OV-driven secretome is linked to the immune response. While these proteins have distinct membership in either EV or EV-depleted fractions, it is their co-secretion that augments the immune response and associates with favorable patient outcomes.
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Daneshmandi L, Shah S, Jafari T, Bhattacharjee M, Momah D, Saveh-Shemshaki N, Lo KWH, Laurencin CT. Emergence of the Stem Cell Secretome in Regenerative Engineering. Trends Biotechnol 2020; 38:1373-1384. [PMID: 32622558 PMCID: PMC7666064 DOI: 10.1016/j.tibtech.2020.04.013] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023]
Abstract
The secretome is defined as the set of molecules and biological factors that are secreted by cells into the extracellular space. In the past decade, secretome-based therapies have emerged as a promising approach to overcome the limitations associated with cell-based therapies for tissue and organ regeneration. Considering the growing number of recent publications related to secretome-based therapies, this review takes a step-by-step engineering approach to evaluate the role of the stem cell secretome in regenerative engineering. We discuss the functional benefits of the secretome, the techniques used to engineer the secretome and tailor its therapeutic effects, and the delivery systems and strategies that have been developed to use the secretome for tissue regeneration.
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Affiliation(s)
- Leila Daneshmandi
- Connecticut Convergence Institute for Translation in Regenerative Engineering, UConn Health, Farmington, CT 06030, USA; Raymond and Beverly Sackler Center for Biomedical, Biological, Physical and Engineering Sciences, UConn Health, Farmington, CT 06030, USA; Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA; Department of Orthopaedic Surgery, UConn Health, Farmington, CT 06030, USA
| | - Shiv Shah
- Connecticut Convergence Institute for Translation in Regenerative Engineering, UConn Health, Farmington, CT 06030, USA; Raymond and Beverly Sackler Center for Biomedical, Biological, Physical and Engineering Sciences, UConn Health, Farmington, CT 06030, USA; Department of Orthopaedic Surgery, UConn Health, Farmington, CT 06030, USA; Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Tahereh Jafari
- Connecticut Convergence Institute for Translation in Regenerative Engineering, UConn Health, Farmington, CT 06030, USA; Raymond and Beverly Sackler Center for Biomedical, Biological, Physical and Engineering Sciences, UConn Health, Farmington, CT 06030, USA; Department of Orthopaedic Surgery, UConn Health, Farmington, CT 06030, USA
| | - Maumita Bhattacharjee
- Connecticut Convergence Institute for Translation in Regenerative Engineering, UConn Health, Farmington, CT 06030, USA; Raymond and Beverly Sackler Center for Biomedical, Biological, Physical and Engineering Sciences, UConn Health, Farmington, CT 06030, USA; Department of Orthopaedic Surgery, UConn Health, Farmington, CT 06030, USA
| | - Deandra Momah
- Connecticut Convergence Institute for Translation in Regenerative Engineering, UConn Health, Farmington, CT 06030, USA; Raymond and Beverly Sackler Center for Biomedical, Biological, Physical and Engineering Sciences, UConn Health, Farmington, CT 06030, USA
| | - Nikoo Saveh-Shemshaki
- Connecticut Convergence Institute for Translation in Regenerative Engineering, UConn Health, Farmington, CT 06030, USA; Raymond and Beverly Sackler Center for Biomedical, Biological, Physical and Engineering Sciences, UConn Health, Farmington, CT 06030, USA; Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA; Department of Orthopaedic Surgery, UConn Health, Farmington, CT 06030, USA
| | - Kevin W-H Lo
- Connecticut Convergence Institute for Translation in Regenerative Engineering, UConn Health, Farmington, CT 06030, USA; Raymond and Beverly Sackler Center for Biomedical, Biological, Physical and Engineering Sciences, UConn Health, Farmington, CT 06030, USA; Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA; Institute of Materials Science, University of Connecticut, Storrs, CT 06269
| | - Cato T Laurencin
- Connecticut Convergence Institute for Translation in Regenerative Engineering, UConn Health, Farmington, CT 06030, USA; Raymond and Beverly Sackler Center for Biomedical, Biological, Physical and Engineering Sciences, UConn Health, Farmington, CT 06030, USA; Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA; Department of Orthopaedic Surgery, UConn Health, Farmington, CT 06030, USA; Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA; Institute of Materials Science, University of Connecticut, Storrs, CT 06269; Department of Materials Science and Engineering, University of Connecticut, Storrs, CT 06269, USA; Department of Medicine, UConn Health, Farmington, CT 06030, USA.
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25
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Poschmann G, Brenig K, Lenz T, Stühler K. Comparative Secretomics Gives Access to High Confident Secretome Data: Evaluation of Different Methods for the Determination of Bona Fide Secreted Proteins. Proteomics 2020; 21:e2000178. [PMID: 33015975 DOI: 10.1002/pmic.202000178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/23/2020] [Indexed: 12/16/2022]
Abstract
Secretome analysis is broadly applied to understand the interplay between cells and their microenvironment. In particular, the unbiased analysis by mass spectrometry-based proteomics of conditioned medium has been successfully applied. In this context, several approaches have been developed allowing to distinguish proteins actively secreted by cells from proteins derived from culture medium or proteins released from dying cells. Here, three different methods comparing conditioned medium and lysate by quantitative mass spectrometry-based proteomics to identify bona fide secreted proteins are evaluated. Evaluation in three different human cell lines reveals that all three methods give access to a similar set of bona fide secreted proteins covering a broad abundance range. In the analyzed primary cells, that is, mesenchymal stromal cells and normal human dermal fibroblasts, more than 70% of the identified proteins are linked to classical secretion pathways. Furthermore, 4-12% are predicted to be released by unconventional secretion pathways. Interestingly, evidence of release by ectodomain shedding in a large number of the remaining candidate proteins is found. In summary, it is convinced that comparative secretomics is currently the method of choice to obtain high-confident secretome data and to identify novel candidates for unconventional protein secretion which have been neglected so far.
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Affiliation(s)
- Gereon Poschmann
- Proteome Research, Institute of Molecular Medicine, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Katrin Brenig
- Proteome Research, Institute of Molecular Medicine, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Thomas Lenz
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Kai Stühler
- Proteome Research, Institute of Molecular Medicine, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany.,Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
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van Neel TL, Berry SB, Berthier E, Theberge AB. Localized Cell-Surface Sampling of a Secreted Factor Using Cell-Targeting Beads. Anal Chem 2020; 92:13634-13640. [PMID: 32941013 DOI: 10.1021/acs.analchem.0c02578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Intercellular communication through the secretion of soluble factors plays a vital role in a wide range of biological processes (e.g., homeostasis, immune response), yet identification and quantification of many of these factors can be challenging due to their degradation or sequestration in cell culture media prior to analysis. Here, we present a customizable bead-based system capable of simultaneously binding to live cells (through antibody-mediated cell tethering) and capturing cell-secreted molecules. Our functionalized beads capture secreted molecules (e.g., hepatocyte growth factor secreted by fibroblasts) that are diminished when sampled via traditional supernatant analysis techniques (p < 0.05), effectively rescuing a reduced signal in the presence of neutralizing components in the cell culture media. Our system enables capture and analysis of molecules integral to chemical communication that would otherwise be markedly decreased prior to analysis.
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Affiliation(s)
- Tammi L van Neel
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Samuel B Berry
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Erwin Berthier
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Ashleigh B Theberge
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States.,Department of Urology, University of Washington, Seattle, Washington 98105, United States
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Shirani I, Zhang H, Zhao G, Lu S, Marawan MA, Dawood A, Chen Y, Chen X, Chen J, Hu C, Chen H, Guo A. In Silico Identification of Novel Immunogenic Secreted Proteins of Mycoplasma bovis from Secretome Data and Experimental Verification. Pathogens 2020; 9:pathogens9090770. [PMID: 32967149 PMCID: PMC7559824 DOI: 10.3390/pathogens9090770] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 01/09/2023] Open
Abstract
Mycoplasma bovis is a major pathogen, responsible for bovine respiratory diseases worldwide. The present lack of effective control measures leaves cattle owners at considerable perpetual risk of M. bovis outbreaks. In this study, we identified M. bovis secreted immunogenic proteins in silico as potential candidates for novel diagnostic agents and vaccines. We used immunoinformatics to analyze 438 M. bovis proteins previously identified with a label-free proteomics analysis of virulent M. bovis HB0801 (P1) and its attenuated P150 strains. The subcellular localization of these proteins was preliminarily screened and 59 proteins were found to be secreted extracellular proteins. Twenty-seven of these proteins contained a large number of predictive T-cell epitopes presented by major histocompatibility complex (MHC) class I and II molecules. Twenty-two of these 27 proteins had a high number of conformational B-cell epitopes, predicted from the corresponding 3D structural templates, including one unique to P1, two unique to P150, and 19 common to both strains. Five proteins were selected for further validation, and two of these, MbovP274 and MbovP570, were successfully expressed and purified. Both were confirmed to be secretory and highly immunogenic proteins that induced a mouse antibody response, reacted with cattle serum positive for M. bovis infection, and significantly increased the production of interleukin 8 (IL-8), IL-12 and interferon γ (IFN-γ) during the secretion of these three cytokines by both M. bovis mutants of these genes. These results should be useful in the development of novel immunological agents against M. bovis infection.
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Affiliation(s)
- Ihsanullah Shirani
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; (I.S.); (H.Z.); (G.Z.); (S.L.); (M.A.M.); (A.D.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan 430070, China; (X.C.); (J.C.)
- Para-Clinic Department, Faculty of Veterinary Medicine, Nangarhar University, Jalalabad 2601, Afghanistan
| | - Hui Zhang
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; (I.S.); (H.Z.); (G.Z.); (S.L.); (M.A.M.); (A.D.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan 430070, China; (X.C.); (J.C.)
| | - Gang Zhao
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; (I.S.); (H.Z.); (G.Z.); (S.L.); (M.A.M.); (A.D.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan 430070, China; (X.C.); (J.C.)
| | - Siyi Lu
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; (I.S.); (H.Z.); (G.Z.); (S.L.); (M.A.M.); (A.D.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan 430070, China; (X.C.); (J.C.)
| | - Marawan A Marawan
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; (I.S.); (H.Z.); (G.Z.); (S.L.); (M.A.M.); (A.D.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan 430070, China; (X.C.); (J.C.)
- Infectious diseases, Animal Medicine Department, Faculty of Veterinary Medicine, Benha University, Qualyobia 13511, Egypt
| | - Ali Dawood
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; (I.S.); (H.Z.); (G.Z.); (S.L.); (M.A.M.); (A.D.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan 430070, China; (X.C.); (J.C.)
- Infectious Diseases, Animal Medicine Department, Faculty of Veterinary Medicine, Sadat City University, Sadat City 32511, Egypt
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; (I.S.); (H.Z.); (G.Z.); (S.L.); (M.A.M.); (A.D.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan 430070, China; (X.C.); (J.C.)
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Chen
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan 430070, China; (X.C.); (J.C.)
| | - Jianguo Chen
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan 430070, China; (X.C.); (J.C.)
| | - Changmin Hu
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; (I.S.); (H.Z.); (G.Z.); (S.L.); (M.A.M.); (A.D.); (Y.C.); (C.H.); (H.C.)
| | - Huanchun Chen
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; (I.S.); (H.Z.); (G.Z.); (S.L.); (M.A.M.); (A.D.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan 430070, China; (X.C.); (J.C.)
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; (I.S.); (H.Z.); (G.Z.); (S.L.); (M.A.M.); (A.D.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan 430070, China; (X.C.); (J.C.)
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: ; Tel.: +86-27-87286861
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Freire PP, Fernandez GJ, de Moraes D, Cury SS, Dal Pai‐Silva M, dos Reis PP, Rogatto SR, Carvalho RF. The expression landscape of cachexia-inducing factors in human cancers. J Cachexia Sarcopenia Muscle 2020; 11:947-961. [PMID: 32125790 PMCID: PMC7432594 DOI: 10.1002/jcsm.12565] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 01/20/2020] [Accepted: 02/09/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Cachexia is a multifactorial syndrome highly associated with specific tumour types, but the causes of variation in cachexia prevalence and severity are unknown. While circulating plasma mediators (soluble cachectic factors) derived from tumours have been implicated with the pathogenesis of the syndrome, these associations were generally based on plasma concentration rather than tissue-specific gene expression levels. Here, we hypothesized that tumour gene expression profiling of cachexia-inducing factors (CIFs) in human cancers with different prevalence of cachexia could reveal potential cancer-specific cachexia mediators and biomarkers of clinical outcome. METHODS First, we combined uniformly processed RNA sequencing data from The Cancer Genome Atlas and Genotype-Tissue Expression databases to characterize the expression profile of secretome genes in 12 cancer types (4651 samples) compared with their matched normal tissues (2737 samples). We systematically investigated the transcriptomic data to assess the tumour expression profile of 25 known CIFs and their predictive values for patient survival. We used the Xena Functional Genomics tool to analyse the gene expression of CIFs according to neoplastic cellularity in pancreatic adenocarcinoma, which is known to present the highest prevalence of cachexia. RESULTS A comprehensive characterization of the expression profiling of secreted genes in different human cancers revealed pathways and mediators with a potential role in cachexia within the tumour microenvironment. Cytokine-related and chemokine-related pathways were enriched in tumour types frequently associated with the syndrome. CIFs presented a tumour-specific expression profile, in which the number of upregulated genes was correlated with the cachexia prevalence (r2 : 0.80; P value: 0.002) and weight loss (r2 : 0.81; P value: 0.002). The distinct gene expression profile, according to tumour type, was significantly associated with prognosis (P value ≤ 1.96 E-06). In pancreatic adenocarcinoma, the upregulated CIF genes were associated with tumours presenting low neoplastic cellularity and high leucocyte fraction and not with tumour grade. CONCLUSIONS Our results present a biological dimension of tumour-secreted elements that are potentially useful to explain why specific cancer types are more likely to develop cachexia. The tumour-specific profile of CIFs may help the future development of better targeted therapies to treat cancer types highly associated with the syndrome.
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Affiliation(s)
- Paula Paccielli Freire
- Department of Structural and Functional Biology, Institute of BiosciencesSão Paulo State University, UNESPBotucatuBrazil
| | - Geysson Javier Fernandez
- Department of Structural and Functional Biology, Institute of BiosciencesSão Paulo State University, UNESPBotucatuBrazil
- Faculty of MedicineUniversity of Antioquia, UdeAMedellínColombia
| | - Diogo de Moraes
- Department of Structural and Functional Biology, Institute of BiosciencesSão Paulo State University, UNESPBotucatuBrazil
| | - Sarah Santiloni Cury
- Department of Structural and Functional Biology, Institute of BiosciencesSão Paulo State University, UNESPBotucatuBrazil
| | - Maeli Dal Pai‐Silva
- Department of Structural and Functional Biology, Institute of BiosciencesSão Paulo State University, UNESPBotucatuBrazil
| | - Patrícia Pintor dos Reis
- Department of Surgery and Orthopedics, Faculty of MedicineSão Paulo State University, UNESPBotucatuBrazil
- Experimental Research Unity, Faculty of MedicineSão Paulo State University, UNESPBotucatuBrazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital, Institute of Regional Health ResearchUniversity of Southern DenmarkVejleDenmark
- Danish Colorectal Cancer Center SouthVejleDenmark
| | - Robson Francisco Carvalho
- Department of Structural and Functional Biology, Institute of BiosciencesSão Paulo State University, UNESPBotucatuBrazil
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Dihazi GH, Eltoweissy M, Jahn O, Tampe B, Zeisberg M, Wülfrath HS, Müller GA, Dihazi H. The Secretome Analysis of Activated Human Renal Fibroblasts Revealed Beneficial Effect of the Modulation of the Secreted Peptidyl-Prolyl Cis-Trans Isomerase A in Kidney Fibrosis. Cells 2020; 9:cells9071724. [PMID: 32708451 PMCID: PMC7407823 DOI: 10.3390/cells9071724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
The secretome is an important mediator in the permanent process of reciprocity between cells and their environment. Components of secretome are involved in a large number of physiological mechanisms including differentiation, migration, and extracellular matrix modulation. Alteration in secretome composition may therefore trigger cell transformation, inflammation, and diseases. In the kidney, aberrant protein secretion plays a central role in cell activation and transition and in promoting renal fibrosis onset and progression. Using comparative proteomic analyses, we investigated in the present study the impact of cell transition on renal fibroblast cells secretome. Human renal cell lines were stimulated with profibrotic hormones and cytokines, and alterations in secretome were investigated using proteomic approaches. We identified protein signatures specific for the fibrotic phenotype and investigated the impact of modeling secretome proteins on extra cellular matrix accumulation. The secretion of peptidyl-prolyl cis-trans isomerase A (PPIA) was demonstrated to be associated with fibrosis phenotype. We showed that the in-vitro inhibition of PPIA with ciclosporin A (CsA) resulted in downregulation of PPIA and fibronectin (FN1) expression and significantly reduced their secretion. Knockdown studies of PPIA in a three-dimensional (3D) cell culture model significantly impaired the secretion and accumulation of the extracellular matrix (ECM), suggesting a positive therapeutic effect on renal fibrosis progression.
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Affiliation(s)
- Gry H. Dihazi
- Institute for Clinical Chemistry/UMG-Laboratories, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (G.H.D.); (H.S.W.)
| | - Marwa Eltoweissy
- Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21500, Egypt;
| | - Olaf Jahn
- Proteomics Group, Max-Planck-Institute of Experimental Medicine, Hermann-Rein-Strasse 3, D-37075 Göttingen, Germany;
| | - Björn Tampe
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (B.T.); (M.Z.); (G.A.M.)
| | - Michael Zeisberg
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (B.T.); (M.Z.); (G.A.M.)
| | - Hauke S. Wülfrath
- Institute for Clinical Chemistry/UMG-Laboratories, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (G.H.D.); (H.S.W.)
| | - Gerhard A. Müller
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (B.T.); (M.Z.); (G.A.M.)
| | - Hassan Dihazi
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (B.T.); (M.Z.); (G.A.M.)
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, D-37075 Göttingen, Germany
- Correspondence: ; Tel.: +49-551-399-1221; Fax: +49-551-399-1039
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30
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Zubair M, Khan FA, Menghwar H, Faisal M, Ashraf M, Rasheed MA, Marawan MA, Dawood A, Chen Y, Chen H, Guo A. Progresses on bacterial secretomes enlighten research on Mycoplasma secretome. Microb Pathog 2020; 144:104160. [PMID: 32194181 DOI: 10.1016/j.micpath.2020.104160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 11/20/2022]
Abstract
Bacterial secretome is a comprehensive catalog of bacterial proteins that are released or secreted outside the cells. They offer a number of factors that possess several significant roles in virulence as well as cell to cell communication and hence play a core role in bacterial pathogenesis. Sometimes these proteins are bounded with membranes giving them the shape of vesicles called extracellular vesicles (EVs) or outer membrane vesicles (OMVs). Bacteria secrete these proteins via Sec and Tat pathways into the periplasm. Secreted proteins have found to be important as diagnostic markers as well as antigenic factors for the development of an effective candidate vaccine. Recently, the research in the field of secretomics is growing up and getting more interesting due to their direct involvement in the pathogenesis of the microorganisms leading to the infection. Many pathogenic bacteria have been studied for their secretome and the results illustrated novel antigens. This review highlights the secretome studies of different pathogenic bacteria in humans and animals, general secretion mechanisms, different approaches and challenges in the secretome of Mycoplasma sp.
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Molloy K, Cagney G, Dillon ET, Wynne K, Greene CM, McElvaney NG. Impaired Airway Epithelial Barrier Integrity in Response to Stenotrophomonas maltophilia Proteases, Novel Insights Using Cystic Fibrosis Bronchial Epithelial Cell Secretomics. Front Immunol 2020; 11:198. [PMID: 32161586 PMCID: PMC7053507 DOI: 10.3389/fimmu.2020.00198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/27/2020] [Indexed: 11/13/2022] Open
Abstract
Stenotrophomonas maltophilia is a Gram-negative opportunistic pathogen that can chronically colonize the lungs of people with cystic fibrosis (CF) and is associated with lethal pulmonary hemorrhage in immunocompromised patients. Its secreted virulence factors include the extracellular serine proteases StmPR1, StmPR2, and StmPR3. To explore the impact of secreted virulence determinants on pulmonary mucosal defenses in CF, we examined the secretome of human CFBE41o- bronchial epithelial cells in response to treatment with S. maltophilia K279a cell culture supernatant (CS) using a liquid-chromatography-tandem mass spectrometry (LC-MS/MS) based label-free quantitative (LFQ) shotgun proteomics approach for global profiling of the cell secretome. Secretome analysis identified upregulated pathways mainly relating to biological adhesion and epithelial cell signaling in infection, whereas no specific pathways relating to the immune response were enriched. Further exploration of the potentially harmful effects of K279a CS on CF bronchial epithelial cells, demonstrated that K279a CS caused CFBE41o- cell condensation and detachment, reversible by the serine protease inhibitor PMSF. K279a CS also decreased trans-epithelial electrical resistance in CFBE41o- cell monolayers suggestive of disruption of tight junction complexes (TJC). This finding was corroborated by an observed increase in fluorescein isothiocyanate (FITC) dextran permeability and by demonstrating PMSF-sensitive degradation of the tight junction proteins ZO-1 and occludin, but not JAM-A or claudin-1. These observations demonstrating destruction of the CFBE41o- TJC provide a novel insight regarding the virulence of S. maltophilia and may explain the possible injurious effects of this bacterium on the CF bronchial epithelium and the pathogenic mechanism leading to lethal pulmonary hemorrhage.
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Affiliation(s)
- Kevin Molloy
- Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Catherine M Greene
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Noel G McElvaney
- Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
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Zhang R, Saredy J, Shao Y, Yao T, Liu L, Saaoud F, Yang WY, Sun Y, Johnson C, Drummer C, Fu H, Lu Y, Xu K, Liu M, Wang J, Cutler E, Yu D, Jiang X, Li Y, Li R, Wang L, Choi ET, Wang H, Yang X. End-stage renal disease is different from chronic kidney disease in upregulating ROS-modulated proinflammatory secretome in PBMCs - A novel multiple-hit model for disease progression. Redox Biol 2020; 34:101460. [PMID: 32179051 PMCID: PMC7327976 DOI: 10.1016/j.redox.2020.101460] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/28/2020] [Accepted: 02/07/2020] [Indexed: 12/17/2022] Open
Abstract
Background The molecular mechanisms underlying chronic kidney disease (CKD) transition to end-stage renal disease (ESRD) and CKD acceleration of cardiovascular and other tissue inflammations remain poorly determined. Methods We conducted a comprehensive data analyses on 7 microarray datasets in peripheral blood mononuclear cells (PBMCs) from patients with CKD and ESRD from NCBI-GEO databases, where we examined the expressions of 2641 secretome genes (SG). Results 1) 86.7% middle class (molecular weight >500 Daltons) uremic toxins (UTs) were encoded by SGs; 2) Upregulation of SGs in PBMCs in patients with ESRD (121 SGs) were significantly higher than that of CKD (44 SGs); 3) Transcriptomic analyses of PBMC secretome had advantages to identify more comprehensive secretome than conventional secretomic analyses; 4) ESRD-induced SGs had strong proinflammatory pathways; 5) Proinflammatory cytokines-based UTs such as IL-1β and IL-18 promoted ESRD modulation of SGs; 6) ESRD-upregulated co-stimulation receptors CD48 and CD58 increased secretomic upregulation in the PBMCs, which were magnified enormously in tissues; 7) M1-, and M2-macrophage polarization signals contributed to ESRD- and CKD-upregulated SGs; 8) ESRD- and CKD-upregulated SGs contained senescence-promoting regulators by upregulating proinflammatory IGFBP7 and downregulating anti-inflammatory TGF-β1 and telomere stabilizer SERPINE1/PAI-1; 9) ROS pathways played bigger roles in mediating ESRD-upregulated SGs (11.6%) than that in CKD-upregulated SGs (6.8%), and half of ESRD-upregulated SGs were ROS-independent. Conclusions Our analysis suggests novel secretomic upregulation in PBMCs of patients with CKD and ESRD, act synergistically with uremic toxins, to promote inflammation and potential disease progression. Our findings have provided novel insights on PBMC secretome upregulation to promote disease progression and may lead to the identification of new therapeutic targets for novel regimens for CKD, ESRD and their accelerated cardiovascular disease, other inflammations and cancers. (Total words: 279).
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Affiliation(s)
- Ruijing Zhang
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA; Department of Nephrology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030013, China; Department of Nephrology, The Affiliated People's Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030012, China
| | - Jason Saredy
- Centers for Metabolic Disease Research, Cardiovascular Research, & Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Ying Shao
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Tian Yao
- Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China
| | - Lu Liu
- Centers for Metabolic Disease Research, Cardiovascular Research, & Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Fatma Saaoud
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | | | - Yu Sun
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Candice Johnson
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Charles Drummer
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Hangfei Fu
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Yifan Lu
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Keman Xu
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Ming Liu
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA; Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China
| | - Jirong Wang
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Elizabeth Cutler
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA; School of Science and Engineering, Tulane University, New Orleans, LA, 70118, USA
| | - Daohai Yu
- Department of Clinical Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Xiaohua Jiang
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Yafeng Li
- Department of Nephrology, The Affiliated People's Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030012, China
| | - Rongshan Li
- Department of Nephrology, The Affiliated People's Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030012, China
| | - Lihua Wang
- Department of Nephrology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030013, China
| | - Eric T Choi
- Division of Vascular and Endovascular Surgery, Department of Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA; Centers for Metabolic Disease Research, Cardiovascular Research, & Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA; Departments of Pharmacology, Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Hong Wang
- Centers for Metabolic Disease Research, Cardiovascular Research, & Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA; Departments of Pharmacology, Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Xiaofeng Yang
- Center for Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA; Centers for Metabolic Disease Research, Cardiovascular Research, & Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA; Departments of Pharmacology, Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.
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Zubair H, Patel GK, Khan MA, Azim S, Zubair A, Singh S, Srivastava SK, Singh AP. Proteomic Analysis of MYB-Regulated Secretome Identifies Functional Pathways and Biomarkers: Potential Pathobiological and Clinical Implications. J Proteome Res 2020; 19:794-804. [PMID: 31928012 DOI: 10.1021/acs.jproteome.9b00641] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Earlier we have shown important roles of MYB in pancreatic tumor pathobiology. To better understand the role of MYB in the tumor microenvironment and identify MYB-associated secreted biomarker proteins, we conducted mass spectrometry analysis of the secretome from MYB-modulated and control pancreatic cancer cell lines. We also performed in silico analyses to determine MYB-associated biofunctions, gene networks, and altered biological pathways. Our data demonstrated significant modulation (p < 0.05) of 337 secreted proteins in MYB-silenced MiaPaCa cells, whereas 282 proteins were differentially present in MYB-overexpressing BxPC3 cells, compared to their respective control cells. Alteration of several phenotypes such as cellular movement, cell death and survival, inflammatory response, protein synthesis, etc. was associated with MYB-induced differentially expressed proteins (DEPs) in secretomes. DEPs from MYB-silenced MiaPaCa PC cells were suggestive of the downregulation of genes primarily associated with glucose metabolism, PI3K/AKT signaling, and oxidative stress response, among others. DEPs from MYB-overexpressing BxPC3 cells suggested the enhanced release of proteins associated with glucose metabolism and cellular motility. We also observed that MYB positively regulated the expression of four proteins with potential biomarker properties, i.e., FLNB, ENO1, ITGB1, and INHBA. Mining of publicly available databases using Oncomine and UALCAN demonstrated that these genes are overexpressed in pancreatic tumors and associated with reduced patient survival. Altogether, these data provide novel avenues for future investigations on diverse biological functions of MYB, specifically in the tumor microenvironment, and could also be exploited for biomarker development.
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Affiliation(s)
- Haseeb Zubair
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Girijesh Kumar Patel
- Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Mohammad Aslam Khan
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Shafquat Azim
- Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Asif Zubair
- Molecular and Computational Biology, School of Biological Sciences, Dornsife College of Letters, Arts and Sciences , University of Southern California , Los Angeles , California 90089 , United States
| | - Seema Singh
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States.,Department of Biochemistry and Molecular Biology, College of Medicine , University of South Alabama , Mobile , Alabama 36688 , United States
| | - Sanjeev Kumar Srivastava
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Ajay Pratap Singh
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States.,Department of Biochemistry and Molecular Biology, College of Medicine , University of South Alabama , Mobile , Alabama 36688 , United States
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Abstract
Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.
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Affiliation(s)
- Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory Timp
- Departments of Electrical Engineering and Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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35
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Schira-Heinen J, Grube L, Waldera-Lupa DM, Baberg F, Langini M, Etemad-Parishanzadeh O, Poschmann G, Stühler K. Pitfalls and opportunities in the characterization of unconventionally secreted proteins by secretome analysis. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2019; 1867:140237. [DOI: 10.1016/j.bbapap.2019.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/04/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023]
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36
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Hernández-Albors A, Castaño AG, Fernández-Garibay X, Ortega MA, Balaguer J, Ramón-Azcón J. Microphysiological sensing platform for an in-situ detection of tissue-secreted cytokines. Biosens Bioelectron X 2019; 2:100025. [PMID: 32904308 PMCID: PMC7453918 DOI: 10.1016/j.biosx.2019.100025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/08/2019] [Accepted: 07/25/2019] [Indexed: 06/11/2023]
Abstract
Understanding the protein-secretion dynamics from single, specific tissues is critical toward the advancement of disease detection and treatments. However, such secretion dynamics remain difficult to measure in vivo due to the uncontrolled contributions from other tissue populations. Here, we describe an integrated platform designed for the reliable, near real-time measurements of cytokines secreted from an in vitro single-tissue model. In our setup, we grow 3D biomimetic tissues to discretize cytokine source, and we separate them from a magnetic microbead-based biosensing system using a Transwell insert. This design integrates physiochemically controlled biological activity, high-sensitivity protein detection (LOD < 20 pg mL-1), and rapid protein diffusion to enable non-invasive, near real-time measurements. To showcase the specificity and sensitivity of the system, we use our setup to probe the inflammatory process related to the protein Interleukine 6 (IL-6) and to the Tumor Necrosis Factor (TNF-α). We show that our setup can monitor the time-dependence profile of IL-6 and TNF-α secretion that results from the electrical and chemical stimulation of 3D skeletal muscle tissues. We demonstrate a novel and affordable methodology for discretizing the secretion kinetics of specific tissues for advancing metabolic-disorder studies and drug-screening applications.
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Affiliation(s)
| | | | - Xiomara Fernández-Garibay
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - María Alejandra Ortega
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Jordina Balaguer
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Javier Ramón-Azcón
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain
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37
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Sukumaran A, Coish JM, Yeung J, Muselius B, Gadjeva M, MacNeil AJ, Geddes-McAlister J. Decoding communication patterns of the innate immune system by quantitative proteomics. J Leukoc Biol 2019; 106:1221-1232. [PMID: 31556465 DOI: 10.1002/jlb.2ri0919-302r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 12/15/2022] Open
Abstract
The innate immune system is a collective network of cell types involved in cell recruitment and activation using a robust and refined communication system. Engagement of receptor-mediated intracellular signaling initiates communication cascades by conveying information about the host cell status to surrounding cells for surveillance and protection. Comprehensive profiling of innate immune cells is challenging due to low cell numbers, high dynamic range of the cellular proteome, low abundance of secreted proteins, and the release of degradative enzymes (e.g., proteases). However, recent advances in mass spectrometry-based proteomics provides the capability to overcome these limitations through profiling the dynamics of cellular processes, signaling cascades, post-translational modifications, and interaction networks. Moreover, integration of technologies and molecular datasets provide a holistic view of a complex and intricate network of communications underscoring host defense and tissue homeostasis mechanisms. In this Review, we explore the diverse applications of mass spectrometry-based proteomics in innate immunity to define communication patterns of the innate immune cells during health and disease. We also provide a technical overview of mass spectrometry-based proteomic workflows, with a focus on bottom-up approaches, and we present the emerging role of proteomics in immune-based drug discovery while providing a perspective on new applications in the future.
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Affiliation(s)
- Arjun Sukumaran
- Molecular and Cellular Biology Department, University of Guelph, Guelph, Ontario, Canada
| | - Jeremia M Coish
- Department of Health Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Jason Yeung
- Molecular and Cellular Biology Department, University of Guelph, Guelph, Ontario, Canada
| | - Benjamin Muselius
- Molecular and Cellular Biology Department, University of Guelph, Guelph, Ontario, Canada
| | - Mihaela Gadjeva
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Adam J MacNeil
- Department of Health Sciences, Brock University, St. Catharines, Ontario, Canada
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da Cunha BR, Domingos C, Stefanini ACB, Henrique T, Polachini GM, Castelo-Branco P, Tajara EH. Cellular Interactions in the Tumor Microenvironment: The Role of Secretome. J Cancer 2019; 10:4574-4587. [PMID: 31528221 PMCID: PMC6746126 DOI: 10.7150/jca.21780] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/25/2019] [Indexed: 02/06/2023] Open
Abstract
Over the past years, it has become evident that cancer initiation and progression depends on several components of the tumor microenvironment, including inflammatory and immune cells, fibroblasts, endothelial cells, adipocytes, and extracellular matrix. These components of the tumor microenvironment and the neoplastic cells interact with each other providing pro and antitumor signals. The tumor-stroma communication occurs directly between cells or via a variety of molecules secreted, such as growth factors, cytokines, chemokines and microRNAs. This secretome, which derives not only from tumor cells but also from cancer-associated stromal cells, is an important source of key regulators of the tumorigenic process. Their screening and characterization could provide useful biomarkers to improve cancer diagnosis, prognosis, and monitoring of treatment responses.
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Affiliation(s)
- Bianca Rodrigues da Cunha
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil.,Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP, Brazil
| | - Célia Domingos
- Department of Biomedical Sciences and Medicine, University of Algarve, Portugal.,Centre for Biomedical Research (CBMR), University of Algarve, Faro, Portugal
| | - Ana Carolina Buzzo Stefanini
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil.,Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP, Brazil
| | - Tiago Henrique
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Giovana Mussi Polachini
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Pedro Castelo-Branco
- Department of Biomedical Sciences and Medicine, University of Algarve, Portugal.,Centre for Biomedical Research (CBMR), University of Algarve, Faro, Portugal.,Algarve Biomedical Center, Gambelas, Faro, Portugal
| | - Eloiza Helena Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil.,Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP, Brazil
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39
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Koltes JE, Arora I, Gupta R, Nguyen DC, Schaid M, Kim JA, Kimple ME, Bhatnagar S. A gene expression network analysis of the pancreatic islets from lean and obese mice identifies complement 1q like-3 secreted protein as a regulator of β-cell function. Sci Rep 2019; 9:10119. [PMID: 31300714 PMCID: PMC6626003 DOI: 10.1038/s41598-019-46219-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 06/24/2019] [Indexed: 12/29/2022] Open
Abstract
Secreted proteins are important metabolic regulators. Identifying and characterizing the role of secreted proteins from small tissue depots such as islets of Langerhans, which are required for the proper control of whole-body energy metabolism, remains challenging. Our objective was to identify islet-derived secreted proteins that affect islet function in obesity. Lean and obese mouse islet expression data were analyzed by weighted gene co-expression network analysis (WGCNA) to identify trait-associated modules. Subsequently, genes within these modules were filtered for transcripts that encode for secreted proteins based on intramodular connectivity, module membership, and differential expression. Complement 1q like-3 (C1ql3) secreted protein was identified as a hub gene affecting islet function in obesity. Co-expression network, hierarchal clustering, and gene-ontology based approaches identified a putative role for C1ql3 in regulating β-cell insulin secretion. Biological validation shows that C1ql3 is expressed in β-cells, it inhibits insulin secretion and key genes that are involved in β-cell function. Moreover, the increased expression of C1ql3 is correlated with the reduced insulin secretion in islets of obese mice. Herein, we demonstrate a streamlined approach to effectively screen and determine the function of secreted proteins in islets, and identified C1ql3 as a putative contributor to reduced insulin secretion in obesity, linking C1ql3 to an increased susceptibility to type 2 diabetes.
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Affiliation(s)
- James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Itika Arora
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine and Comprehensive Diabetes Center, University of Alabama, Birmingham, AL, 35294, USA
| | - Rajesh Gupta
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine and Comprehensive Diabetes Center, University of Alabama, Birmingham, AL, 35294, USA
| | - Dan C Nguyen
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine and Comprehensive Diabetes Center, University of Alabama, Birmingham, AL, 35294, USA
| | - Michael Schaid
- Interdisciplinary Graduate Program in Nutritional Sciences, University of Wisconsin-Madison College of Agriculture and Life Sciences, Madison, WI, 53706, USA.,Research Service, William S Middleton Memorial VA Hospital, Madison, WI, 53705, USA
| | - Jeong-A Kim
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine and Comprehensive Diabetes Center, University of Alabama, Birmingham, AL, 35294, USA
| | - Michelle E Kimple
- Interdisciplinary Graduate Program in Nutritional Sciences, University of Wisconsin-Madison College of Agriculture and Life Sciences, Madison, WI, 53706, USA.,Divison of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, 53705, USA.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, 53705, USA.,Department of Academic Affairs, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, 53705, USA.,Research Service, William S Middleton Memorial VA Hospital, Madison, WI, 53705, USA
| | - Sushant Bhatnagar
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine and Comprehensive Diabetes Center, University of Alabama, Birmingham, AL, 35294, USA.
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Goodarzi P, Alavi-Moghadam S, Payab M, Larijani B, Rahim F, Gilany K, Bana N, Tayanloo-Beik A, Foroughi Heravani N, Hadavandkhani M, Arjmand B. Metabolomics Analysis of Mesenchymal Stem Cells. Int J Mol Cell Med 2019; 8:30-40. [PMID: 32351907 PMCID: PMC7175611 DOI: 10.22088/ijmcm.bums.8.2.30] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/20/2019] [Indexed: 12/12/2022]
Abstract
Various mesenchymal stem cells as easily accessible and multipotent cells can share different essential signaling pathways related to their stemness ability. Understanding the mechanism of stemness ability can be useful for controlling the stem cells for regenerative medicine targets. In this context, OMICs studies can analyze the mechanism of different stem cell properties or stemness ability via a broad range of current high-throughput techniques. This field is fundamentally directed toward the analysis of whole genome (genomics), mRNAs (transcriptomics), proteins (proteomics) and metabolites (metabolomics) in biological samples. According to several studies, metabolomics is more effective than other OMICs ّfor various system biology concerns. Metabolomics can elucidate the biological mechanisms of various mesenchymal stem cell function by measuring their metabolites such as their secretome components. Analyzing the metabolic alteration of mesenchymal stem cells can be useful to promote their regenerative medicine application.
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Affiliation(s)
- Parisa Goodarzi
- Brain and Spinal Cord Injury Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sepideh Alavi-Moghadam
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Moloud Payab
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical sciences, Tehran, Iran
| | - Fakher Rahim
- Health Research Institute, Thalassemia and Hemoglobinopathies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran .,Department of Biomedical Sciences, University of Antwerp, Belgium
| | - Nikoo Bana
- Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular- Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Najmeh Foroughi Heravani
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdieh Hadavandkhani
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran .,Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular- Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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41
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Canto LMD, Cury SS, Barros-Filho MC, Kupper BEC, Begnami MDFDS, Scapulatempo-Neto C, Carvalho RF, Marchi FA, Olsen DA, Madsen JS, Havelund BM, Aguiar S, Rogatto SR. Locally advanced rectal cancer transcriptomic-based secretome analysis reveals novel biomarkers useful to identify patients according to neoadjuvant chemoradiotherapy response. Sci Rep 2019; 9:8702. [PMID: 31213644 PMCID: PMC6582145 DOI: 10.1038/s41598-019-45151-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/31/2019] [Indexed: 12/24/2022] Open
Abstract
Most patients with locally advanced rectal cancer (LARC) present incomplete pathological response (pIR) to neoadjuvant chemoradiotherapy (nCRT). Despite the efforts to predict treatment response using tumor-molecular features, as differentially expressed genes, no molecule has proved to be a strong biomarker. The tumor secretome analysis is a promising strategy for biomarkers identification, which can be assessed using transcriptomic data. We performed transcriptomic-based secretome analysis to select potentially secreted proteins using an in silico approach. The tumor expression profile of 28 LARC biopsies collected before nCRT was compared with normal rectal tissues (NT). The expression profile showed no significant differences between complete (pCR) and incomplete responders to nCRT. Genes with increased expression (pCR = 106 and pIR = 357) were used for secretome analysis based on public databases (Vesiclepedia, Human Cancer Secretome, and Plasma Proteome). Seventeen potentially secreted candidates (pCR = 1, pIR = 13 and 3 in both groups) were further investigated in two independent datasets (TCGA and GSE68204) confirming their over-expression in LARC and association with nCRT response (GSE68204). The expression of circulating amphiregulin and cMET proteins was confirmed in serum from 14 LARC patients. Future studies in liquid biopsies could confirm the utility of these proteins for personalized treatment in LARC patients.
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Affiliation(s)
- Luisa Matos do Canto
- International Research Center - CIPE, A.C.Camargo Cancer Center, Sao Paulo, 04002-010, Brazil.,Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, 7100, Denmark
| | - Sarah Santiloni Cury
- Department of Morphology - Institute of Bioscience, São Paulo State University (UNESP), Botucatu, 18618689, Brazil
| | | | | | | | | | - Robson Francisco Carvalho
- Department of Morphology - Institute of Bioscience, São Paulo State University (UNESP), Botucatu, 18618689, Brazil
| | | | - Dorte Aalund Olsen
- Department of Biochemistry and Immunology, University Hospital of Southern Denmark, Vejle, 7100, Denmark
| | - Jonna Skov Madsen
- Department of Biochemistry and Immunology, University Hospital of Southern Denmark, Vejle, 7100, Denmark.,Danish Colorectal Cancer Center South, Vejle, 7100, Denmark.,Institute of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Vejle, 7100, Denmark
| | - Birgitte Mayland Havelund
- Danish Colorectal Cancer Center South, Vejle, 7100, Denmark.,Department of Oncology, University Hospital of Southern Denmark, 7100, Vejle, Denmark
| | - Samuel Aguiar
- Department of Pelvic Surgery, A.C.Camargo Cancer Center, Sao Paulo, 04002-010, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, 7100, Denmark. .,Danish Colorectal Cancer Center South, Vejle, 7100, Denmark. .,Institute of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Vejle, 7100, Denmark.
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42
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Affiliation(s)
- Carol A. Eisenberg
- New York Medical College / Westchester Medical Center Stem Cell Laboratory, Departments of Physiology and Medicine, New York Medical College, Valhalla, NY 10595, United States
| | - Leonard M. Eisenberg
- New York Medical College / Westchester Medical Center Stem Cell Laboratory, Departments of Physiology and Medicine, New York Medical College, Valhalla, NY 10595, United States
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43
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Abstract
Secreted proteins serve as crucial mediators of many physiology processes, and beginning with the discovery of insulin, studies have revealed numerous context-specific regulatory networks across various cell types. Here, we review “omics” approaches to deconvolute the complex milieu of proteins that are released from the cell. We emphasize a novel “systems genetics” approach our laboratory has developed to investigate mechanisms of tissue-tissue communication using population-based datasets. Finally, we highlight potential future directions for these studies, discuss several caveats, and propose new ways to investigate modes of endocrine communication.
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Affiliation(s)
- Marcus M Seldin
- Departments of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Aldons J Lusis
- Departments of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 .,Human Genetics University of California, Los Angeles, Los Angeles, CA 90095.,Microbiology, Immunology, and Molecular Genetics University of California, Los Angeles, Los Angeles, CA 90095
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44
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Abstract
In order to overcome the limitations of classic imaging in Histology during the actually era of multiomics, the multi-color "molecular microscope" by its emerging "molecular pictures" offers quantitative and spatial information about thousands of molecular profiles without labeling of potential targets. Healthy and diseased human tissues, as well as those of diverse invertebrate and vertebrate animal models, including genetically engineered species and cultured cells, can be easily analyzed by histology-directed MALDI imaging mass spectrometry. The aims of this review are to discuss a range of proteomic information emerging from MALDI mass spectrometry imaging comparative to classic histology, histochemistry and immunohistochemistry, with applications in biology and medicine, concerning the detection and distribution of structural proteins and biological active molecules, such as antimicrobial peptides and proteins, allergens, neurotransmitters and hormones, enzymes, growth factors, toxins and others. The molecular imaging is very well suited for discovery and validation of candidate protein biomarkers in neuroproteomics, oncoproteomics, aging and age-related diseases, parasitoproteomics, forensic, and ecotoxicology. Additionally, in situ proteome imaging may help to elucidate the physiological and pathological mechanisms involved in developmental biology, reproductive research, amyloidogenesis, tumorigenesis, wound healing, neural network regeneration, matrix mineralization, apoptosis and oxidative stress, pain tolerance, cell cycle and transformation under oncogenic stress, tumor heterogeneity, behavior and aggressiveness, drugs bioaccumulation and biotransformation, organism's reaction against environmental penetrating xenobiotics, immune signaling, assessment of integrity and functionality of tissue barriers, behavioral biology, and molecular origins of diseases. MALDI MSI is certainly a valuable tool for personalized medicine and "Eco-Evo-Devo" integrative biology in the current context of global environmental challenges.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania.
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45
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de Almeida Fuzeta M, de Matos Branco AD, Fernandes-Platzgummer A, da Silva CL, Cabral JMS. Addressing the Manufacturing Challenges of Cell-Based Therapies. Adv Biochem Eng Biotechnol 2019; 171:225-278. [PMID: 31844924 DOI: 10.1007/10_2019_118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Exciting developments in the cell therapy field over the last decades have led to an increasing number of clinical trials and the first cell products receiving marketing authorization. In spite of substantial progress in the field, manufacturing of cell-based therapies presents multiple challenges that need to be addressed in order to assure the development of safe, efficacious, and cost-effective cell therapies.The manufacturing process of cell-based therapies generally requires tissue collection, cell isolation, culture and expansion (upstream processing), cell harvest, separation and purification (downstream processing), and, finally, product formulation and storage. Each one of these stages presents significant challenges that have been the focus of study over the years, leading to innovative and groundbreaking technological advances, as discussed throughout this chapter.Delivery of cell-based therapies relies on defining product targets while controlling process variable impact on cellular features. Moreover, commercial viability is a critical issue that has had damaging consequences for some therapies. Implementation of cost-effectiveness measures facilitates healthy process development, potentially being able to influence end product pricing.Although cell-based therapies represent a new level in bioprocessing complexity in every manufacturing stage, they also show unprecedented levels of therapeutic potential, already radically changing the landscape of medical care.
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Affiliation(s)
- Miguel de Almeida Fuzeta
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - André Dargen de Matos Branco
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Fernandes-Platzgummer
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Cláudia Lobato da Silva
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.
| | - Joaquim M S Cabral
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
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46
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Juan-Colás J, Hitchcock IS, Coles M, Johnson S, Krauss TF. Quantifying single-cell secretion in real time using resonant hyperspectral imaging. Proc Natl Acad Sci U S A 2018; 115:13204-9. [PMID: 30530663 DOI: 10.1073/pnas.1814977115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cell communication is primarily regulated by secreted proteins, whose inhomogeneous secretion often indicates physiological disorder. Parallel monitoring of innate protein-secretion kinetics from individual cells is thus crucial to unravel systemic malfunctions. Here, we report a label-free, high-throughput method for parallel, in vitro, and real-time analysis of specific single-cell signaling using hyperspectral photonic crystal resonant technology. Heterogeneity in physiological thrombopoietin expression from individual HepG2 liver cells in response to platelet desialylation was quantified demonstrating how mapping real-time protein secretion can provide a simple, yet powerful approach for studying complex physiological systems regulating protein production at single-cell resolution.
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47
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Pearce SC, Coia HG, Karl JP, Pantoja-Feliciano IG, Zachos NC, Racicot K. Intestinal in vitro and ex vivo Models to Study Host-Microbiome Interactions and Acute Stressors. Front Physiol 2018; 9:1584. [PMID: 30483150 PMCID: PMC6240795 DOI: 10.3389/fphys.2018.01584] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/23/2018] [Indexed: 12/16/2022] Open
Abstract
The gut microbiome is extremely important for maintaining homeostasis with host intestinal epithelial, neuronal, and immune cells and this host-microbe interaction is critical during times of stress or disease. Environmental, nutritional, and cognitive stress are just a few factors known to influence the gut microbiota and are thought to induce microbial dysbiosis. Research on this bidirectional relationship as it pertains to health and disease is extensive and rapidly expanding in both in vivo and in vitro/ex vivo models. However, far less work has been devoted to studying effects of host-microbe interactions on acute stressors and performance, the underlying mechanisms, and the modulatory effects of different stressors on both the host and the microbiome. Additionally, the use of in vitro/ex vivo models to study the gut microbiome and human performance has not been researched extensively nor reviewed. Therefore, this review aims to examine current evidence concerning the current status of in vitro and ex vivo host models, the impact of acute stressors on gut physiology/microbiota as well as potential impacts on human performance and how we can parlay this information for DoD relevance as well as the broader scientific community. Models reviewed include widely utilized intestinal cell models from human and animal models that have been applied in the past for stress or microbiology research as well as ex vivo organ/tissue culture models and new innovative models including organ-on-a-chip and co-culture models.
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Affiliation(s)
- Sarah C Pearce
- Performance Nutrition Team, Combat Feeding Directorate, Natick Soldier Research, Development and Engineering Center, Natick, MA, United States
| | - Heidi G Coia
- National Research Council, The National Academies of Sciences, Engineering, and Medicine, Washington, DC, United States.,711th Human Performance Wing, Airforce Research Laboratory, Airman Systems Directorate, Human-Centered ISR Division, Molecular Mechanisms Branch, Wright-Patterson Air Force Base, Dayton, OH, United States
| | - J P Karl
- Military Nutrition Division, U.S. Army Research Institute of Environmental Medicine, Natick, MA, United States
| | - Ida G Pantoja-Feliciano
- Soldier Protection and Optimization Directorate, Natick Soldier Research, Development and Engineering Center, Natick, MA, United States
| | - Nicholas C Zachos
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kenneth Racicot
- Performance Nutrition Team, Combat Feeding Directorate, Natick Soldier Research, Development and Engineering Center, Natick, MA, United States
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48
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Curran AM, Scott-Boyer MP, Kaput J, Ryan MF, Drummond E, Gibney ER, Gibney MJ, Roche HM, Brennan L. A proteomic signature that reflects pancreatic beta-cell function. PLoS One 2018; 13:e0202727. [PMID: 30161145 PMCID: PMC6117012 DOI: 10.1371/journal.pone.0202727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/08/2018] [Indexed: 01/08/2023] Open
Abstract
AIM Proteomics has the potential to enhance early identification of beta-cell dysfunction, in conjunction with monitoring the various stages of type 2 diabetes onset. The most routine method of assessing pancreatic beta-cell function is an oral glucose tolerance test, however this method is time consuming and carries a participant burden. The objectives of this research were to identify protein signatures and pathways related to pancreatic beta-cell function in fasting blood samples. METHODS Beta-cell function measures were calculated for MECHE study participants who completed an oral glucose tolerance test and had proteomic data (n = 100). Information on 1,129 protein levels was obtained using the SOMAscan assay. Receiver operating characteristic curves were used to assess discriminatory ability of proteins of interest. Subsequent in vitro experiments were performed using the BRIN-BD11 pancreatic beta-cell line. Replication of findings were achieved in a second human cohort where possible. RESULTS Twenty-two proteins measured by aptamer technology were significantly associated with beta-cell function/HOMA-IR while 17 proteins were significantly associated with the disposition index (p ≤ 0.01). Receiver operator characteristic curves determined the protein panels to have excellent discrimination between low and high beta-cell function. Linear regression analysis determined that beta-endorphin and IL-17F have strong associations with beta-cell function/HOMA-IR, β = 0.039 (p = 0.005) and β = -0.027 (p = 0.013) respectively. Calcineurin and CRTAM were strongly associated with the disposition index (β = 0.005 and β = 0.005 respectively, p = 0.012). In vitro experiments confirmed that IL-17F modulated insulin secretion in the BRIN-BD11 cell line, with the lower concentration of 10 ng/mL significantly increasing glucose stimulated insulin secretion (p = 0.043). CONCLUSIONS Early detection of compromised beta-cell function could allow for implementation of nutritional and lifestyle interventions before progression to type 2 diabetes.
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Affiliation(s)
- Aoife M. Curran
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Food for Health Ireland (FHI), University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
| | - Marie Pier Scott-Boyer
- The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Jim Kaput
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Miriam F. Ryan
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
| | - Elaine Drummond
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Food for Health Ireland (FHI), University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
| | - Eileen R. Gibney
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Food for Health Ireland (FHI), University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
| | - Michael J. Gibney
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Food for Health Ireland (FHI), University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
| | - Helen M. Roche
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Food for Health Ireland (FHI), University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Nutrigenomics Research Group, UCD Conway Institute of Biomolecular and Biomedical Research and UCD Institute of Food and Health, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin, Republic of Ireland
| | - Lorraine Brennan
- Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- Food for Health Ireland (FHI), University College Dublin, Belfield, Ireland University College Dublin, Dublin, Republic of Ireland
- * E-mail:
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49
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Kennedy E, Hokmabadi M, Dong Z, McKelvey K, Nelson EM, Timp G. Method for Dynamically Detecting Secretions from Single Cells Using a Nanopore. Nano Lett 2018; 18:4263-4272. [PMID: 29870666 DOI: 10.1021/acs.nanolett.8b01257] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Secreted proteins mediate cell-to-cell communications. Thus, eavesdropping on the secretome could reveal the cellular phenotype, but it is challenging to detect the proteins because they are secreted only in minute amounts and then diluted in blood plasma or contaminated by cell culture medium or the lysate. In this pilot study, it is demonstrated that secretions from single cancer cells can be detected and dynamically analyzed through measurements of blockades in the electrolytic current due to single molecules translocating through a nanopore in a thin inorganic membrane. It is established that the distribution of blockades can be used to differentiate three different cancer cell lines (U937, MDA-MB-231, and MCF-7) in real time and quickly (<20 s). Importantly, the distinctive blockades associated with the chemokine CCL5, a prognostic factor for disease progression in breast cancer, along with other low-mass biomarkers of breast cancer (PI3, TIMP1, and MMP1) were identified in the context of the secretome of these three cell types, tracked with time, and used to provide information on the cellular phenotype.
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50
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Celińska E, Borkowska M, Białas W, Korpys P, Nicaud JM. Robust signal peptides for protein secretion in Yarrowia lipolytica: identification and characterization of novel secretory tags. Appl Microbiol Biotechnol 2018; 102:5221-5233. [PMID: 29704042 PMCID: PMC5959983 DOI: 10.1007/s00253-018-8966-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/13/2018] [Accepted: 03/24/2018] [Indexed: 12/18/2022]
Abstract
Upon expression of a given protein in an expression host, its secretion into the culture medium or cell-surface display is frequently advantageous in both research and industrial contexts. Hence, engineering strategies targeting folding, trafficking, and secretion of the proteins gain considerable interest. Yarrowia lipolytica has emerged as an efficient protein expression platform, repeatedly proved to be a competitive secretor of proteins. Although the key role of signal peptides (SPs) in secretory overexpression of proteins and their direct effect on the final protein titers are widely known, the number of reports on manipulation with SPs in Y. lipolytica is rather scattered. In this study, we assessed the potential of ten different SPs for secretion of two heterologous proteins in Y. lipolytica. Genomic and transcriptomic data mining allowed us to select five novel, previously undescribed SPs for recombinant protein secretion in Y. lipolytica. Their secretory potential was assessed in comparison with known, widely exploited SPs. We took advantage of Golden Gate approach, for construction of expression cassettes, and micro-volume enzymatic assays, for functional screening of large libraries of recombinant strains. Based on the adopted strategy, we identified novel secretory tags, characterized their secretory capacity, indicated the most potent SPs, and suggested a consensus sequence of a potentially robust synthetic SP to expand the molecular toolbox for engineering Y. lipolytica.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
| | - Monika Borkowska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Paulina Korpys
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Jean-Marc Nicaud
- INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Domaine de Vilvert, Micalis Institute, 78352, Jouy-en-Josas, France
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