1
|
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: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
2
|
Makthal N, Do H, Wendel BM, Olsen RJ, Helmann JD, Musser JM, Kumaraswami M. Group A Streptococcus AdcR Regulon Participates in Bacterial Defense against Host-Mediated Zinc Sequestration and Contributes to Virulence. Infect Immun 2020; 88:e00097-20. [PMID: 32393509 PMCID: PMC7375770 DOI: 10.1128/iai.00097-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
Colonization by pathogenic bacteria depends on their ability to overcome host nutritional defenses and acquire nutrients. The human pathogen group A streptococcus (GAS) encounters the host defense factor calprotectin (CP) during infection. CP inhibits GAS growth in vitro by imposing zinc (Zn) limitation. However, GAS counterstrategies to combat CP-mediated Zn limitation and the in vivo relevance of CP-GAS interactions to bacterial pathogenesis remain unknown. Here, we report that GAS upregulates the AdcR regulon in response to CP-mediated Zn limitation. The AdcR regulon includes genes encoding Zn import (adcABC), Zn sparing (rpsN.2), and Zn scavenging systems (adcAII, phtD, and phtY). Each gene in the AdcR regulon contributes to GAS Zn acquisition and CP resistance. The ΔadcC and ΔrpsN.2 mutant strains were the most susceptible to CP, whereas the ΔadcA, ΔadcAII, and ΔphtD mutant strains displayed less CP sensitivity during growth in vitro However, the ΔphtY mutant strain did not display an increased CP sensitivity. The varied sensitivity of the mutant strains to CP-mediated Zn limitation suggests distinct roles for individual AdcR regulon genes in GAS Zn acquisition. GAS upregulates the AdcR regulon during necrotizing fasciitis infection in WT mice but not in S100a9-/- mice lacking CP. This suggests that CP induces Zn deficiency in the host. Finally, consistent with the in vitro results, several of the AdcR regulon genes are critical for GAS virulence in WT mice, whereas they are dispensable for virulence in S100a9-/- mice, indicating the direct competition for Zn between CP and proteins encoded by the GAS AdcR regulon during infection.
Collapse
Affiliation(s)
- Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Brian M Wendel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| |
Collapse
|
3
|
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] [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.
Collapse
|
4
|
Streptococcus pyogenes Transcriptome Changes in the Inflammatory Environment of Necrotizing Fasciitis. Appl Environ Microbiol 2019; 85:AEM.01428-19. [PMID: 31471300 PMCID: PMC6803311 DOI: 10.1128/aem.01428-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/23/2019] [Indexed: 12/31/2022] Open
Abstract
Necrotizing fasciitis, a life-threatening subcutaneous soft-tissue infection, is principally caused by S. pyogenes. The inflammatory environment at the site of infection causes global gene expression changes for survival of the bacterium and pathogenesis. However, no known study regarding transcriptomic profiling of S. pyogenes in cases of necrotizing fasciitis has been presented. We identified 483 bacterial genes whose expression was consistently altered during infection. Our results showed that S. pyogenes infection induces drastic upregulation of the expression of virulence-associated genes and shifts metabolic pathway usage. In particular, high-level expression of toxins, such as cytolysins, proteases, and nucleases, was observed at infection sites. In addition, genes identified as consistently enriched included those related to metabolism of arginine and histidine as well as carbohydrate uptake and utilization. Conversely, genes associated with the oxidative stress response and cell division were consistently downregulated during infection. The present findings provide useful information for establishing novel treatment strategies. Streptococcus pyogenes is a major cause of necrotizing fasciitis, a life-threatening subcutaneous soft-tissue infection. At the host infection site, the local environment and interactions between the host and bacteria have effects on bacterial gene expression profiles, while the gene expression pattern of S. pyogenes related to this disease remains unknown. In this study, we used a mouse model of necrotizing fasciitis and performed RNA-sequencing (RNA-seq) analysis of S. pyogenes M1T1 strain 5448 by isolating total RNA from infected hind limbs obtained at 24, 48, and 96 h postinfection. RNA-seq analysis results identified 483 bacterial genes whose expression was consistently altered in the infected hindlimbs compared to their expression under in vitro conditions. Genes showing consistent enrichment during infection included 306 encoding molecules involved in virulence, carbohydrate utilization, amino acid metabolism, trace-metal transport, and the vacuolar ATPase transport system. Surprisingly, drastic upregulation of 3 genes, encoding streptolysin S precursor (sagA), cysteine protease (speB), and secreted DNase (spd), was noted in the present mouse model (log2 fold change, >6.0, >9.4, and >7.1, respectively). Conversely, the number of consistently downregulated genes was 177, including those associated with the oxidative stress response and cell division. These results suggest that in necrotizing fasciitis, S. pyogenes shows an altered metabolism, decreased cell proliferation, and upregulation of expression of major toxins. Our findings are considered to provide critical information for developing novel treatment strategies and vaccines for necrotizing fasciitis. IMPORTANCE Necrotizing fasciitis, a life-threatening subcutaneous soft-tissue infection, is principally caused by S. pyogenes. The inflammatory environment at the site of infection causes global gene expression changes for survival of the bacterium and pathogenesis. However, no known study regarding transcriptomic profiling of S. pyogenes in cases of necrotizing fasciitis has been presented. We identified 483 bacterial genes whose expression was consistently altered during infection. Our results showed that S. pyogenes infection induces drastic upregulation of the expression of virulence-associated genes and shifts metabolic pathway usage. In particular, high-level expression of toxins, such as cytolysins, proteases, and nucleases, was observed at infection sites. In addition, genes identified as consistently enriched included those related to metabolism of arginine and histidine as well as carbohydrate uptake and utilization. Conversely, genes associated with the oxidative stress response and cell division were consistently downregulated during infection. The present findings provide useful information for establishing novel treatment strategies.
Collapse
|
5
|
Edwards RJ, Pyzio M, Gierula M, Turner CE, Abdul-Salam VB, Sriskandan S. Proteomic analysis at the sites of clinical infection with invasive Streptococcus pyogenes. Sci Rep 2018; 8:5950. [PMID: 29654237 PMCID: PMC5899161 DOI: 10.1038/s41598-018-24216-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/20/2018] [Indexed: 01/09/2023] Open
Abstract
Invasive Streptococcus pyogenes infections are rare, with often-unexplained severity. Prompt diagnosis is desirable, as deaths can occur rapidly following onset and there is an increased, but preventable, risk to contacts. Here, proteomic analyses of clinical samples from invasive human S. pyogenes infections were undertaken to determine if novel diagnostic targets could be detected, and to augment our understanding of disease pathogenesis. Fluid samples from 17 patients with confirmed invasive S. pyogenes infection (empyema, septic arthritis, necrotising fasciitis) were analysed by proteomics for streptococcal and human proteins; 16/17 samples had detectable S. pyogenes DNA. Nineteen unique S. pyogenes proteins were identified in just 6/17 samples, and 15 of these were found in a single pleural fluid sample including streptococcal inhibitor of complement, trigger factor, and phosphoglycerate kinase. In contrast, 469 human proteins were detected in patient fluids, 177 (38%) of which could be identified as neutrophil proteins, including alpha enolase and lactotransferrin which, together, were found in all 17 samples. Our data suggest that streptococcal proteins are difficult to detect in infected fluid samples. A vast array of human proteins associated with leukocyte activity are, however, present in samples that deserve further evaluation as potential biomarkers of infection.
Collapse
Affiliation(s)
| | - Marta Pyzio
- Faculty of Medicine, Imperial College London, London, U.K
| | | | - Claire E Turner
- Faculty of Medicine, Imperial College London, London, U.K.,Molecular Biology & Biotechnology, Firth Court, University of Sheffield, Sheffield, U.K
| | | | | |
Collapse
|
6
|
Ding DC, Wen YT, Tsai RK. Pigment epithelium-derived factor from ARPE19 promotes proliferation and inhibits apoptosis of human umbilical mesenchymal stem cells in serum-free medium. Exp Mol Med 2017; 49:e411. [PMID: 29244789 PMCID: PMC5750476 DOI: 10.1038/emm.2017.219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 05/24/2017] [Accepted: 06/23/2017] [Indexed: 12/22/2022] Open
Abstract
Clinical expansion of mesenchymal stem cells (MSCs) is hampered by the lack of knowledge regarding how to prevent MSC apoptosis and promote their proliferation in serum-free medium. Our in vitro studies demonstrated that human umbilical cord MSCs (HUCMSCs) underwent apoptosis in the serum-free medium. When HUCMSCs were co-cultured with retinal pigment epithelial cells (ARPE19), however, HUCMSCs exhibited normal growth and morphology in serum-free medium. Their colony formation was promoted by the conditioned medium (CM) of ARPE19 cells on Matrigel. Proteomics analysis showed that pigment epithelium-derived factor (PEDF) was one of the most abundant extracellular proteins in the ARPE19 CM, whereas enzyme-linked immunosorbent assay confirmed that large amounts of PEDF was secreted from ARPE19 cells. Adding anti-PEDF-blocking antibodies to the co-culture of HUCMSCs with ARPE19 cells increased apoptosis of HUCMSCs. Conversely, treatment with PEDF significantly reduced apoptosis and increased proliferation of HUCMSCs in serum-free medium. PEDF was further demonstrated to exert this anti-apoptotic effect by inhibiting P53 expression to suppress caspase activation. In vivo studies demonstrated that co-injection of HUCMSCs with ARPE19 cells in immunocompromised NOD-SCID mice also increased survival and decreased apoptosis of HUCMSCs. PEDF also showed no negative effect on the mesoderm differentiation capability of HUCMSCs. In conclusion, this study is the first to demonstrate that PEDF promotes HUCMSC proliferation and protects them from apoptosis by reducing p53 expression in the serum-free medium. This study provides crucial information for clinical-scale expansion of HUCMSCs.
Collapse
Affiliation(s)
- Dah-Ching Ding
- Department of Obstetrics and Gynecology, Tzu Chi University, Hualien, Taiwan.,Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
| | - Yao-Tseng Wen
- Institute of Eye Research, Buddhist Tzu Chi General Hospital, Tzu Chi University, Hualien, Taiwan
| | - Rong-Kung Tsai
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan.,Institute of Eye Research, Buddhist Tzu Chi General Hospital, Tzu Chi University, Hualien, Taiwan
| |
Collapse
|
7
|
Fels U, Gevaert K, Van Damme P. Proteogenomics in Aid of Host-Pathogen Interaction Studies: A Bacterial Perspective. Proteomes 2017; 5:E26. [PMID: 29019919 PMCID: PMC5748561 DOI: 10.3390/proteomes5040026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/02/2017] [Accepted: 10/08/2017] [Indexed: 12/17/2022] Open
Abstract
By providing useful tools to study host-pathogen interactions, next-generation omics has recently enabled the study of gene expression changes in both pathogen and infected host simultaneously. However, since great discriminative power is required to study pathogen and host simultaneously throughout the infection process, the depth of quantitative gene expression profiling has proven to be unsatisfactory when focusing on bacterial pathogens, thus preferentially requiring specific strategies or the development of novel methodologies based on complementary omics approaches. In this review, we focus on the difficulties encountered when making use of proteogenomics approaches to study bacterial pathogenesis. In addition, we review different omics strategies (i.e., transcriptomics, proteomics and secretomics) and their applications for studying interactions of pathogens with their host.
Collapse
Affiliation(s)
- Ursula Fels
- VIB-UGent Center for Medical Biotechnology, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
| | - Petra Van Damme
- VIB-UGent Center for Medical Biotechnology, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
| |
Collapse
|
8
|
Abstract
SIGNIFICANCE Secreted proteins are important both as signaling molecules and potential biomarkers. Recent Advances: Protein can undergo different types of oxidation, both in physiological conditions or under oxidative stress. Several redox proteomics techniques have been successfully applied to the identification of glutathionylated proteins, an oxidative post-translational modification consisting in the formation of a mixed disulfide between a protein cysteine and glutathione. Redox proteomics has also been used to study other forms of protein oxidation. CRITICAL ISSUES Because of the highest proportion of free cysteines in the cytosol, redox proteomics of protein thiols has focused, so far, on intracellular proteins. However, plasma proteins, such as transthyretin and albumin, have been described as glutathionylated or cysteinylated. The present review discusses the redox state of protein cysteines in relation to their cellular distribution. We describe the various approaches used to detect secreted glutathionylated proteins, the only thiol modification studied so far in secreted proteins, and the specific problems presented in the study of the secretome. FUTURE DIRECTIONS This review focusses on glutathionylated proteins secreted under inflammatory conditions and that may act as soluble mediators (cytokines). Future studies on the redox secretome (including other forms of oxidation) might identify new soluble mediators and biomarkers of oxidative stress. Antioxid. Redox Signal. 26, 299-312.
Collapse
Affiliation(s)
- Pietro Ghezzi
- 1 Brighton & Sussex Medical School , Brighton, United Kingdom
| | - Philippe Chan
- 2 PISSARO Proteomic Platform, Institute for Research and Innovation in Biomedicine, University of Rouen , Rouen, France
| |
Collapse
|
9
|
Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A Streptococcus Biofilms. mSystems 2016; 1:mSystems00149-16. [PMID: 27933318 PMCID: PMC5141267 DOI: 10.1128/msystems.00149-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 11/01/2016] [Indexed: 11/20/2022] Open
Abstract
Prokaryotes are thought to regulate their proteomes largely at the level of transcription. However, the results from this first set of global transcriptomic and proteomic analyses of paired microbial samples presented here show that this assumption is false for the majority of genes and their products in S. pyogenes. In addition, the tenuousness of the link between transcription and translation becomes even more pronounced when microbes exist in a biofilm or a stationary planktonic state. Since the transcriptome level does not usually equal the proteome level, the validity attributed to gene expression studies as well as proteomic studies in microbial analyses must be brought into question. Therefore, the results attained by either approach, whether RNA-seq or shotgun proteomics, must be taken in context and evaluated with particular care since they are by no means interchangeable. To gain a better understanding of the genes and proteins involved in group A Streptococcus (GAS; Streptococcus pyogenes) biofilm growth, we analyzed the transcriptome, cellular proteome, and cell wall proteome from biofilms at different stages and compared them to those of plankton-stage GAS. Using high-throughput RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) shotgun proteomics, we found distinct expression profiles in the transcriptome and proteome. A total of 46 genes and 41 proteins showed expression across the majority of biofilm time points that was consistently higher or consistently lower than that seen across the majority of planktonic time points. However, there was little overlap between the genes and proteins on these two lists. In line with other studies comparing transcriptomic and proteomic data, the overall correlation between the two data sets was modest. Furthermore, correlation was poorest for biofilm samples. This suggests a high degree of regulation of protein expression by nontranscriptional mechanisms. This report illustrates the benefits and weaknesses of two different approaches to global expression profiling, and it also demonstrates the advantage of using proteomics in conjunction with transcriptomics to gain a more complete picture of global expression within biofilms. In addition, this report provides the fullest characterization of expression patterns in GAS biofilms currently available. IMPORTANCE Prokaryotes are thought to regulate their proteomes largely at the level of transcription. However, the results from this first set of global transcriptomic and proteomic analyses of paired microbial samples presented here show that this assumption is false for the majority of genes and their products in S. pyogenes. In addition, the tenuousness of the link between transcription and translation becomes even more pronounced when microbes exist in a biofilm or a stationary planktonic state. Since the transcriptome level does not usually equal the proteome level, the validity attributed to gene expression studies as well as proteomic studies in microbial analyses must be brought into question. Therefore, the results attained by either approach, whether RNA-seq or shotgun proteomics, must be taken in context and evaluated with particular care since they are by no means interchangeable.
Collapse
|
10
|
Crotti S, Piccoli M, Rizzolio F, Giordano A, Nitti D, Agostini M. Extracellular Matrix and Colorectal Cancer: How Surrounding Microenvironment Affects Cancer Cell Behavior? J Cell Physiol 2016; 232:967-975. [PMID: 27775168 DOI: 10.1002/jcp.25658] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 10/20/2016] [Indexed: 12/12/2022]
Abstract
Colorectal cancer (CRC) whit more than a million of new cases per year is one of the most common registered cancers worldwide with few treatment options especially for advanced and metastatic patients.The tumor microenvironment is composed by extracellular matrix (ECM), cells, and interstitial fluids. Among all these constituents, in the last years an increased interest around the ECM and its potential role in cancer tumorigenesis is arisen. During cancer progression the ECM structure and composition became disorganized, allowing cellular transformation and metastasis. Up to now, the focus has mainly been on the characterization of CRC microenvironment analyzing separately structural ECM components or cell secretome modifications. A more extensive view that interconnects these aspects should be addressed. In this review, biochemical (secretome) and biomechanical (structure and architecture) changes of tumor microenvironment will be discussed, giving suggestions on how these changes can affect cancer cell behavior. J. Cell. Physiol. 232: 967-975, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Sara Crotti
- Institute of Paediatric Research-Città della Speranza, Corso Stati Uniti 4, Padova, Italy
| | - Martina Piccoli
- Institute of Paediatric Research-Città della Speranza, Corso Stati Uniti 4, Padova, Italy
| | - Flavio Rizzolio
- Department of Translational Research, IRCCS-National Cancer Institute, Aviano, Italy
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania.,Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - Donato Nitti
- First Surgical Clinic Section, Department of Surgical, Oncological and Gastroenterological Sciences, University of Padua, Via Nicolo Giustiniani 2, Padova, Italy
| | - Marco Agostini
- Institute of Paediatric Research-Città della Speranza, Corso Stati Uniti 4, Padova, Italy.,First Surgical Clinic Section, Department of Surgical, Oncological and Gastroenterological Sciences, University of Padua, Via Nicolo Giustiniani 2, Padova, Italy
| |
Collapse
|
11
|
Santos GBD, Monteiro KM, da Silva ED, Battistella ME, Ferreira HB, Zaha A. Excretory/secretory products in the Echinococcus granulosus metacestode: is the intermediate host complacent with infection caused by the larval form of the parasite? Int J Parasitol 2016; 46:843-856. [PMID: 27771257 DOI: 10.1016/j.ijpara.2016.07.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 12/11/2022]
Abstract
The genus Echinococcus consists of parasites that have a life cycle with two mammalian hosts. Their larval stage, called the hydatid cyst, develops predominantly in the liver and lungs of intermediate hosts. The hydatid cyst is the causative agent of cystic hydatid disease and the species Echinococcus granulosus, G1 haplotype, is responsible for the vast majority of cases in humans, cattle and sheep. Protein characterization in hydatid cysts is essential for better understanding of the host-parasite relationship and the fertility process of Echinococcus. The aims of this work were the identification and quantitative comparison of proteins found in hydatid fluid from fertile and infertile cysts from E. granulosus, in order to highlight possible mechanisms involved in cyst fertility or infertility. Hydatid fluid samples containing proteins from both E. granulosus and Bos taurus were analysed by LC-MS/MS. Our proteomic analysis of fertile and infertile cysts allowed identification of a total of 498 proteins, of which 153 proteins were exclusively identified in the fertile cyst, 271 in the infertile cyst, and 74 in both. Functional in silico analysis allowed us to highlight some important aspects: (i) clues about the possible existence of an "arms race" involving parasite and host responses in fertile and infertile cysts; (ii) a number of proteins in hydatid fluid without functional annotation or with possible alternative functions; (iii) the presence of extracellular vesicles such as exosomes, which was confirmed by transmission electron microscopy.
Collapse
Affiliation(s)
- Guilherme B Dos Santos
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Caixa Postal 15005, CEP 91501-970 Porto Alegre, RS, Brazil
| | - Karina M Monteiro
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Caixa Postal 15005, CEP 91501-970 Porto Alegre, RS, Brazil; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, CEP 91501-970 Porto Alegre, RS, Brazil
| | - Edileuza Danieli da Silva
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Caixa Postal 15005, CEP 91501-970 Porto Alegre, RS, Brazil
| | - Maria Eduarda Battistella
- Graduação em Biotecnologia, Universidade Federal do Rio Grande do Sul, Caixa Postal 15005, CEP 91501-970 Porto Alegre, RS, Brazil
| | - Henrique B Ferreira
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Caixa Postal 15005, CEP 91501-970 Porto Alegre, RS, Brazil; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, CEP 91501-970 Porto Alegre, RS, Brazil
| | - Arnaldo Zaha
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Caixa Postal 15005, CEP 91501-970 Porto Alegre, RS, Brazil; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, CEP 91501-970 Porto Alegre, RS, Brazil.
| |
Collapse
|
12
|
Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG. Proteomic investigation of the secretome ofCellvibrio japonicusduring growth on chitin. Proteomics 2016; 16:1904-14. [DOI: 10.1002/pmic.201500419] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 04/05/2016] [Accepted: 05/09/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Tina Rise Tuveng
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Magnus Øverlie Arntzen
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Oskar Bengtsson
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Jeffrey G. Gardner
- Department of Biological Sciences; University of Maryland - Baltimore County; Baltimore MD USA
| | - Gustav Vaaje-Kolstad
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Vincent G.H. Eijsink
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| |
Collapse
|
13
|
Marco-Ramell A, de Almeida AM, Cristobal S, Rodrigues P, Roncada P, Bassols A. Proteomics and the search for welfare and stress biomarkers in animal production in the one-health context. MOLECULAR BIOSYSTEMS 2016; 12:2024-35. [DOI: 10.1039/c5mb00788g] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stress and welfare are important factors in animal production in the context of growing production optimization and scrutiny by the general public.
Collapse
Affiliation(s)
- A. Marco-Ramell
- Departament de Bioquímica i Biologia Molecular
- Facultat de Veterinària
- Universitat Autònoma de Barcelona
- 08193 Cerdanyola del Vallès
- Spain
| | - A. M. de Almeida
- Instituto de Biologia Experimental e Tecnologica
- Oeiras
- Portugal
- CIISA/FMV – Centro Interdisciplinar de Investigação em Sanidade Animal
- Faculdade de Medicina Veterinária
| | - S. Cristobal
- Department of Clinical and Experimental Medicine
- Cell Biology
- Faculty of Medicine
- Linköping University
- Linköping
| | - P. Rodrigues
- CCMAR
- Center of Marine Science
- University of Algarve
- 8005-139 Faro
- Portugal
| | - P. Roncada
- Istituto Sperimentale Italiano L. Spallanzani
- Milano
- Italy
| | - A. Bassols
- Departament de Bioquímica i Biologia Molecular
- Facultat de Veterinària
- Universitat Autònoma de Barcelona
- 08193 Cerdanyola del Vallès
- Spain
| |
Collapse
|