1
|
Barbosa JMG, Filho NRA. The human volatilome meets cancer diagnostics: past, present, and future of noninvasive applications. Metabolomics 2024; 20:113. [PMID: 39375265 DOI: 10.1007/s11306-024-02180-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 09/22/2024] [Indexed: 10/09/2024]
Abstract
BACKGROUND Cancer is a significant public health problem, causing dozens of millions of deaths annually. New cancer screening programs are urgently needed for early cancer detection, as this approach can improve treatment outcomes and increase patient survival. The search for affordable, noninvasive, and highly accurate cancer detection methods revealed a valuable source of tumor-derived metabolites in the human metabolome through the exploration of volatile organic compounds (VOCs) in noninvasive biofluids. AIM OF REVIEW This review discusses volatilomics-based approaches for cancer detection using noninvasive biomatrices (breath, saliva, skin secretions, urine, feces, and earwax). We presented the historical background, the latest approaches, and the required stages for clinical validation of volatilomics-based methods, which are still lacking in terms of making noninvasive methods available and widespread to the population. Furthermore, insights into the usefulness and challenges of volatilomics in clinical implementation steps for each biofluid are highlighted. KEY SCIENTIFIC CONCEPTS OF REVIEW We outline the methodologies for using noninvasive biomatrices with up-and-coming clinical applications in cancer diagnostics. Several challenges and advantages associated with the use of each biomatrix are discussed, aiming at encouraging the scientific community to strengthen efforts toward the necessary steps to speed up the clinical translation of volatile-based cancer detection methods, as well as discussing in favor of (i) hybrid applications (i.e., using more than one biomatrix) to describe metabolite modulations that can be "cancer volatile fingerprints" and (ii) in multi-omics approaches integrating genomics, transcriptomics, and proteomics into the volatilomic data, which might be a breakthrough for diagnostic purposes, onco-pathway assessment, and biomarker validations.
Collapse
Affiliation(s)
- João Marcos G Barbosa
- Laboratório de Métodos de Extração E Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus II - Samambaia, Goiânia, GO, 74690-900, Brazil.
| | - Nelson R Antoniosi Filho
- Laboratório de Métodos de Extração E Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus II - Samambaia, Goiânia, GO, 74690-900, Brazil.
| |
Collapse
|
2
|
Xia YQ, Yang Y, Liu Y, Li CH, Liu PF. Investigation of copper-induced intestinal damage and proteome alterations in Takifugu rubripes: Potential health risks and environmental toxicology detection. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 282:116718. [PMID: 39024957 DOI: 10.1016/j.ecoenv.2024.116718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 07/06/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Abstract
Copper is one of the predominant water pollutants. Excessive exposure to copper can cause harm to animal health, affecting the central nervous system and causing blood abnormalities. Cuproptosis is a novel form of cell death that differs from previous programmed cell death methods. However, the impact of copper on the intestines remains unclear. Therefore, we investigated the effects of different concentrations of copper exposure on the intestinal proteome of Takifugu rubripes (T. rubripes). Relevant biomarkers were used to detect cuproptosis. We revealed the crosstalk relationship between cuproptosis and self-rescue at different concentrations, and discussed the feasibility of using potential cuproptosis indicators as anti-infection factors. We observed intestinal damage in the three copper exposure groups, especially in T. rubripes treated with 100 and 500 μg/L copper, with shedding and breakage of intestinal villus and fuzzy and loose structure of intestinal mucosa. The presence of copper stress not only causes cuproptosis but also oxidative damage caused by reactive oxygen species (ROS). The results of quantitative proteomics by TMT showed that compared to the 50 and 100 μg/L copper exposure groups, the expression of glutaminase, pyruvate kinase, and skin mucus lectin in the 500 μg/L group was significantly increased. The positive mediators COX5A and CTNNB1, as well as the negative mediators CD4 and FDXR, were found to be differentially expressed. Using the protein expression trends of cuproptosis indicator factors FDX1 and DLAT to indicate the concentration of copper ions in the environment. In addition, we found a new effect of promoting ferroptosis: providing additional copper ions can activate the phenomenon of ferroptosis. Our results expand our understanding of the potential health risks of copper in T. rubripes. At the same time, it is of great significance for the process of copper poisoning and the development of new environmental toxicology detection reagents.
Collapse
Affiliation(s)
- Yu-Qing Xia
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China; Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian 116023, PR China
| | - Yi Yang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian 116023, PR China; College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, PR China
| | - Ying Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian 116023, PR China; College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China
| | - Cheng-Hua Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Peng-Fei Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian 116023, PR China; College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, PR China.
| |
Collapse
|
3
|
Paes Leme AF, Yokoo S, Normando AGC, Ormonde JVS, Domingues RR, Cruz FF, Silva PL, Souza BSF, Dos Santos CC, Castro-Faria-Neto H, Martins CM, Lopes-Pacheco M, Rocco PRM. Proteomics of serum-derived extracellular vesicles are associated with the severity and different clinical profiles of patients with COVID-19: An exploratory secondary analysis. Cytotherapy 2024; 26:444-455. [PMID: 38363248 DOI: 10.1016/j.jcyt.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND AIMS Coronavirus disease 2019 (COVID-19) is characterized by a broad spectrum of clinical manifestations with the potential to progress to multiple organ dysfunction in severe cases. Extracellular vesicles (EVs) carry a range of biological cargoes, which may be used as biomarkers of disease state. METHODS An exploratory secondary analysis of the SARITA-2 and SARITA-1 datasets (randomized clinical trials on patients with mild and moderate/severe COVID-19) was performed. Serum-derived EVs were used for proteomic analysis to identify enriched biological processes and key proteins, thus providing insights into differences in disease severity. Serum-derived EVs were separated from patients with COVID-19 by size exclusion chromatography and nanoparticle tracking analysis was used to determine particle concentration and diameter. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was performed to identify and quantify protein signatures. Bioinformatics and multivariate statistical analysis were applied to distinguish candidate proteins associated with disease severity (mild versus moderate/severe COVID-19). RESULTS No differences were observed in terms of the concentration and diameter of enriched EVs between mild (n = 14) and moderate/severe (n = 30) COVID-19. A total of 414 proteins were found to be present in EVs, of which 360 were shared while 48 were uniquely present in severe/moderate compared to mild COVID-19. The main biological signatures in moderate/severe COVID-19 were associated with platelet degranulation, exocytosis, complement activation, immune effector activation, and humoral immune response. Von Willebrand factor, serum amyloid A-2 protein, histone H4 and H2A type 2-C, and fibrinogen β-chain were the most differentially expressed proteins between severity groups. CONCLUSION Exploratory proteomic analysis of serum-derived EVs from patients with COVID-19 detected key proteins related to immune response and activation of coagulation and complement pathways, which are associated with disease severity. Our data suggest that EV proteins may be relevant biomarkers of disease state and prognosis.
Collapse
Affiliation(s)
- Adriana F Paes Leme
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, São Paulo, Brazil
| | - Sami Yokoo
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, São Paulo, Brazil
| | - Ana Gabriela C Normando
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, São Paulo, Brazil
| | - João Vitor S Ormonde
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, São Paulo, Brazil
| | - Romenia Ramos Domingues
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, São Paulo, Brazil
| | - Fernanda F Cruz
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Institute of Science and Technology for Regenerative Medicine, Rio de Janeiro, Brazil; Rio de Janeiro Innovation Network in Nanosystems for Health-NanoSaúde, Research Support Foundation of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro L Silva
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Institute of Science and Technology for Regenerative Medicine, Rio de Janeiro, Brazil; Rio de Janeiro Innovation Network in Nanosystems for Health-NanoSaúde, Research Support Foundation of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno S F Souza
- Goncalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil; D'Or Institute for Research and Education (IDOR), Salvador, Bahia, Brazil; Center for Biotechnology and Cell Therapy, São Rafael Hospital, Salvador, Bahia, Brazil
| | - Claudia C Dos Santos
- The Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Toronto, Ontario, Canada; Institute of Medical Sciences and Interdepartmental Division of Critical Care, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Miquéias Lopes-Pacheco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Patricia R M Rocco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Institute of Science and Technology for Regenerative Medicine, Rio de Janeiro, Brazil; Rio de Janeiro Innovation Network in Nanosystems for Health-NanoSaúde, Research Support Foundation of the State of Rio de Janeiro, Rio de Janeiro, Brazil.
| |
Collapse
|
4
|
Bruszel B, Tóth-Molnár E, Janáky T, Szabó Z. Sources of Variance in Human Tear Proteomic Samples: Statistical Evaluation, Quality Control, Normalization, and Biological Insight. Int J Mol Sci 2024; 25:1559. [PMID: 38338841 PMCID: PMC10855525 DOI: 10.3390/ijms25031559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Human tear fluid contains numerous compounds, which are present in highly variable amounts owing to the dynamic and multipurpose functions of tears. A better understanding of the level and sources of variance is essential for determining the functions of the different tear components and the limitations of tear samples as a potential biomarker source. In this study, a quantitative proteomic method was used to analyze variations in the tear protein profiles of healthy volunteers. High day-to-day and inter-eye personal variances were observed in the tear volumes, protein content, and composition of the tear samples. Several normalization and outlier exclusion approaches were evaluated to decrease variances. Despite the intrapersonal variances, statistically significant differences and cluster analysis revealed that proteome profile and immunoglobulin composition of tear fluid present personal characteristics. Using correlation analysis, we could identify several correlating protein clusters, mainly related to the source of the proteins. Our study is the first attempt to achieve more insight into the biochemical background of human tears by statistical evaluation of the experimentally observed dynamic behavior of the tear proteome. As a pilot study for determination of personal protein profiles of the tear fluids of individual patients, it contributes to the application of this noninvasively collectible body fluid in personal medicine.
Collapse
Affiliation(s)
- Bella Bruszel
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (B.B.); (T.J.)
| | - Edit Tóth-Molnár
- Department of Ophtalmology, Albert Szent-Györgyi Health Centre, University of Szeged, Korányi Fasor 10-11, H-6720 Szeged, Hungary;
| | - Tamás Janáky
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (B.B.); (T.J.)
| | - Zoltán Szabó
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (B.B.); (T.J.)
| |
Collapse
|
5
|
Yang Y, Liu Y, Xia Y, Cheng J, Liu P. Tandem mass tag (TMT) quantitative proteomics and phosphoproteomic of Takifugu rubripes infected with Cryptocaryon irritans. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101124. [PMID: 37647835 DOI: 10.1016/j.cbd.2023.101124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
In this study, we identified the differentially expressed proteins in gills stimulated by infected ciliates and analyzed the immune mechanisms of T. rubripes infected with the ciliate Cryptocaryon irritans. Through liquid chromatography analysis, a total of 144 proteins were identified with significant differences, of which 58 were upregulated and 86 were downregulated. Among phosphorylated proteins, we identified a total of 167 significantly different phosphorylated proteins, of which 44 were upregulated, 123 were downregulated, 60 were upregulated, and 208 were downregulated. We analyzed the data of proteomics and Phosphorylated proteome quantification protein omics to finally identify three phosphorylated proteins (RPS27, eNOS and CaM) and two phosphorylated protein kinases(CaMKII and MAPK1) as potential biomarkers for T. rubripes immune responses. We finally identified three phosphorylated proteins (RPS27, eNOS and CaM) and two phosphorylated protein kinases (CaMKII and MAPK1) as potential biomarkers of immune response of T. rubripes. Our research findings provide new insights into the immune mechanism of T. rubripes, which may serve as an effective indicator of C. irritans infection in T. rubripes.
Collapse
Affiliation(s)
- Yi Yang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China
| | - Yanyun Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China
| | - Yuqing Xia
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jianxin Cheng
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Pengfei Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China.
| |
Collapse
|
6
|
Zawrotniak M, Juszczak M, Mosio-Wójcik J, Rapala-Kozik M. Neutrophil extracellular traps in upper respiratory tract secretions: insights into infectious and allergic rhinitis. Front Immunol 2023; 14:1295921. [PMID: 38077338 PMCID: PMC10702990 DOI: 10.3389/fimmu.2023.1295921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction Neutrophil extracellular traps (NETs) are structures released by neutrophils in response to various infections. NETs have a biocidal role and have been demonstrated to be effective against bacteria, fungi, viruses, and parasites. Depending on the situation, NETs can protect the host from pathogen invasion or contribute to the development of autoimmune diseases such as cystic fibrosis and rheumatoid arthritis. In this study, we aimed to investigate the occurrence of NET as one of the components in upper respiratory tract secretions in infectious and allergic diseases. Methods Nasal mucus was collected from donors diagnosed with infectious rhinitis or allergic rhinitis. The extracellular DNA content was determined using SytoxGreen staining, and the total protein pool was determined using the microBCA method. Micrococcal nuclease was used to digest the samples and ELISA was employed to identify the NET proteins. The enzymatic activity of elastase was determined. Results Our findings showed that nasal mucus collected from patients with infectious rhinosinusitis contained extracellular DNA that could come from a variety of sources, responsible for increasing the density and viscosity of secretions, as well as NETs proteins. The identified enzymatic activity of NET elastase indicates the possible irritation of nasal tissues. However, the DNA content was not identified in the samples from allergic patients. In addition, we have shown in preliminary studies that therapy using N-acetylcysteine can liquefy nasal secretions. Discussion The study suggests that the composition of nasal mucus varies according to the cause of mucosal irritation. The presence of DNA and NET proteins can have severe consequences for the therapeutic process prolonging treatment. The low viscosity of nasal mucus in allergic patients facilitates mucosal flushing and the removal of allergens. Understanding the occurrence and role of NETs in various respiratory diseases is critical for developing effective treatment strategies that consider the complex interaction between the immune system and pathogens. The results of this study suggest that NETs may be present in upper respiratory tract secretions with an infectious background, supporting basic defense mechanisms using eosinophils and EETs. Further research is needed to explore the potential of NETs as a therapeutic target in respiratory diseases.
Collapse
Affiliation(s)
- Marcin Zawrotniak
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Magdalena Juszczak
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | | | - Maria Rapala-Kozik
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| |
Collapse
|
7
|
Pant P, Sircar R, Prasad R, Prasad HO, Chitme HR. Protein Expression and Bioinformatics Study of Granulosa Cells of Polycystic Ovary Syndrome Expressed Under the Influence of DHEA. Clin Med Insights Endocrinol Diabetes 2023; 16:11795514231206732. [PMID: 38023736 PMCID: PMC10644732 DOI: 10.1177/11795514231206732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023] Open
Abstract
Background The reproductive system is heavily dependent on ovarian follicles, which are made up of germ cells (oocytes) and granulosa cells (GCs), including cumulus granulosa cells (CGCs) and mural granulosa cells (MGCs). Understanding their normal and steroid-induced functions is the key to understanding the pathophysiology of endocrinal diseases in women. Objective This study investigated the differentially expressed proteins by CGCs and MGCs of patients with polycystic ovarian syndrome (PCOS) and without subsequent exposure to dehydroepiandrosterone sulfate (DHEAS) and functional differentiation. Design The present study was observational and experimental study carried out in hospital involving 80 female patients undergoing IVF for infertility. Methods In this study, we isolated CGCs and MGCs from the follicular fluid of both PCOS and non-PCOS patients undergoing in vitro fertilization (IVF). The cells were cultured and treated with DHEAS for 48 hours, and these cells were extracted, digested, and analyzed by tandem mass spectrometry followed by processing of the results using open-source bioinformatics tools. Results The present investigation discovered 276 and 341 proteins in CGCs and MGCs, respectively. DHEAS reduced the number of proteins expressed by CGCs and MGCs to 34 and 57 from 91 and 94, respectively. Venn results of CGCs revealed 49, 53, 36, and 21 proteins in normal CGCs, PCOS-CGCs, post-DHEAS, and PCOS-CGCs, respectively. Venn analysis of MGCs showed 51 proteins specific to PCOS and 29 shared by normal and PCOS samples after DHEAS therapy. MGCs express the most binding and catalytic proteins, whereas CGCs express transporter-related proteins. A protein pathway study demonstrated considerable differences between normal and PCOS samples, while DHEAS-treated samples of both cell lines showed distinct pathways. String findings identified important network route components such as albumin, actin, apolipoprotein, complement component C3, and heat shock protein. Conclusion This is the first study to show how DHEAS-induced stress affects the expression of proteins by MGCs and CGCs isolated from normal and PCOS patients. Further studies are recommended to identify PCOS biomarkers from CGCs and MGCs expressed under the influence of DHEAS.
Collapse
Affiliation(s)
- Pankaj Pant
- Faculty of Pharmacy, DIT University, Dehradun, Uttarakhand, India
| | - Reema Sircar
- Indira IVF Hospital, Dehradun, Uttarakhand, India
| | - Ritu Prasad
- Morpheus Prasad International Hospital, Dehradun, Uttarakhand, India
| | - Hari Om Prasad
- Morpheus Prasad International Hospital, Dehradun, Uttarakhand, India
| | | |
Collapse
|
8
|
Kalló G, Bertalan PM, Márton I, Kiss C, Csősz É. Salivary Chemical Barrier Proteins in Oral Squamous Cell Carcinoma-Alterations in the Defense Mechanism of the Oral Cavity. Int J Mol Sci 2023; 24:13657. [PMID: 37686462 PMCID: PMC10487546 DOI: 10.3390/ijms241713657] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is one of the most frequent types of head and neck cancer. Despite the genetic and environmental risk factors, OSCC is also associated with microbial infections and/or dysbiosis. The secreted saliva serves as the chemical barrier of the oral cavity and, since OSCC can alter the protein composition of saliva, our aim was to analyze the effect of OSCC on the salivary chemical barrier proteins. Publicly available datasets regarding the analysis of salivary proteins from patients with OSCC and controls were collected and examined in order to identify differentially expressed chemical barrier proteins. Network analysis and gene ontology (GO) classification of the differentially expressed chemical barrier proteins were performed as well. One hundred and twenty-seven proteins showing different expression pattern between the OSCC and control groups were found. Protein-protein interaction networks of up- and down-regulated proteins were constructed and analyzed. The main hub proteins (IL-6, IL-1B, IL-8, TNF, APOA1, APOA2, APOB, APOC3, APOE, and HP) were identified and the enriched GO terms were examined. Our study highlighted the importance of the chemical barrier of saliva in the development of OSCC.
Collapse
Affiliation(s)
- Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (P.M.B.); (I.M.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Petra Magdolna Bertalan
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (P.M.B.); (I.M.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Ildikó Márton
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (P.M.B.); (I.M.); (É.C.)
| | - Csongor Kiss
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, 4032 Debrecen, Hungary;
| | - Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (P.M.B.); (I.M.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| |
Collapse
|
9
|
Shama A, Soni T, Jawanda IK, Upadhyay G, Sharma A, Prabha V. The Latest Developments in Using Proteomic Biomarkers from Urine and Serum for Non-Invasive Disease Diagnosis and Prognosis. Biomark Insights 2023; 18:11772719231190218. [PMID: 37528936 PMCID: PMC10387783 DOI: 10.1177/11772719231190218] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/10/2023] [Indexed: 08/03/2023] Open
Abstract
Due to diagnostic improvements, medical diagnostics is demanding non-invasive or minimally invasive methods. Non-invasively obtained body fluids (eg., Urine, serum) can replace cerebral fluid, amniotic fluid, synovial fluid, bronchoalveolar lavage fluid, and others for diagnostic reasons. Many illnesses are induced by perturbations of cellular signaling pathways and associated pathway networks as a result of genetic abnormalities. These disturbances are represented by a shift in the protein composition of the fluids surrounding the tissues and organs that is, tissue interstitial fluid (TIF). These variant proteins may serve as diagnostic "signatures" for a variety of disorders. This review provides a concise summary of urine and serum biomarkers that may be used for the diagnosis and prognosis of a variety of disorders, including cancer, brain diseases, kidney diseases, and other system diseases. The studies reviewed in this article suggest that serum and urine biomarkers of various illnesses may be therapeutically useful for future diagnostics. Correct illness management is crucial for disease prognosis, hence non-invasive serum and urine biomarkers have been extensively studied for diagnosis, subclassification, monitoring disease activity, and predicting treatment results and consequences.
Collapse
Affiliation(s)
- Anurag Shama
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Thomson Soni
- Department of Microbiology, Panjab University, Chandigarh, India
| | | | - Garima Upadhyay
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Anshika Sharma
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Vijay Prabha
- Department of Microbiology, Panjab University, Chandigarh, India
| |
Collapse
|
10
|
Pagani L, Chinello C, Risca G, Capitoli G, Criscuolo L, Lombardi A, Ungaro R, Mangioni D, Piga I, Muscatello A, Blasi F, Favalli A, Martinovic M, Gori A, Bandera A, Grifantini R, Magni F. Plasma Proteomic Variables Related to COVID-19 Severity: An Untargeted nLC-MS/MS Investigation. Int J Mol Sci 2023; 24:ijms24043570. [PMID: 36834989 PMCID: PMC9962231 DOI: 10.3390/ijms24043570] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection leads to a wide range of clinical manifestations and determines the need for personalized and precision medicine. To better understand the biological determinants of this heterogeneity, we explored the plasma proteome of 43 COVID-19 patients with different outcomes by an untargeted liquid chromatography-mass spectrometry approach. The comparison between asymptomatic or pauci-symptomatic subjects (MILDs), and hospitalised patients in need of oxygen support therapy (SEVEREs) highlighted 29 proteins emerged as differentially expressed: 12 overexpressed in MILDs and 17 in SEVEREs. Moreover, a supervised analysis based on a decision-tree recognised three proteins (Fetuin-A, Ig lambda-2chain-C-region, Vitronectin) that are able to robustly discriminate between the two classes independently from the infection stage. In silico functional annotation of the 29 deregulated proteins pinpointed several functions possibly related to the severity; no pathway was associated exclusively to MILDs, while several only to SEVEREs, and some associated to both MILDs and SEVEREs; SARS-CoV-2 signalling pathway was significantly enriched by proteins up-expressed in SEVEREs (SAA1/2, CRP, HP, LRG1) and in MILDs (GSN, HRG). In conclusion, our analysis could provide key information for 'proteomically' defining possible upstream mechanisms and mediators triggering or limiting the domino effect of the immune-related response and characterizing severe exacerbations.
Collapse
Affiliation(s)
- Lisa Pagani
- Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Clizia Chinello
- Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
- Correspondence: ; Tel.:+39-333-5905725
| | - Giulia Risca
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre—B4, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Giulia Capitoli
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre—B4, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Lucrezia Criscuolo
- Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Andrea Lombardi
- Department of Pathophysiology and Transplantation, University of Milano, 20122 Milano, Italy
- Infectious Diseases Unit, IRCCS Ca’ Granda Ospedale Maggiore Policlinico Foundation, 20122 Milano, Italy
| | - Riccardo Ungaro
- Infectious Diseases Unit, IRCCS Ca’ Granda Ospedale Maggiore Policlinico Foundation, 20122 Milano, Italy
| | - Davide Mangioni
- Department of Pathophysiology and Transplantation, University of Milano, 20122 Milano, Italy
- Infectious Diseases Unit, IRCCS Ca’ Granda Ospedale Maggiore Policlinico Foundation, 20122 Milano, Italy
| | - Isabella Piga
- Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Antonio Muscatello
- Infectious Diseases Unit, IRCCS Ca’ Granda Ospedale Maggiore Policlinico Foundation, 20122 Milano, Italy
| | - Francesco Blasi
- Department of Pathophysiology and Transplantation, University of Milano, 20122 Milano, Italy
- Respiratory Unit and Cystic Fibrosis Adult Center, Internal Medicine Department, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy
| | - Andrea Favalli
- Istituto Nazionale di Genetica Molecolare (INGM), 20122 Milano, Italy
| | | | - Andrea Gori
- Department of Pathophysiology and Transplantation, University of Milano, 20122 Milano, Italy
- Infectious Diseases Unit, IRCCS Ca’ Granda Ospedale Maggiore Policlinico Foundation, 20122 Milano, Italy
| | - Alessandra Bandera
- Department of Pathophysiology and Transplantation, University of Milano, 20122 Milano, Italy
- Infectious Diseases Unit, IRCCS Ca’ Granda Ospedale Maggiore Policlinico Foundation, 20122 Milano, Italy
| | - Renata Grifantini
- Istituto Nazionale di Genetica Molecolare (INGM), 20122 Milano, Italy
| | - Fulvio Magni
- Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| |
Collapse
|
11
|
Wang S, Yang M, Li R, Bai J. Current advances in noninvasive methods for the diagnosis of oral squamous cell carcinoma: a review. Eur J Med Res 2023; 28:53. [PMID: 36707844 PMCID: PMC9880940 DOI: 10.1186/s40001-022-00916-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/28/2022] [Indexed: 01/28/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC), one of the most common types of cancers worldwide, is diagnosed mainly through tissue biopsy. However, owing to the tumor heterogeneity and other drawbacks, such as the invasiveness of the biopsy procedure and high cost and limited usefulness of longitudinal surveillance, there has been a focus on adopting more rapid, economical, and noninvasive screening methods. Examples of these include liquid biopsy, optical detection systems, oral brush cytology, microfluidic detection, and artificial intelligence auxiliary diagnosis, which have their own strengths and weaknesses. Extensive research is being performed on various liquid biopsy biomarkers, including novel microbiome components, noncoding RNAs, extracellular vesicles, and circulating tumor DNA. The majority of these elements have demonstrated encouraging clinical outcomes in early OSCC detection. This review summarizes the screening methods for OSCC with a focus on providing new guiding strategies for the diagnosis of the disease.
Collapse
Affiliation(s)
- Shan Wang
- grid.443397.e0000 0004 0368 7493Department of Oral Pathology, School of Stomatology, Hainan Medical College, Haikou, 571199 People’s Republic of China ,grid.443397.e0000 0004 0368 7493Department of Stomatology, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216 People’s Republic of China
| | - Mao Yang
- grid.13291.380000 0001 0807 1581West China School of Stomatology, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Ruiying Li
- grid.443397.e0000 0004 0368 7493Department of Oral Pathology, School of Stomatology, Hainan Medical College, Haikou, 571199 People’s Republic of China
| | - Jie Bai
- grid.13402.340000 0004 1759 700XDepartment of Ophthalmology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000 People’s Republic of China
| |
Collapse
|
12
|
O'Sullivan EM, Dowling P, Swandulla D, Ohlendieck K. Proteomic Identification of Saliva Proteins as Noninvasive Diagnostic Biomarkers. Methods Mol Biol 2023; 2596:147-167. [PMID: 36378438 DOI: 10.1007/978-1-0716-2831-7_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Many biomedically relevant biomarkers are proteins with characteristic biochemical properties and a relatively restricted subcellular distribution. The comparative and mass spectrometry-based proteomic analysis of body fluids can be particularly instrumental for the targeted identification of novel protein biomarkers with pathological relevance. In this respect, new research efforts in biomarker discovery focus on the systematic mapping of the human saliva proteome, as well as the pathobiochemical identification of disease-related modifications or concentration changes in specific saliva proteins. As a product of exocrine secretion, saliva can be considered an ideal source for the biochemical identification of new disease indicators. Importantly, saliva represents a body fluid that is continuously available for diagnostic and prognostic assessments. This chapter gives an overview of saliva proteomics, including a discussion of the usefulness of both liquid chromatography and two-dimensional gel electrophoresis for efficient protein separation in saliva proteomics.
Collapse
Affiliation(s)
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
13
|
Ponzini E, Santambrogio C, De Palma A, Mauri P, Tavazzi S, Grandori R. Mass spectrometry-based tear proteomics for noninvasive biomarker discovery. MASS SPECTROMETRY REVIEWS 2022; 41:842-860. [PMID: 33759206 PMCID: PMC9543345 DOI: 10.1002/mas.21691] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 05/05/2023]
Abstract
The lacrimal film has attracted increasing interest in the last decades as a potential source of biomarkers of physiopathological states, due to its accessibility, moderate complexity, and responsiveness to ocular and systemic diseases. High-performance liquid chromatography-mass spectrometry (LC-MS) has led to effective approaches to tear proteomics, despite the intrinsic limitations in sample amounts. This review focuses on the recent progress in strategy and technology, with an emphasis on the potential for personalized medicine. After an introduction on lacrimal-film composition, examples of applications to biomarker discovery are discussed, comparing approaches based on pooled-sample and single-tear analysis. Then, the most critical steps of the experimental pipeline, that is, tear collection, sample fractionation, and LC-MS implementation, are discussed with reference to proteome-coverage optimization. Advantages and challenges of the alternative procedures are highlighted. Despite the still limited number of studies, tear quantitative proteomics, including single-tear investigation, could offer unique contributions to the identification of low-invasiveness, sustained-accessibility biomarkers, and to the development of personalized approaches to therapy and diagnosis.
Collapse
Affiliation(s)
- Erika Ponzini
- Materials Science DepartmentUniversity of Milano‐BicoccaMilanItaly
| | - Carlo Santambrogio
- Department of Biotechnology and BiosciencesUniversity of Milano‐BicoccaMilanItaly
| | - Antonella De Palma
- Institute for Biomedical TechnologiesNational Research Council (ITB‐CNR)Segrate (MI)Italy
| | - Pierluigi Mauri
- Institute for Biomedical TechnologiesNational Research Council (ITB‐CNR)Segrate (MI)Italy
| | - Silvia Tavazzi
- Materials Science DepartmentUniversity of Milano‐BicoccaMilanItaly
- COMiBUniversity of Milano‐BicoccaMilanItaly
| | - Rita Grandori
- Department of Biotechnology and BiosciencesUniversity of Milano‐BicoccaMilanItaly
| |
Collapse
|
14
|
Kalló G, Kumar A, Tőzsér J, Csősz É. Chemical Barrier Proteins in Human Body Fluids. Biomedicines 2022; 10:biomedicines10071472. [PMID: 35884778 PMCID: PMC9312486 DOI: 10.3390/biomedicines10071472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022] Open
Abstract
Chemical barriers are composed of those sites of the human body where potential pathogens can contact the host cells. A chemical barrier is made up by different proteins that are part of the antimicrobial and immunomodulatory protein/peptide (AMP) family. Proteins of the AMP family exert antibacterial, antiviral, and/or antifungal activity and can modulate the immune system. Besides these proteins, a wide range of proteases and protease inhibitors can also be found in the chemical barriers maintaining a proteolytic balance in the host and/or the pathogens. In this review, we aimed to identify the chemical barrier components in nine human body fluids. The interaction networks of the chemical barrier proteins in each examined body fluid were generated as well.
Collapse
Affiliation(s)
- Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (A.K.); (J.T.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Correspondence: ; Tel.: +36-52-416432
| | - Ajneesh Kumar
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (A.K.); (J.T.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - József Tőzsér
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (A.K.); (J.T.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (A.K.); (J.T.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| |
Collapse
|
15
|
Mukherjee A, Pednekar CB, Kolke SS, Kattimani M, Duraisamy S, Burli AR, Gupta S, Srivastava S. Insights on Proteomics-Driven Body Fluid-Based Biomarkers of Cervical Cancer. Proteomes 2022; 10:proteomes10020013. [PMID: 35645371 PMCID: PMC9149910 DOI: 10.3390/proteomes10020013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 02/04/2023] Open
Abstract
Cervical cancer is one of the top malignancies in women around the globe, which still holds its place despite being preventable at early stages. Gynecological conditions, even maladies like cervical cancer, still experience scrutiny from society owing to prevalent taboo and invasive screening methods, especially in developing economies. Additionally, current diagnoses lack specificity and sensitivity, which prolong diagnosis until it is too late. Advances in omics-based technologies aid in discovering differential multi-omics profiles between healthy individuals and cancer patients, which could be utilized for the discovery of body fluid-based biomarkers. Body fluids are a promising potential alternative for early disease detection and counteracting the problems of invasiveness while also serving as a pool of potential biomarkers. In this review, we will provide details of the body fluids-based biomarkers that have been reported in cervical cancer. Here, we have presented our perspective on proteomics for global biomarker discovery by addressing several pertinent problems, including the challenges that are confronted in cervical cancer. Further, we also used bioinformatic methods to undertake a meta-analysis of significantly up-regulated biomolecular profiles in CVF from cervical cancer patients. Our analysis deciphered alterations in the biological pathways in CVF such as immune response, glycolytic processes, regulation of cell death, regulation of structural size, protein polymerization disease, and other pathways that can cumulatively contribute to cervical cancer malignancy. We believe, more extensive research on such biomarkers, will speed up the road to early identification and prevention of cervical cancer in the near future.
Collapse
Affiliation(s)
- Amrita Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India;
| | | | - Siddhant Sujit Kolke
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India;
| | - Megha Kattimani
- Undergraduate Department, Indian Institute of Science, Bengaluru 560012, India;
| | - Subhiksha Duraisamy
- Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, India;
| | - Ananya Raghu Burli
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India;
| | - Sudeep Gupta
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Hospital, Mumbai 400012, India;
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India;
- Correspondence: ; Tel.: +91-22-2576-7779
| |
Collapse
|
16
|
Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
Collapse
Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| |
Collapse
|
17
|
Kim JW, Jung JY, Lee SW, Baek WY, Kim HA, Suh CH. S100A8 in Serum, Urine, and Saliva as a Potential Biomarker for Systemic Lupus Erythematosus. Front Immunol 2022; 13:886209. [PMID: 35529863 PMCID: PMC9073082 DOI: 10.3389/fimmu.2022.886209] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/28/2022] [Indexed: 01/02/2023] Open
Abstract
ObjectivesThis study aimed to elucidate the potential of serum, urine, and saliva S100 calcium-binding protein A8 protein (S100A8) levels as biomarkers for systemic lupus erythematosus (SLE).MethodsSerum, urine, and saliva samples were obtained from 249 patients with SLE from the Ajou lupus cohort and 52 age- and sex-matched healthy controls (HCs). The concentrations of S100A8 were quantified using an ELISA, and a receiver operating characteristic curve was used to analyze whether they may be used as biomarkers for diagnosing SLE.ResultsAmong 249 SLE patients included in our study, the mean SLE disease activity index (SLEDAI)-2K was 7.16 ± 5.61, and the number of patients with lupus flare was 11. Patients with SLE showed a 2.7-fold increase in serum S100A8 levels compared with that in HCs (1,890.6 vs. 709 pg/ml, p < 0.001). In urine and saliva, the average S100A8 levels were significantly higher in patients with SLE compared with those in HCs (urine, 2,029.4 vs. 1,096.7 pg/ml, p = 0.001; saliva, 290,496.3 vs. 47,742 pg/ml, p < 0.001). For SLE diagnosis, the area under the receiver operating characteristic curve was 0.831 for serum S100A8 (95% CI, 0.765–0.897), 0.751 for urine S100A8 (95% CI, 0.648–0.854), and 0.729 for salivary S100A8 (95% CI, 0.646–0.812). Pearson’s correlation analysis showed that S100A8 in serum, urine, and saliva was significantly associated with the SLEDAI (r = 0.267, p < 0.001; r = 0.274, p < 0.001; and r = 0.629, p < 0.001, respectively). Among the clinical manifestations, nephritis was the most influential factor related to SLE in the concentration of S100A8 in serum, urine, and saliva.ConclusionThis is the first study to show that the expression of S100A8 in serum, urine, and saliva is significantly higher in patients with SLE than in HCs and is associated with disease activity markers. Therefore, we suggest that S100A8 protein could be a potential biomarker for SLE.
Collapse
Affiliation(s)
- Ji-Won Kim
- Department of Rheumatology, Ajou University School of Medicine, Suwon, South Korea
| | - Ju-Yang Jung
- Department of Rheumatology, Ajou University School of Medicine, Suwon, South Korea
| | - Sang-Won Lee
- Department of Rheumatology, Ajou University School of Medicine, Suwon, South Korea
| | - Wook-Young Baek
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Hyoun-Ah Kim
- Department of Rheumatology, Ajou University School of Medicine, Suwon, South Korea
| | - Chang-Hee Suh
- Department of Rheumatology, Ajou University School of Medicine, Suwon, South Korea
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- *Correspondence: Chang-Hee Suh,
| |
Collapse
|
18
|
Fast and Sensitive Quantification of AccQ-Tag Derivatized Amino Acids and Biogenic Amines by UHPLC-UV Analysis from Complex Biological Samples. Metabolites 2022; 12:metabo12030272. [PMID: 35323715 PMCID: PMC8949038 DOI: 10.3390/metabo12030272] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 01/27/2023] Open
Abstract
Metabolomic analysis of different body fluids bears high importance in medical sciences. Our aim was to develop and validate a fast UHPLC-UV method for the analysis of 33 amino acids and biogenic amines from complex biological samples. AccQ-Tag derivatization was conducted on target molecules and the derivatized targets were analyzed by UHPLC-UV. The detection of the analytes was carried out with UV analysis and by Selected Reaction Monitoring (SRM)-based targeted mass spectrometry. The method was validated according to the FDA guidelines. Serum and non-stimulated tear samples were collected from five healthy individuals and the samples were analyzed by the method. The method was successfully validated with appropriate accuracy and precision for all 33 biomolecules. A total of 29 analytes were detected in serum samples and 26 of them were quantified. In the tears, 30 amino acids and biogenic amines were identified and 20 of them were quantified. The developed and validated UHPLC-UV method enables the fast and precise analysis of amino acids and biogenic amines from complex biological samples.
Collapse
|
19
|
Raposo AC, Lebrilla C, Portela RW, Xu G, Oriá AP. The glycoproteomics of hawk and caiman tears. BMC Vet Res 2021; 17:381. [PMID: 34886864 PMCID: PMC8656020 DOI: 10.1186/s12917-021-03088-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 11/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycoproteins are important tear components that participate in the stability of the ocular surface. However, the glycopeptides that are present in the tears of wild animals have not yet been described. This work aimed to describe the glycoproteomic profile of roadside hawk (Rupornis magnirostris) and caiman (Caiman latirostris) tears. METHODS Tears collected from 10 hawks and 70 caimans using Schirmer tear test strips were used in this study. The samples were submitted to trypsin digestion and separated using a reverse-phase column coupled to a mass spectrometer associated to a nanospray ionization source. The glycoproteins were categorized as: cellular components, biological processes and molecular function, according to the UniProt Knowledgebase. RESULTS As shown by the liquid chromatography-mass spectrometry, all glycopeptides found were classified as N-type. Of the 51 glycoproteins that were identified in the hawk tear film, the most abundant were ovotransferrin, globulins and complement system proteins. In the caiman tear film, 29 glycoproteins were identified. The most abundant caiman glycoproteins were uncharacterized proteins, ATPases, globulins and proteasome components. Ontological characterization revealed that the glycoproteins were extracellular, and the most identified molecular function was endopeptidase activity for both species. CONCLUSION Glycoproteins are abundant in the tear film of the bird and reptile species studied herein, and all these molecules were shown to have N-type modifications. Location at the extracellular space and an endopeptidase inhibitor activity were the main cell component and molecular function for both species, respectively. These profiles showed differences when compared to human tears, are possibly linked to adaptive processes and can be the basis for further studies on the search of disease biomarkers.
Collapse
Affiliation(s)
- Ana Cláudia Raposo
- School of Veterinary Medicine, Federal University of Bahia, Brazil, Salvador, 40.110-060, Brazil
| | - Carlito Lebrilla
- Chemistry Department, Mass Spectrometry Facilities Campus, University of California, Davis, CA, 95616-8585, USA
| | - Ricardo Wagner Portela
- Institute of Health Sciences, Federal University of Bahia, Brazil, Salvador, 40.110-100, Brazil
| | - Gege Xu
- Chemistry Department, Mass Spectrometry Facilities Campus, University of California, Davis, CA, 95616-8585, USA
| | - Arianne Pontes Oriá
- School of Veterinary Medicine, Federal University of Bahia, Brazil, Salvador, 40.110-060, Brazil.
| |
Collapse
|
20
|
Apolipoprotein E is an effective biomarker for orthodontic tooth movement in patients treated with transmission straight wire appliances. Am J Orthod Dentofacial Orthop 2021; 161:255-262.e1. [PMID: 34756485 DOI: 10.1016/j.ajodo.2020.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 08/01/2020] [Accepted: 08/01/2020] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Orthodontic tooth movement (OTM) is the core component of orthodontic treatment and is increasingly popular for treating malocclusions. In this study, we aimed to investigate the role of apolipoprotein E (ApoE) in OTM. METHODS Thirty patients treated with transmission straight wire technology were selected and longitudinally tracked at 2 different stages of orthodontic treatment (initial 2 months and 12 months of orthodontic treatment). Total saliva was collected and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Western blotting was used to detect the difference in ApoE expression in the saliva samples of the 2 groups. The expression of ApoE was further verified by immunohistochemical staining in a mouse model of tooth movement. RESULTS The results of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry showed significant differences in the components of the salivary peptides in the 2 groups and peptides with a molecular weight of 2010.7 Da were predicted to be ApoE by database analysis. Western blotting further verified a significant difference in the expression of salivary ApoE in the 2 groups. In addition, an OTM model was successfully constructed in mice. The immunohistochemical staining results showed that ApoE expression significantly increased after force loading in the OTM model. CONCLUSIONS This study indicated that ApoE participated in and played a role during OTM in patients treated with transmission straight wire technology. This relationship might be related to alveolar bone reconstruction and root resorption. The results provide new ideas for research on the mechanism of tooth movement using precision medicine based on saliva detection.
Collapse
|
21
|
Burat B, Reynaerts A, Baiwir D, Fléron M, Eppe G, Leal T, Mazzucchelli G. Characterization of the Human Eccrine Sweat Proteome-A Focus on the Biological Variability of Individual Sweat Protein Profiles. Int J Mol Sci 2021; 22:ijms221910871. [PMID: 34639210 PMCID: PMC8509809 DOI: 10.3390/ijms221910871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 12/17/2022] Open
Abstract
The potential of eccrine sweat as a bio-fluid of interest for diagnosis and personalized therapy has not yet been fully evaluated, due to the lack of in-depth sweat characterization studies. Thanks to recent developments in omics, together with the availability of accredited sweat collection methods, the analysis of human sweat may now be envisioned as a standardized, non-invasive test for individualized monitoring and personalized medicine. Here, we characterized individual sweat samples, collected from 28 healthy adult volunteers under the most standardized sampling methodology, by applying optimized shotgun proteomics. The thorough characterization of the sweat proteome allowed the identification of 983 unique proteins from which 344 were identified across all samples. Annotation-wise, the study of the sweat proteome unveiled the over-representation of newly addressed actin dynamics, oxidative stress and proteasome-related functions, in addition to well-described proteolysis and anti-microbial immunity. The sweat proteome composition correlated with the inter-individual variability of sweat secretion parameters. In addition, both gender-exclusive proteins and gender-specific protein abundances were highlighted, despite the high similarity between human female and male sweat proteomes. In conclusion, standardized sample collection coupled with optimized shotgun proteomics significantly improved the depth of sweat proteome coverage, far beyond previous similar studies. The identified proteins were involved in many diverse biological processes and molecular functions, indicating the potential of this bio-fluid as a valuable biological matrix for further studies. Addressing sweat variability, our results prove the proteomic profiling of sweat to be a promising bio-fluid analysis for individualized, non-invasive monitoring and personalized medicine.
Collapse
Affiliation(s)
- Bastien Burat
- Mass Spectrometry Laboratory, MolSys Research Unit, Liège Université, B-4000 Liège, Belgium;
- Correspondence: (B.B.); (G.M.); Tel.: +32-(0)-4-366-34-11; Fax: +32-(0)-4-366-43-8 (G.M.)
| | - Audrey Reynaerts
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, B-1200 Brussels, Belgium; (A.R.); (T.L.)
| | - Dominique Baiwir
- GIGA Proteomics Facility, Liège Université, B-4000 Liège, Belgium; (D.B.); (M.F.)
| | - Maximilien Fléron
- GIGA Proteomics Facility, Liège Université, B-4000 Liège, Belgium; (D.B.); (M.F.)
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, Liège Université, B-4000 Liège, Belgium;
| | - Teresinha Leal
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, B-1200 Brussels, Belgium; (A.R.); (T.L.)
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, Liège Université, B-4000 Liège, Belgium;
- Correspondence: (B.B.); (G.M.); Tel.: +32-(0)-4-366-34-11; Fax: +32-(0)-4-366-43-8 (G.M.)
| |
Collapse
|
22
|
Karimi MR, Karimi AH, Abolmaali S, Sadeghi M, Schmitz U. Prospects and challenges of cancer systems medicine: from genes to disease networks. Brief Bioinform 2021; 23:6361045. [PMID: 34471925 PMCID: PMC8769701 DOI: 10.1093/bib/bbab343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/20/2022] Open
Abstract
It is becoming evident that holistic perspectives toward cancer are crucial in deciphering the overwhelming complexity of tumors. Single-layer analysis of genome-wide data has greatly contributed to our understanding of cellular systems and their perturbations. However, fundamental gaps in our knowledge persist and hamper the design of effective interventions. It is becoming more apparent than ever, that cancer should not only be viewed as a disease of the genome but as a disease of the cellular system. Integrative multilayer approaches are emerging as vigorous assets in our endeavors to achieve systemic views on cancer biology. Herein, we provide a comprehensive review of the approaches, methods and technologies that can serve to achieve systemic perspectives of cancer. We start with genome-wide single-layer approaches of omics analyses of cellular systems and move on to multilayer integrative approaches in which in-depth descriptions of proteogenomics and network-based data analysis are provided. Proteogenomics is a remarkable example of how the integration of multiple levels of information can reduce our blind spots and increase the accuracy and reliability of our interpretations and network-based data analysis is a major approach for data interpretation and a robust scaffold for data integration and modeling. Overall, this review aims to increase cross-field awareness of the approaches and challenges regarding the omics-based study of cancer and to facilitate the necessary shift toward holistic approaches.
Collapse
Affiliation(s)
| | | | | | - Mehdi Sadeghi
- Department of Cell & Molecular Biology, Semnan University, Semnan, Iran
| | - Ulf Schmitz
- Department of Molecular & Cell Biology, James Cook University, Townsville, QLD 4811, Australia
| |
Collapse
|
23
|
Kalló G, Varga AK, Szabó J, Emri M, Tőzsér J, Csutak A, Csősz É. Reduced Level of Tear Antimicrobial and Immunomodulatory Proteins as a Possible Reason for Higher Ocular Infections in Diabetic Patients. Pathogens 2021; 10:pathogens10070883. [PMID: 34358033 PMCID: PMC8308669 DOI: 10.3390/pathogens10070883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022] Open
Abstract
(1) Background: Diabetes mellitus is one of the most common metabolic disorders and a risk factor for bacterial ocular infections. Our aim was to examine the antibacterial activity of tears from patients with diabetes mellitus with and without diabetic retinopathy and to link this activity to the level of tear proteins. (2) Methods: Non-stimulated basal tears were collected from 39 eyes of 35 subjects. The antibacterial activity of tear pools was tested against pathogenic Staphylococcus aureus ATCC 29213, Escherichia coli ATCC 26922 and Pseudomonas aeruginosa ATCC 27853 strains. The levels of 10 antimicrobial and immunomodulatory proteins were analyzed in the individual tear samples of the studied groups by SRM-based targeted mass spectrometry analysis. (3) Results: Disease stage-specific antimicrobial effect was observed in case of Staphylococcus aureus ATCC 29213 strain, and a non-disease specific inhibitory effect was observed in case of Pseudomonas aeruginosa ATCC 27853 strain. Changes in the levels of the studied antimicrobial and immunomodulatory proteins in the tears of the studied groups were also observed. (4) Conclusions: The higher ocular infection rate observed in diabetic patients may be the consequence of the decreased antimicrobial activity of tears possibly caused by the changes in the levels of antimicrobial and immunomodulatory proteins.
Collapse
Affiliation(s)
- Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (G.K.); (A.K.V.); (J.T.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Anita Katalin Varga
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (G.K.); (A.K.V.); (J.T.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Judit Szabó
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, 4032 Debrecen, Hungary;
| | - Miklós Emri
- Department of Medical Imaging, Division of Nuclear Medicine and Translational Imaging Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary;
| | - József Tőzsér
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (G.K.); (A.K.V.); (J.T.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Adrienne Csutak
- Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary;
- Department of Ophthalmology, Faculty of Medicine, University of Pécs, Rákóczi út 2, 7623 Pécs, Hungary
| | - Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (G.K.); (A.K.V.); (J.T.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Correspondence: ; Tel.: +36-52-416-432; Fax: +36-52-314-989
| |
Collapse
|
24
|
Jenei A, Kalló G, Dajnoki Z, Gáspár K, Szegedi A, Kapitány A, Csősz É. Detection of Antimicrobial Peptides in Stratum Corneum by Mass Spectrometry. Int J Mol Sci 2021; 22:ijms22084233. [PMID: 33921817 PMCID: PMC8073585 DOI: 10.3390/ijms22084233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/02/2022] Open
Abstract
Antimicrobial and immunomodulatory peptides (AMPs) are considered as the key players in the maintenance of skin barrier functions. Here, we developed a novel approach for the examination of AMPs in the outermost layer of the epidermis, namely stratum corneum (SC). The SC sample collection by tape stripping was coupled with detection by highly specific and sensitive parallel reaction monitoring (PRM)-based mass spectrometry. We found that hexane-free processing of SC samples produced higher protein yield compared to hexane-based extraction. Of the 18 investigated peptides, 9 could be detected either in healthy or in inflamed skin specimens. Regarding the amount of S100A8, LCN2, LACRT and LYZ significant topographical differences were described among gland poor (GP), sebaceous gland rich (SGR) and apocrine gland rich (AGR) healthy skin regions. We applied a minimally invasive, reproducible approach for sampling, which can be assessed for research and diagnostic purposes and for monitoring the effectiveness of therapies in skin diseases.
Collapse
Affiliation(s)
- Adrienn Jenei
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (A.J.); (Z.D.); (K.G.); (A.S.); (A.K.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
- Department of Neurosurgery, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
- Gyula Petrányi Doctoral School of Allergy and Clinical Immunology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Zsolt Dajnoki
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (A.J.); (Z.D.); (K.G.); (A.S.); (A.K.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Krisztián Gáspár
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (A.J.); (Z.D.); (K.G.); (A.S.); (A.K.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Andrea Szegedi
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (A.J.); (Z.D.); (K.G.); (A.S.); (A.K.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Anikó Kapitány
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (A.J.); (Z.D.); (K.G.); (A.S.); (A.K.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary;
- Correspondence: ; Tel.: +36-52-411-717 (ext. 55734)
| |
Collapse
|
25
|
Chantada-Vázquez MDP, García Vence M, Serna A, Núñez C, Bravo SB. SWATH-MS Protocols in Human Diseases. Methods Mol Biol 2021; 2259:105-141. [PMID: 33687711 DOI: 10.1007/978-1-0716-1178-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Identification of molecular biomarkers for human diseases is one of the most important disciplines in translational science as it helps to elucidate their origin and early progression. Thus, it is a key factor in better diagnosis, prognosis, and treatment. Proteomics can help to solve the problem of sample complexity when the most common primary sample specimens were analyzed: organic fluids of easy access. The latest developments in high-throughput and label-free quantitative proteomics (SWATH-MS), together with more advanced liquid chromatography, have enabled the analysis of large sample sets with the sensitivity and depth needed to succeed in this task. In this chapter, we show different sample processing methods (major protein depletion, digestion, etc.) and a micro LC-SWATH-MS protocol to identify/quantify several proteins in different types of samples (serum/plasma, saliva, urine, tears).
Collapse
Affiliation(s)
| | - María García Vence
- Proteomic Unit, Instituto de Investigaciones Sanitarias-IDIS, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | | | - Cristina Núñez
- Research Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), Lugo, Spain.
| | - Susana B Bravo
- Proteomic Unit, Instituto de Investigaciones Sanitarias-IDIS, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain.
| |
Collapse
|
26
|
Scholtz B, Vo Minh D, Kiss C, Tar I, Kumar A, Tőzsér J, Csősz É, Márton I. Examination of Oral Squamous Cell Carcinoma and Precancerous Lesions Using Proximity Extension Assay and Salivary RNA Quantification. Biomedicines 2020; 8:biomedicines8120610. [PMID: 33327496 PMCID: PMC7764999 DOI: 10.3390/biomedicines8120610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/24/2022] Open
Abstract
Saliva is an easy-to access body fluid with high diagnostic potential. The utilization of saliva for oral cancer diagnosis can be an attractive possibility. Besides the oral cancer, it is important to better understand the precancerous lesions such as oral lichen planus (OLP) and leukoplakia (OLK). In order to examine the changes of salivary proteins in controls, patients with oral cancer, and patients with precancerous conditions, proximity extension assay was utilized. Some proteins and functions were characteristic to the examined groups and can serve as a starting point for further biomarker studies. The different nature of OLK and OLP was demonstrated, showing the malignant transformation and the inflammation as the prominent biological processes in the OLK and OLP, respectively. The salivary level of IL6 was verified using quantitative ELISA and the mRNA level was also studied. Elevated IL6 levels could be detected in precancerous groups compared to controls.
Collapse
Affiliation(s)
- Beáta Scholtz
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Doan Vo Minh
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (D.V.M.); (A.K.)
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Csongor Kiss
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Ildikó Tar
- Department of Oral Medicine, Faculty of Dentistry, University of Debrecen, 4032 Debrecen, Hungary;
| | - Ajneesh Kumar
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (D.V.M.); (A.K.)
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- Doctoral School of Molecular Cell and Immune Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - József Tőzsér
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Éva Csősz
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (D.V.M.); (A.K.)
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- Correspondence: (É.C.); (I.M.); Tel.: +36-52-416432 (É.C.)
| | - Ildikó Márton
- Department of Restorative Dentistry, Faculty of Dentistry, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (É.C.); (I.M.); Tel.: +36-52-416432 (É.C.)
| |
Collapse
|
27
|
Michalik M, Samet A, Dmowska-Koroblewska A, Podbielska-Kubera A, Waszczuk-Jankowska M, Struck-Lewicka W, Markuszewski MJ. An Overview of the Application of Systems Biology in an Understanding of Chronic Rhinosinusitis (CRS) Development. J Pers Med 2020; 10:jpm10040245. [PMID: 33255995 PMCID: PMC7712485 DOI: 10.3390/jpm10040245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is an inflammatory disease of the paranasal sinuses. It is defined as the presence of a minimum of two out of four main symptoms such as hyposmia, facial pain, nasal blockage, and discharge, which last for 8–12 weeks. CRS significantly impairs a patient’s quality of life. It needs special treatment mainly focusing on preventing local infection/inflammation with corticosteroid sprays or improving sinus drainage using nasal saline irrigation. When other treatments fail, endoscopic sinus surgery is considered an effective option. According to the state-of-the-art knowledge of CRS, there is more evidence suggesting that it is more of an inflammatory disease than an infectious one. This condition is also treated as a multifactorial inflammatory disorder as it may be triggered by various factors, such as bacterial or fungal infections, airborne irritants, defects in innate immunity, or the presence of concomitant diseases. Due to the incomplete understanding of the pathological processes of CRS, there is a continuous search for new indicators that are directly related to the pathogenesis of this disease—e.g., in the field of systems biology. The studies adopting systems biology search for possible factors responsible for the disease at genetic, transcriptomic, proteomic, and metabolomic levels. The analyses of the changes in the genome, transcriptome, proteome, and metabolome may reveal the dysfunctional pathways of inflammatory regulation and provide a clear insight into the pathogenesis of this disease. Therefore, in the present paper, we have summarized the state-of-the-art knowledge of the application of systems biology in the pathology and development of CRS.
Collapse
Affiliation(s)
- Michał Michalik
- Medical Center MML, Bagno 2, 00-112 Warsaw, Poland; (M.M.); (A.S.); (A.D.-K.); (A.P.-K.)
| | - Alfred Samet
- Medical Center MML, Bagno 2, 00-112 Warsaw, Poland; (M.M.); (A.S.); (A.D.-K.); (A.P.-K.)
| | | | | | - Małgorzata Waszczuk-Jankowska
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland; (M.W.-J.); (W.S.-L.)
| | - Wiktoria Struck-Lewicka
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland; (M.W.-J.); (W.S.-L.)
| | - Michał J. Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland; (M.W.-J.); (W.S.-L.)
- Correspondence: ; Tel.: +48-(58)-349-1493
| |
Collapse
|
28
|
Buccitelli C, Selbach M. mRNAs, proteins and the emerging principles of gene expression control. Nat Rev Genet 2020; 21:630-644. [PMID: 32709985 DOI: 10.1038/s41576-020-0258-4] [Citation(s) in RCA: 542] [Impact Index Per Article: 135.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2020] [Indexed: 12/15/2022]
Abstract
Gene expression involves transcription, translation and the turnover of mRNAs and proteins. The degree to which protein abundances scale with mRNA levels and the implications in cases where this dependency breaks down remain an intensely debated topic. Here we review recent mRNA-protein correlation studies in the light of the quantitative parameters of the gene expression pathway, contextual confounders and buffering mechanisms. Although protein and mRNA levels typically show reasonable correlation, we describe how transcriptomics and proteomics provide useful non-redundant readouts. Integrating both types of data can reveal exciting biology and is an essential step in refining our understanding of the principles of gene expression control.
Collapse
Affiliation(s)
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany. .,Charité - Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
29
|
Chiaradia E, Miller I. In slow pace towards the proteome of equine body fluids. J Proteomics 2020; 225:103880. [PMID: 32569818 DOI: 10.1016/j.jprot.2020.103880] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022]
Abstract
Equine medicine represents a relevant field of veterinary science and the horse industry generates a significant economic impact. Horses can be involved in different sport disciplines, meat production, work and recreational purposes. Horses are also important for human health as they can be used as animal models for studying human diseases and in equine-assisted therapy. This review summarizes the data related to body fluids such as plasma/serum, urine, cerebrospinal fluid, synovial fluid, saliva, bronchoalveolar lavage fluid and peritoneal fluid obtained using proteomic analysis. Horse body fluid proteome analysis under various physiological and pathological conditions is a useful method for identifying new biomarkers for horse diseases which are still difficult to diagnose, but with serious consequences on equine health and welfare. The findings reported here reveal that further proteomic studies on equine body fluids collected from diseased animals are required. SIGNIFICANCE: Body fluids are sources of potential protein biomarkers for diagnosis and therapeutic target identification. Indeed, they contain proteins that play a crucial role in cell functions and whose presence or relative abundance are indicative of the health status of tissues/organs. The review reports the data on the equine body fluids obtained using proteomic analysis, including those which are commonly used to obtain a correct diagnosis and prognosis of horse diseases which still pose a significant challenge. For equine medicine, new biomarkers are needed to formulate early diagnosis and to distinguish among diseases with similar clinical signs.
Collapse
Affiliation(s)
- Elisabetta Chiaradia
- Laboratory of proteomics, Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, via San Costanzo, 4, 06126 Perugia, Italy.
| | - Ingrid Miller
- Institut für Medizinische Biochemie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria.
| |
Collapse
|
30
|
Piñeyro-Ruiz C, Serrano H, Pérez-Brayfield MR, Jorge JC. New frontiers on the molecular underpinnings of hypospadias according to severity. Arab J Urol 2020; 18:257-266. [PMID: 33312738 PMCID: PMC7717703 DOI: 10.1080/2090598x.2020.1760589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Hypospadias, which is characterised by the displacement of the urethral meatus from its typical anatomical location in males, shows various degrees of severity. In this systematic review, we surveyed our current understanding of the genetics of isolated hypospadias in humans according to the severity of the condition. We found that sequencing and genotyping approaches were the preferred methods of study and that single nucleotide polymorphisms were the most common finding associated with hypospadias. Most genes fell into four gene-pathway categories related to androgens, oestrogens, growth factors, or transcription factors. Few hypospadias studies classify their findings by severity. Taken together, we argue that it is advantageous to take into consideration the severity of the condition in search of novel candidates in the aetiology of hypospadias. Abbreviations: AR: androgen receptor; ATF3: activating transcription factor 3; BMP4: bone morphogenetic protein 4; BMP7: bone morphogenetic protein 7; CYP17: steroid 17-alpha-hydroxylase/17,20 lyase; CYP1A1: cytochrome P450 1A1; CYP3A4: cytochrome P450 3A4; CNVs: copy number variants; DGKK: diacylglycerol kinase kappa; ESR1: oestrogen receptor 1; ESR2: oestrogen receptor 2; FGF8: fibroblast growth factor 8; FGF10: fibroblast growth factor 10; FGFR2: fibroblast growth factor receptor 2; HOXA4: homeobox protein Hox-A4; HOXB6: homeobox protein Hox-B6; HSD17B3: hydroxysteroid 17-beta dehydrogenase 3; MAMLD1: mastermind-like domain-containing protein 1; SF-1: splicing factor 1; SHH: sonic hedgehog; SNPs: single nucleotide polymorphisms; SOX9: SRY-box 9; SRD5A2: steroid 5 alpha-reductase 2; SRY: sex-determining region Y protein; STAR: steroidogenic acute regulatory protein; STARD3: StAR-related lipid transfer protein 3; STS: steryl-sulfatase; WT1: Wilms tumour protein; ZEB1: zinc finger oestrogen-box binding homeobox 1.
Collapse
Affiliation(s)
- Coriness Piñeyro-Ruiz
- Department of Anatomy and Neurobiology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico, USA
| | - Horacio Serrano
- Department of Internal Medicine and Department of Biochemistry, University of Puerto Rico, San Juan, Puerto Rico, USA
| | - Marcos R Pérez-Brayfield
- Department of Surgery, Section of Urology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico, USA
| | - Juan Carlos Jorge
- Department of Anatomy and Neurobiology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico, USA
| |
Collapse
|
31
|
Gargan S, Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Identification of marker proteins of muscular dystrophy in the urine proteome from the mdx-4cv model of dystrophinopathy. Mol Omics 2020; 16:268-278. [PMID: 32211681 DOI: 10.1039/c9mo00182d] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the protein constituents of urine present a dynamic proteome that can reflect a variety of disease-related alterations in the body, the mass spectrometric survey of proteome-wide changes in urine promises new insights into pathogenic mechanisms. Urine can be investigated in a completely non-invasive way and provides valuable biomedical information on body-wide changes. In this report, we have focused on the urine proteome in X-linked muscular dystrophy using the established mdx-4cv mouse model of dystrophinopathy. In order to avoid potential artefacts due to the manipulation of the biofluid proteome prior to mass spectrometry, crude urine specimens were analyzed without the prior usage of centrifugation steps or concentration procedures. Comparative proteomics revealed 21 increased and 8 decreased proteins out of 870 identified urinary proteoforms using 50 μl of biofluid per investigated sample, i.e. 14 wild type versus 14 mdx-4cv specimens. Promising marker proteins that were almost exclusively found in mdx-4cv urine included nidogen, parvalbumin and titin. Interestingly, the mass spectrometric identification of urine-associated titin revealed a wide spread of peptides over the sequence of this giant muscle protein. The newly established urinomic signature of dystrophinopathy might be helpful for the design of non-invasive assays to improve diagnosis, prognosis, therapy-monitoring and evaluation of potential harmful side effects of novel treatments in the field of muscular dystrophy research.
Collapse
Affiliation(s)
- Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth W23F2H6, Co. Kildare, Ireland.
| | | | | | | | | |
Collapse
|
32
|
Serum proteomics of active tuberculosis patients and contacts reveals unique processes activated during Mycobacterium tuberculosis infection. Sci Rep 2020; 10:3844. [PMID: 32123229 PMCID: PMC7052228 DOI: 10.1038/s41598-020-60753-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/17/2020] [Indexed: 01/24/2023] Open
Abstract
Tuberculosis (TB) is the most lethal infection among infectious diseases. The specific aim of this study was to establish panels of serum protein biomarkers representative of active TB patients and their household contacts who were either infected (LTBI) or uninfected (EMI-TB Discovery Cohort, Pontevedra Region, Spain). A TMT (Tamdem mass tags) 10plex-based quantitative proteomics study was performed in quintuplicate containing a total of 15 individual serum samples per group. Peptides were analyzed in an LC-Orbitrap Elite platform, and raw data were processed using Proteome Discoverer 2.1. A total of 418 proteins were quantified. The specific protein signature of active TB patients was characterized by an accumulation of proteins related to complement activation, inflammation and modulation of immune response and also by a decrease of a small subset of proteins, including apolipoprotein A and serotransferrin, indicating the importance of lipid transport and iron assimilation in the progression of the disease. This signature was verified by the targeted measurement of selected candidates in a second cohort (EMI-TB Verification Cohort, Maputo Region, Mozambique) by ELISA and nephelometry techniques. These findings will aid our understanding of the complex metabolic processes associated with TB progression from LTBI to active disease.
Collapse
|
33
|
Deng W, Rao J, Chen X, Li D, Zhang Z, Liu D, Liu J, Wang Y, Huang O. Metabolomics study of serum and urine samples reveals metabolic pathways and biomarkers associated with pelvic organ prolapse. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1136:121882. [PMID: 31809960 DOI: 10.1016/j.jchromb.2019.121882] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/24/2019] [Accepted: 11/12/2019] [Indexed: 12/17/2022]
Abstract
Pelvic organ prolapse (POP) is a common medical condition among women and involves complicated diagnostics and controversial surgical management. The exact molecular mechanism underlying POP is poorly understood, especially at the metabolism level. To explore the metabolic mechanism underlying POP and discover potential biomarkers for POP diagnosis, we applied a non-targeted metabolomics approach using ultra-high performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UHPLC-Q-TOF-MS). Metabolomics study of serum samples from patients with POP (n = 24) and controls (n = 22) revealed a total of 59 metabolites that are significantly different (VIP ≥ 1 and p ≤ 0.05) between the two groups. Between urine samples from POP patients (n = 45) and controls (n = 59), 33 metabolites differed significantly (VIP ≥ 1 and p ≤ 0.05). Metabolic pathways affected by these differentially expressed metabolites were analyzed. In both serum and urine samples, three pathways including arginine biosynthesis and purine metabolism were found to be significantly related to POP. Six metabolites including GPC, 1-methyladenosine, maleic acid, L-pyroglutamic acid, inosine, and citrate are significantly changed (VIP ≥ 1 and p ≤ 0.05) in both serum and urine samples from patients with POP. Receiver operating characteristics (ROC) curve analysis showed that using these six metabolites as a biomarker could distinguish patients with POP from controls with good accuracy in both serum (AUC = 1) and urine samples (AUC = 0.854). Collectively, these results further extended our understanding of key regulatory metabolic pathways involved in the pathophysiology of POP, as well as provided some promising biomarkers for effective POP diagnosis.
Collapse
Affiliation(s)
- Wei Deng
- Nanchang University, Nanchang 330006, Jiangxi, China; Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang 330006, Jiangxi, China
| | - Jun Rao
- Jiangxi Provincial Key Laboratory of Translational Medicine and Oncology, Jiangxi Cancer Hospital, Jiangxi Cancer Center, Nanchang 330029, China
| | - Xiaodan Chen
- Jiangxi Provincial Key Laboratory of Translational Medicine and Oncology, Jiangxi Cancer Hospital, Jiangxi Cancer Center, Nanchang 330029, China
| | - Dongqing Li
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang 330006, Jiangxi, China
| | - Ziyu Zhang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang 330006, Jiangxi, China
| | - Dan Liu
- Jiangxi Provincial Key Laboratory of Basic Pharmacology, Nanchang University School of Pharmaceutical Science, Nanchang 330006, China
| | - Jun Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang 330006, Jiangxi, China
| | - Yaoqing Wang
- Nanchang University, Nanchang 330006, Jiangxi, China; Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang 330006, Jiangxi, China
| | - Ouping Huang
- Nanchang University, Nanchang 330006, Jiangxi, China; Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang 330006, Jiangxi, China.
| |
Collapse
|
34
|
Carvalho LB, Capelo-Martínez JL, Lodeiro C, Wiśniewski JR, Santos HM. Snap-heated freeze-free preservation and processing of the urine proteome using the combination of stabilizor-based technology and filter aided sample preparation. Anal Chim Acta 2019; 1076:82-90. [DOI: 10.1016/j.aca.2019.05.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/19/2019] [Accepted: 05/22/2019] [Indexed: 10/26/2022]
|
35
|
Tian A, Pu K, Li B, Li M, Liu X, Gao L, Mao X. Weighted gene coexpression network analysis reveals hub genes involved in cholangiocarcinoma progression and prognosis. Hepatol Res 2019; 49:1195-1206. [PMID: 31177590 PMCID: PMC6899837 DOI: 10.1111/hepr.13386] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 04/09/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022]
Abstract
AIM Cholangiocarcinoma (CCA) is a highly malignant tumor found in the bile duct epithelial cells, and the second most common primary tumor of the liver. However, the pivotal roles of molecular biomarkers in oncogenesis of CCA are unclear. Therefore, we aim to explore the underlying mechanisms of progression and screen for novel prognostic biomarkers and treatment targets. METHOD The data of mRNA sequencing and clinical information of CCA patients in The Cancer Genome Atlas was analyzed by weighted gene coexpression network analysis (WGCNA). Modules and clinical traits were constructed according to Pearson's correlation analysis, and Gene Ontology and pathway enrichment analysis were applied. Hub genes of these modules were screened by intramodule analysis; Cytoscape with Search Tool for the Retrieval of Interacting Genes was utilized to visualize protein-protein interaction of these modules; hub genes of these modules were validated afterwards. Furthermore, the significance of these genes was confirmed by survival analysis. RESULTS Genes MRPS18A, CST1, and SCP2 were identified as candidate genes in the module, which was associated with clinical traits including pathological stage, histological grade, and liver function and which also affected overall survival of CCA patients. Nineteen hub genes were analyzed together and were associated with progression and prognosis of CCA. Survival analyses found that several of the multiple genes could serve as biomarkers to stratify CCA patients into low- and high-risk groups. CONCLUSION These candidate genes could be involved in progression of CCA, which could serve as novel prognostic markers and treatment targets. Moreover, most of them were first reported in CCA and deserve further research.
Collapse
Affiliation(s)
| | - Ke Pu
- Key Laboratory for Gastrointestinal Diseases of Gansu Province
| | | | - Min Li
- Departments of Infectious Diseases
| | - Xiaoguang Liu
- RheumatologyThe First Hospital of Lanzhou University
| | - Liping Gao
- The First Clinical Medical CollegeLanzhou UniversityLanzhouChina
| | - Xiaorong Mao
- Departments of Infectious Diseases,The First Clinical Medical CollegeLanzhou UniversityLanzhouChina
| |
Collapse
|
36
|
Csősz É, Deák E, Tóth N, Traverso CE, Csutak A, Tőzsér J. Comparative analysis of cytokine profiles of glaucomatous tears and aqueous humour reveals potential biomarkers for trabeculectomy complications. FEBS Open Bio 2019; 9:1020-1028. [PMID: 30959565 PMCID: PMC6487689 DOI: 10.1002/2211-5463.12637] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/11/2019] [Accepted: 04/05/2019] [Indexed: 12/11/2022] Open
Abstract
Glaucoma is a multifactorial neurodegenerative disease that causes impaired vision and, in advanced cases, blindness. The increasing prevalence of glaucoma due to an ageing population has necessitated the identification of suitable biomarkers for the early detection of the disease. Aqueous humour (AH) has been proposed as a source of biomarkers, but it can only be collected using a minor, yet invasive surgical intervention. Tears, however, are constantly available and can be collected any time via noninvasive methods. In order to examine the utility of tear as a surrogate for aqueous humour in biomarker development, we compared the levels of 27 cytokines and chemokines in paired samples of tear and aqueous humour using a Luminex multiplex immunobead-based technique. Significantly higher levels of cytokines in tear compared to aqueous humour were detected suggesting that tear and aqueous humour are not identical in terms of inflammation response. Furthermore, the levels of IFN-γ, GM-CSF and IL-5 in tear were significantly lower in patients who developed complications after one year, but no statistically significant changes in cytokine levels were observed in aqueous humour. These three molecules may have potential as predictive biomarkers for the appearance of late flap-related complications of trabeculectomy.
Collapse
Affiliation(s)
- Éva Csősz
- Biomarker Research GroupDepartment of Biochemistry and Molecular BiologyFaculty of MedicineUniversity of DebrecenHungary
- Proteomics Core FacilityDepartment of Biochemistry and Molecular BiologyFaculty of MedicineUniversity of DebrecenHungary
| | - Eszter Deák
- Biomarker Research GroupDepartment of Biochemistry and Molecular BiologyFaculty of MedicineUniversity of DebrecenHungary
- Department of OphthalmologyFaculty of MedicineUniversity of DebrecenHungary
| | - Noémi Tóth
- Biomarker Research GroupDepartment of Biochemistry and Molecular BiologyFaculty of MedicineUniversity of DebrecenHungary
- Department of OphthalmologyFaculty of MedicineUniversity of DebrecenHungary
| | - Carlo Enrico Traverso
- Clinica OculisticaDiNOGMIUniversity of Genoa and IRCCS Ospedale Policlinico San MartinoGenovaItaly
| | - Adrienne Csutak
- Department of OphthalmologyFaculty of MedicineUniversity of DebrecenHungary
| | - József Tőzsér
- Biomarker Research GroupDepartment of Biochemistry and Molecular BiologyFaculty of MedicineUniversity of DebrecenHungary
- Proteomics Core FacilityDepartment of Biochemistry and Molecular BiologyFaculty of MedicineUniversity of DebrecenHungary
| |
Collapse
|
37
|
|
38
|
Mateos J, Estévez O, González-Fernández Á, Anibarro L, Pallarés Á, Reljic R, Gallardo JM, Medina I, Carrera M. High-resolution quantitative proteomics applied to the study of the specific protein signature in the sputum and saliva of active tuberculosis patients and their infected and uninfected contacts. J Proteomics 2019; 195:41-52. [PMID: 30660769 DOI: 10.1016/j.jprot.2019.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/05/2018] [Accepted: 01/13/2019] [Indexed: 12/11/2022]
Abstract
Our goal was to establish panels of protein biomarkers that are characteristic of patients with microbiologically confirmed pulmonary tuberculosis (TB) and their contacts, including latent TB-infected (LTBI) and uninfected patients. Since the first pathogen-host contact occurs in the oral and nasal passages the saliva and sputum were chosen as the biological fluids to be studied. Quantitative shotgun proteomics was performed using a LTQ-Orbitrap-Elite platform. For active TB patients, both fluids exhibited a specific accumulation of proteins that were related to complement activation, inflammation and modulation of immune response. In the saliva of TB patients, a decrease of in proteins related to glucose and lipid metabolism was detected. In contrast, the sputum of uninfected contacts presented a specific proteomic signature that was composed of proteins involved in the perception of bitter taste, defense against pathogens and innate immune response, suggesting that those are key events during the initial entry of the pathogen in the host. SIGNIFICANCE: This is the first study to compare the saliva and sputum from active TB patients and their contacts. Our findings strongly suggest that TB patients show not only an activation of processes that are related to complement activation and modulation of inflammation but also an imbalance in carbohydrate and lipid metabolism. In addition, those individuals who do not get infected after direct exposure to the pathogen display a typical proteomic signature in the sputum, which is a reflection of the secretion from the nasal and oral mucosa, the first immunological barriers that M. tuberculosis encounters in the host. Thus, this result indicates the importance of the processes related to the innate immune response in fighting the initial events of the infection.
Collapse
Affiliation(s)
- Jesús Mateos
- Spanish National Research Council (CSIC), Vigo, Pontevedra, Spain.
| | - Olivia Estévez
- Biomedical Research Centre (CINBIO), Galician Singular Center of Research, Galicia Sur Health Research Institute (IIS-GS), University of Vigo, Vigo, Pontevedra, Spain
| | - África González-Fernández
- Biomedical Research Centre (CINBIO), Galician Singular Center of Research, Galicia Sur Health Research Institute (IIS-GS), University of Vigo, Vigo, Pontevedra, Spain
| | - Luis Anibarro
- Biomedical Research Centre (CINBIO), Galician Singular Center of Research, Galicia Sur Health Research Institute (IIS-GS), University of Vigo, Vigo, Pontevedra, Spain; Tuberculosis Unit, Infectious Diseases, Internal Medicine Service, Complexo Hospitalario Universitario de Pontevedra, Galicia Sur Health Research Institute (IIS-GS), Pontevedra, Spain; Mycobacterial Infections Study Group (GEIM) of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Ángeles Pallarés
- Tuberculosis Unit, Infectious Diseases, Internal Medicine Service, Complexo Hospitalario Universitario de Pontevedra, Galicia Sur Health Research Institute (IIS-GS), Pontevedra, Spain
| | | | - José M Gallardo
- Spanish National Research Council (CSIC), Vigo, Pontevedra, Spain
| | - Isabel Medina
- Spanish National Research Council (CSIC), Vigo, Pontevedra, Spain
| | - Mónica Carrera
- Spanish National Research Council (CSIC), Vigo, Pontevedra, Spain.
| |
Collapse
|
39
|
Kim YS, Han D, Kim J, Kim DW, Kim YM, Mo JH, Choi HG, Park JW, Shin HW. In-Depth, Proteomic Analysis of Nasal Secretions from Patients With Chronic Rhinosinusitis and Nasal Polyps. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2019; 11:691-708. [PMID: 31332980 PMCID: PMC6658407 DOI: 10.4168/aair.2019.11.5.691] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/22/2019] [Accepted: 05/08/2019] [Indexed: 12/19/2022]
Abstract
Purpose Chronic rhinosinusitis (CRS) is a complex immunological condition, and novel experimental modalities are required to explore various clinical and pathophysiological endotypes; mere evaluation of nasal polyp (NP) status is inadequate. Therefore, we collected patient nasal secretions on filter paper and characterized the proteomes. Methods We performed liquid chromatography-mass spectrometry (MS)/MS in the data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes. Nasal secretions were collected from 10 controls, 10 CRS without NPs (CRSsNP) and 10 CRS with NPs (CRSwNP). We performed Orbitrap MS-based proteomic analysis in the DDA (5 controls, 5 CRSsNP and 5 CRSwNP) and the DIA (5 controls, 5 CRSsNP and 5 CRSwNP) modes, followed by a statistical analysis and a hierarchical clustering to identify differentially expressed proteins in the 3 groups. Results We identified 2,020 proteins in nasal secretions. Canonical pathway analysis and gene ontology (GO) evaluation revealed that interleukin (IL)-7, IL-9, IL-17A and IL-22 signaling and neutrophil-mediated immune responses like neutrophil degranulation and activation were significantly increased in CRSwNP compared to control. The GO terms related to the iron ion metabolism that may be associated with CRS and NP development. Conclusions Collection of nasal secretions on the filter paper is a practical and non-invasive method for in-depth study of nasal proteomics. Our proteomic signatures also support that Asian NPs could be characterized as non-eosinophilic inflammation features. Therefore, the proteomic profiling of nasal secretions from CRS patients may enhance our understanding of CRS endotypes.
Collapse
Affiliation(s)
- Yi Sook Kim
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea.,Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - Dohyun Han
- Proteomics core facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - JinYoup Kim
- Department of Otorhinolaryngology, Armed Forces Capital Hospital, Seongnam, Korea
| | - Dae Woo Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Boramae Medical Center, Seoul, Korea.,Clinical Mucosal Immunology Study Group, Seoul, Korea
| | - Yong Min Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Chungnam National University Hospital, Daejeon, Korea.,Clinical Mucosal Immunology Study Group, Seoul, Korea
| | - Ji Hun Mo
- Department of Otorhinolaryngology-Head and Neck Surgery, Dankook University Hospital, Cheonan, Korea.,Clinical Mucosal Immunology Study Group, Seoul, Korea
| | - Hyo Geun Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University Hospital, Pyongchon, Korea
| | - Jong Wan Park
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea.,Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.,Ischemic/hypoxic disease institute, Seoul National University College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Woo Shin
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea.,Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.,Ischemic/hypoxic disease institute, Seoul National University College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.,Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, Korea.,Clinical Mucosal Immunology Study Group, Seoul, Korea.
| |
Collapse
|
40
|
Guhl C, Birklein F, Hirsch S. Sweating disorders in mice with and without nerve lesions. Eur J Pain 2018; 23:835-842. [PMID: 30582875 DOI: 10.1002/ejp.1352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 12/12/2018] [Accepted: 12/18/2018] [Indexed: 11/11/2022]
Abstract
BACKGROUND Hypersensitivity and altered sweating are often present in neuropathy patients. Nerve lesions are known to produce sudomotor dysfunctions but also patients suffering from complex regional pain syndrome, CRPS1-a condition without a nerve lesion-present with sweating disorders. METHODS Using proton nuclear magnetic resonance of sweat water, we quantified sweat output of mice suffering from a nerve lesion or a bone fracture without nerve lesion and correlated their sweating with behavioural paw hypersensitivity accessed in von Frey testings, water applications and weight-bearing measured with an incapacitance metre. RESULTS Lesioned animals sweat less and are hypersensitive compared to healthy controls, as expected. Fractured animals on the injured side sweat less acutely after the injury but more in the chronic phase. They are hypersensitive acutely as well as chronically after the fracture. These findings resemble human bone trauma patients in the acute phase and CRPS patients in the chronic phase. CONCLUSIONS Sweating disorders are present both in neuropathic animals and in those with a bone fracture without nerve lesions, and autonomic dysfunctions might be considered as an important component in the aetiology of neuropathies. SIGNIFICANCE Sweat output changes in mice after bone trauma, potentially indicative of posttraumatic processes leading to CRPS in humans.
Collapse
Affiliation(s)
- Charlotte Guhl
- Klinik und Poliklinik für Neurologie, Unimedizin Mainz, Mainz, Germany
| | - Frank Birklein
- Klinik und Poliklinik für Neurologie, Unimedizin Mainz, Mainz, Germany
| | - Silke Hirsch
- Klinik und Poliklinik für Neurologie, Unimedizin Mainz, Mainz, Germany
| |
Collapse
|
41
|
Csősz É, Tóth N, Deák E, Csutak A, Tőzsér J. Wound-Healing Markers Revealed by Proximity Extension Assay in Tears of Patients following Glaucoma Surgery. Int J Mol Sci 2018; 19:ijms19124096. [PMID: 30567303 PMCID: PMC6321131 DOI: 10.3390/ijms19124096] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/26/2018] [Accepted: 12/11/2018] [Indexed: 02/07/2023] Open
Abstract
Tears are a constantly available and highly valuable body fluid collectable by non-invasive techniques. Although it can give information on ocular status and be used for follow-ups, tear analysis is challenging due to the low amount of sample that is available. Proximity extension assay (PEA) allows for a sensitive and scalable analysis of multiple proteins in a single run from a one-µL sample, so we applied this technique and examined the amount of 184 proteins in tears collected at different time points after trabeculectomy. The success rate of this surgical intervention highly depends on proper wound healing; therefore, information on the process is indispensable. We observed significantly higher levels of IL-6 and MMP1 at the early time points (day one, two, and four) following trabeculectomy, and the protein amounts went back to the level observed before the surgery three months after the intervention. Patients with or without complications were tested, and proteins that have roles in the immune response and wound healing could be observed with altered frequency and amounts in the cases of patients with complications. Our results highlight the importance of inflammation in wound-healing complications, and at the same time, indicate the utility of PEA in tear analysis.
Collapse
Affiliation(s)
- Éva Csősz
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1., 4032 Debrecen, Hungary.
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1., 4032 Debrecen, Hungary.
| | - Noémi Tóth
- Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98., 4032 Debrecen, Hungary.
| | - Eszter Deák
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1., 4032 Debrecen, Hungary.
- Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98., 4032 Debrecen, Hungary.
| | - Adrienne Csutak
- Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98., 4032 Debrecen, Hungary.
| | - József Tőzsér
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1., 4032 Debrecen, Hungary.
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1., 4032 Debrecen, Hungary.
| |
Collapse
|
42
|
Lorenzo-Pouso AI, Pérez-Sayáns M, Bravo SB, López-Jornet P, García-Vence M, Alonso-Sampedro M, Carballo J, García-García A. Protein-Based Salivary Profiles as Novel Biomarkers for Oral Diseases. DISEASE MARKERS 2018; 2018:6141845. [PMID: 30524521 PMCID: PMC6247606 DOI: 10.1155/2018/6141845] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/26/2018] [Accepted: 10/04/2018] [Indexed: 12/11/2022]
Abstract
The Global Burden of Oral Diseases affects 3.5 billion people worldwide, representing the number of people affected by the burden of untreated dental caries, severe periodontal disease, and edentulism. Thus, much more efforts in terms of diagnostics and treatments must be provided in the fight of these outcomes. In this sense, recently, the study of saliva as biological matrix has been identified as a new landmark initiative in the search of novel and useful biomarkers to prevent and diagnose these conditions. Specifically, saliva is a rich reservoir of different proteins and peptides and accessible due to recent advances in molecular biology and specially in targeted and unbiased proteomics technologies. Nonetheless, emerging barriers are an obstacle to the study of the salivary proteome in an effective way. This review aims at giving an overall perspective of salivary biomarkers identified in several oral diseases by means of molecular biology approaches.
Collapse
Affiliation(s)
- Alejandro I. Lorenzo-Pouso
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Mario Pérez-Sayáns
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Susana B. Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Pía López-Jornet
- Department of Oral Medicine, Faculty of Medicine, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Espinardo, Murcia, Spain
| | - María García-Vence
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Manuela Alonso-Sampedro
- Department of Internal Medicine and Clinical Epidemiology, Santiago de Compostela University Hospital Complex (CHUS), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
| | - Javier Carballo
- Department of Food Technology, Faculty of Sciences, University of Vigo-Ourense Campus, Ourense, Spain
| | - Abel García-García
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| |
Collapse
|
43
|
Ortuño-Lizarán I, Beach TG, Serrano GE, Walker DG, Adler CH, Cuenca N. Phosphorylated α-synuclein in the retina is a biomarker of Parkinson's disease pathology severity. Mov Disord 2018; 33:1315-1324. [PMID: 29737566 PMCID: PMC6146055 DOI: 10.1002/mds.27392] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/01/2018] [Accepted: 03/04/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND PD patients often have visual alterations, for example, loss of visual acuity, contrast sensitivity or motion perception, and diminished electroretinogram responses. PD pathology is mainly characterized by the accumulation of pathological α-synuclein deposits in the brain, but little is known about how synucleinopathy affects the retina. OBJECTIVE To study the correlation between α-synuclein deposits in the retina and brain of autopsied subjects with PD and incidental Lewy body disease. METHODS We evaluated the presence of phosphorylated α-synuclein in the retina of autopsied subjects with PD (9 subjects), incidental Lewy body disease (4 subjects), and controls (6 subjects) by immunohistochemistry and compared the retinal synucleinopathy with brain disease severity indicators. RESULTS Whereas controls did not show any phosphorylated α-synuclein immunoreactivity in their retina, all PD subjects and 3 of 4 incidental Lewy body disease subjects had phosphorylated α-synuclein deposits in ganglion cell perikarya, dendrites, and axons, some of them resembling brain Lewy bodies and Lewy neurites. The Lewy-type synucleinopathy density in the retina significantly correlated with Lewy-type synucleinopathy density in the brain, with the Unified Parkinson's disease pathology stage and with the motor UPDRS. CONCLUSION These data suggest that phosphorylated α-synuclein accumulates in the retina in parallel with that in the brain, including in early stages preceding development of clinical signs of parkinsonism or dementia. Therefore, the retina may provide an in vivo indicator of brain pathology severity, and its detection could help in the diagnosis and monitoring of disease progression. © 2018 International Parkinson and Movement Disorder Society.
Collapse
Affiliation(s)
| | - Thomas G. Beach
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | | | | | - Nicolás Cuenca
- Department of Physiology, Genetics and Microbiology, University of Alicante, Spain
| |
Collapse
|
44
|
Murphy S, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K. Proteomic identification of elevated saliva kallikrein levels in the mdx-4cv mouse model of Duchenne muscular dystrophy. Biochem Biophys Rep 2018; 18:100541. [PMID: 31193643 PMCID: PMC6537026 DOI: 10.1016/j.bbrep.2018.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/30/2018] [Accepted: 05/23/2018] [Indexed: 12/21/2022] Open
Abstract
Dystrophinopathies are multi-system disorders that affect the skeletal musculature, the cardio-respiratory system and the central nervous system. The systematic screening of suitable biofluids for released or altered proteins promises new insights into the highly complex pathophysiology of X-linked muscular dystrophy. However, standard detection approaches using antibody-based assays often fail to reproducibly detect low-abundance protein isoforms in dilute biological fluids. In contrast, mass spectrometric screening approaches enable the proteome-wide identification of minor protein changes in biofluids. This report describes the findings from the comparative proteomic analysis of whole saliva samples from wild type versus the established mdx-4cv mouse model of highly progressive muscular dystrophy, focusing on the kallikrein protein family. Kallikrein-1 (Klk1) and 13 Klk1-related peptidases were identified in saliva and serum from normal mice. Comparative proteomics revealed elevated saliva levels of the Klk1-related peptidases Klk1-b1, Klk1-b5 and Klk-b22, as well as an increased Klk-1 concentration, which agrees with higher Klk-1 levels in serum from mdx-4cv mice. This indicates altered cellular signaling, extracellular matrix remodeling and an altered immune response in the mdx-4cv mouse, and establishes liquid biopsy procedures as suitable bioanalytical tools for the systematic survey of complex pathobiochemical changes in animal models of muscular dystrophy.
Collapse
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, D53115 Bonn, Germany
| | - Rustam R Mundegar
- Institute of Physiology II, University of Bonn, D53115 Bonn, Germany
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| |
Collapse
|
45
|
Paulo JA, Jedrychowski MP, Chouchani ET, Kazak L, Gygi SP. Multiplexed Isobaric Tag-Based Profiling of Seven Murine Tissues Following In Vivo Nicotine Treatment Using a Minimalistic Proteomics Strategy. Proteomics 2018; 18:e1700326. [PMID: 29660237 PMCID: PMC5992107 DOI: 10.1002/pmic.201700326] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/24/2017] [Indexed: 12/18/2022]
Abstract
Nicotine is a major addictive compound in tobacco and a component of smoking-related products, such as e-cigarettes. Once internalized, nicotine can perturb many cellular pathways and can induce alterations in proteins across different cell types; however, the mechanisms thereof remain undetermined. The authors hypothesize that both tissue-specific and global protein abundance alterations result from nicotine exposure. Presented here is the first proteomic profiling of multiple tissues from mice treated orally with nicotine. Proteins extracted from seven tissues (brain, heart, kidney, liver, lung, pancreas, and spleen) from treated (n = 5) and untreated control (n = 5) mice are assembled into a TMT10-plex experiment. A minimalistic proteomics strategy is employed using TMT reagents efficiently and centrifugation-based reversed-phase columns to streamline sample preparation. Combined, over 11 000 non-redundant proteins from over 138 000 different peptides are quantified in seven TMT10-plex experiments. Between 7 and 126 proteins are significantly altered in tissues from nicotine-exposed mice, 11 which are altered in two or more tissues. Our data showcase the vast extent of nicotine exposure across murine tissue.
Collapse
Affiliation(s)
- Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Mark P. Jedrychowski
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
| | - Edward T. Chouchani
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
| | - Lawrence Kazak
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| |
Collapse
|
46
|
Galiana‐Simal A, Muñoz‐Martinez V, Calero‐Bueno P, Vela‐Romero M, Beato‐Fernandez L. Towards a future molecular diagnosis of autism: Recent advances in biomarkers research from saliva samples. Int J Dev Neurosci 2018; 67:1-5. [DOI: 10.1016/j.ijdevneu.2018.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 01/17/2023] Open
Affiliation(s)
- Adrian Galiana‐Simal
- Clínica Centro de Desarrollo Infantil de Ciudad Real (CDICR)Calle Eras del Cerrillo n°813004Ciudad RealSpain
- Grupo de Investigación en Trastornos del Neurodesarrollo de Ciudad Real (TNDCR)Ciudad RealSpain
| | - Victoria Muñoz‐Martinez
- Hospital General Universitario de Ciudad Real (HGUCR), Servicio de PsiquiatríaCalle Obispo Rafael Torija s/n13005Ciudad RealSpain
- Grupo de Investigación en Trastornos del Neurodesarrollo de Ciudad Real (TNDCR)Ciudad RealSpain
| | - Paloma Calero‐Bueno
- Universidad de Castilla‐La Mancha (UCLM)Facultad de Terapia Ocupacional, Logopedia y EnfermeríaAvda. Real Fábrica de Seda, s/n, 45600Talavera de la ReinaToledoSpain
- Grupo de Investigación en Trastornos del Neurodesarrollo de Ciudad Real (TNDCR)Ciudad RealSpain
| | - Maria Vela‐Romero
- Clínica Centro de Desarrollo Infantil de Ciudad Real (CDICR)Calle Eras del Cerrillo n°813004Ciudad RealSpain
- Grupo de Investigación en Trastornos del Neurodesarrollo de Ciudad Real (TNDCR)Ciudad RealSpain
| | - Luis Beato‐Fernandez
- Hospital General Universitario de Ciudad Real (HGUCR), Servicio de PsiquiatríaCalle Obispo Rafael Torija s/n13005Ciudad RealSpain
- Grupo de Investigación en Trastornos del Neurodesarrollo de Ciudad Real (TNDCR)Ciudad RealSpain
| |
Collapse
|
47
|
Csősz É, Márkus B, Darula Z, Medzihradszky KF, Nemes J, Szabó E, Tőzsér J, Kiss C, Márton I. Salivary proteome profiling of oral squamous cell carcinoma in a Hungarian population. FEBS Open Bio 2018; 8:556-569. [PMID: 29632809 PMCID: PMC5881539 DOI: 10.1002/2211-5463.12391] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/23/2017] [Accepted: 01/15/2018] [Indexed: 12/13/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the seventh most common malignancy and the ninth most frequent cause of cancer death in Europe. Within Europe, Hungary has one of the highest rates of OSCC incidence and mortality. Thus, there is an urgent need to improve early detection. Saliva, as a readily available body fluid, became an increasingly important substance for the detection of biomarkers for many diseases. Different research groups have identified salivary biomarkers specific for OSCC for different countries. In this study, saliva samples of Hungarian patients with OSCC were studied to discover disease‐specific and perhaps region‐specific biomarkers. LC‐mass spectrometry (MS)/MS analysis on a linear ion trap‐Orbitrap mass spectrometer was used for qualitative and quantitative salivary protein profiling. More than 500 proteins were identified from saliva by shotgun proteomics. The up‐ and downregulated proteins in the saliva of patients with OSCC highlighted the importance of protein–protein interaction networks involving the immune system and proteolysis in disease development. Two potential biomarkers from our shotgun analysis and a third candidate reported earlier by a Taiwanese group were further examined by ELISA on a larger reference set of samples. Resistin, a biomarker reported in Taiwan but not validated in our study, highlights the necessity of application of standardized analysis methods in different ethnic or geographical populations to identify biomarkers with sufficient specificity and sensitivity.
Collapse
Affiliation(s)
- Éva Csősz
- Proteomics Core Facility Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary.,Biomarker Research Group Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary
| | - Bernadett Márkus
- Proteomics Core Facility Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary.,Biomarker Research Group Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary
| | - Zsuzsanna Darula
- Laboratory of Proteomics Research Biological Research Centre of the Hungarian Academy of Sciences Szeged Hungary
| | - Katalin F Medzihradszky
- Laboratory of Proteomics Research Biological Research Centre of the Hungarian Academy of Sciences Szeged Hungary
| | - Judit Nemes
- Department of Pedodontics Faculty of Dentistry University of Debrecen Hungary
| | - Emese Szabó
- Proteomics Core Facility Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary.,Biomarker Research Group Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary
| | - József Tőzsér
- Proteomics Core Facility Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary.,Biomarker Research Group Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary
| | - Csongor Kiss
- Department of Pediatrics Faculty of Medicine University of Debrecen Hungary
| | - Ildikó Márton
- Department of Restorative Dentistry Faculty of Dentistry University of Debrecen Hungary
| |
Collapse
|
48
|
Murphy S, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K. Proteomic serum biomarkers for neuromuscular diseases. Expert Rev Proteomics 2018; 15:277-291. [DOI: 10.1080/14789450.2018.1429923] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
| | - Margit Zweyer
- Department of Physiology II, University of Bonn, Bonn, Germany
| | | | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
| |
Collapse
|
49
|
Torres SMF, Furrow E, Souza CP, Granick JL, de Jong EP, Griffin TJ, Wang X. Salivary proteomics of healthy dogs: An in depth catalog. PLoS One 2018; 13:e0191307. [PMID: 29329347 PMCID: PMC5766244 DOI: 10.1371/journal.pone.0191307] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/02/2018] [Indexed: 12/19/2022] Open
Abstract
Objective To provide an in-depth catalog of the salivary proteome and endogenous peptidome of healthy dogs, evaluate proteins and peptides with antimicrobial properties, and compare the most common salivary proteins and peptides between different breed phylogeny groups. Methods 36 healthy dogs without evidence of periodontal disease representing four breed phylogeny groups, based upon single nucleotide polymorphism haplotypes (ancient, herding/sighthound, and two miscellaneous groups). Saliva collected from dogs was pooled by phylogeny group and analyzed using nanoscale liquid chromatography-tandem mass spectrometry. Resulting tandem mass spectra were compared to databases for identification of endogenous peptides and inferred proteins. Results 2,491 proteins and endogenous peptides were found in the saliva of healthy dogs with no periodontal disease. All dog phylogeny groups’ saliva was rich in proteins and peptides with antimicrobial functions. The ancient breeds group was distinct in that it contained unique proteins and was missing many proteins and peptides present in the other groups. Conclusions and clinical relevance Using a sophisticated nanoscale liquid chromatography-tandem mass spectrometry, we were able to identify 10-fold more salivary proteins than previously reported in dogs. Seven of the top 10 most abundant proteins or peptides serve immune functions and many more with various antimicrobial mechanisms were found. This is the most comprehensive analysis of healthy canine saliva to date, and will provide the groundwork for future studies analyzing salivary proteins and endogenous peptides in disease states.
Collapse
Affiliation(s)
- Sheila M. F. Torres
- Veterinary Clinical Sciences Department, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
- * E-mail:
| | - Eva Furrow
- Veterinary Clinical Sciences Department, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Clarissa P. Souza
- Veterinary Clinical Sciences Department, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
- Clinical Sciences Department, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jennifer L. Granick
- Veterinary Clinical Sciences Department, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Ebbing P. de Jong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry and Molecular Biochemistry, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Xiong Wang
- Department of Veterinary Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, United States of America
- Minnesota Department of Health, Saint Paul, Minnesota, United States of America
| |
Collapse
|
50
|
Redox regulation of leukocyte-derived microparticle release and protein content in response to cold physical plasma-derived oxidants. CLINICAL PLASMA MEDICINE 2017. [DOI: 10.1016/j.cpme.2017.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|