1
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Ahmad P, Hussain A, Siqueira WL. Mass spectrometry-based proteomic approaches for salivary protein biomarkers discovery and dental caries diagnosis: A critical review. MASS SPECTROMETRY REVIEWS 2024; 43:826-856. [PMID: 36444686 DOI: 10.1002/mas.21822] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Dental caries is a multifactorial chronic disease resulting from the intricate interplay among acid-generating bacteria, fermentable carbohydrates, and several host factors such as saliva. Saliva comprises several proteins which could be utilized as biomarkers for caries prevention, diagnosis, and prognosis. Mass spectrometry-based salivary proteomics approaches, owing to their sensitivity, provide the opportunity to investigate and unveil crucial cariogenic pathogen activity and host indicators and may demonstrate clinically relevant biomarkers to improve caries diagnosis and management. The present review outlines the published literature of human clinical proteomics investigations on caries and extensively elucidates frequently reported salivary proteins as biomarkers. This review also discusses important aspects while designing an experimental proteomics workflow. The protein-protein interactions and the clinical relevance of salivary proteins as biomarkers for caries, together with uninvestigated domains of the discipline are also discussed critically.
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Affiliation(s)
- Paras Ahmad
- College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ahmed Hussain
- College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Walter L Siqueira
- College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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2
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Shen A, Feng X, Wang D, Liu Y, Zhang K, Wang J, Li Y, Ali MM, Hu L. High-throughput proteomic analysis of extracellular vesicles from saliva by chemical probe-based array. Anal Chim Acta 2024; 1309:342699. [PMID: 38772652 DOI: 10.1016/j.aca.2024.342699] [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: 04/15/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
Extracellular vesicles (EVs) are cell-released, nucleus-free particles with a double-membrane structure that effectively prevents degradation of internal components by a variety of salivary enzymes. Saliva is an easily accessible biofluid that contains a wealth of valuable information for disease diagnosis and monitoring and especially reflect respiratory and digestive tract diseases. However, the lack of efficient and high-throughput methods for proteomic analysis of salivary biomarkers poses a significant challenge. Herein, we designed a salivary EV amphiphile-dendrimer supramolecular probe (SEASP) array which enables efficient enrichment and in situ detection of EVs protein biomarkers. Detergent Tween-20 washing of SEASP arrays removes high abundance of heteroproteins from saliva well. This array shows good analytical performance in the linear range of 10 μL-150 μL (LOD = 0.4 μg protein, or 10 μL saliva), exhibiting a good recovery (80.0 %). Compared to ultracentrifugation (UC), this procedure provides simple and convenient access to high-purity EVs (1.3 × 109 particles per mg protein) with good physiological status and structure. Coupling with mass spectrometry based proteomic analysis, differentially expressed proteins as selected asthma biomarkers have been screened. Then, we validated the proteomics primary screening results through clinical samples (100 μL each) using the SEASP array. Utilizing the dual antibody fluorescence technology, SEASP enables the simultaneous high-throughput detection of two proteins. Therefore, the EVs marker protein CD81 could be used as an internal standard to normalize the number of EVs, which was stably expressed in EVs. Proteomics and array results suggested that HNRNPU (P = 4.9 * 10-6) and MUC5B (P = 4.7 * 10-11) are promising protein biomarkers for infantile asthma. HNRNPU and MUC5B may be associated with disease onset and subtypes. The SEASP arrays provide a significant advancement in the field of salivary biomarker. The array enables high-throughput in situ protein detection for highly viscous and complex biological samples. It provides a rapid, low-cost, highly specific screening procedure and experimental basis for early disease screening and diagnosis in the field of liquid biopsy.
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Affiliation(s)
- Ao Shen
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Xin Feng
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Dongxue Wang
- Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, China; The π-HuB Project Infrastructure, International Academy of Phronesis Medicine, Guangzhou, China
| | - Yuanyuan Liu
- Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, China; The π-HuB Project Infrastructure, International Academy of Phronesis Medicine, Guangzhou, China
| | - Kaifu Zhang
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Jiliang Wang
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yanan Li
- Department of Pediatrics Children's Medical Center, The First Hospital of Jilin University, Changchun, 130021, China.
| | - Muhammad Mujahid Ali
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, 210096, China.
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China.
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3
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Granato DC, Carnielli CM, Trino LD, Busso-Lopes AF, Câmara GA, Normando AGC, Filho HVR, Domingues R, Yokoo S, Pauletti BA, Patroni FM, Santos-Silva AR, Lopes MA, Brandão TB, Prado-Ribeiro AC, Lopes-de Oliveira PS, Telles GP, Paes Leme AF. Mapping Conformational Changes in the Saliva Proteome Potentially Associated with Oral Cancer Aggressiveness. J Proteome Res 2024; 23:2148-2159. [PMID: 38785273 PMCID: PMC11166140 DOI: 10.1021/acs.jproteome.4c00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/19/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
Diverse proteomics-based strategies have been applied to saliva to quantitatively identify diagnostic and prognostic targets for oral cancer. Considering that these targets may be regulated by events that do not imply variation in protein abundance levels, we hypothesized that changes in protein conformation can be associated with diagnosis and prognosis, revealing biological processes and novel targets of clinical relevance. For this, we employed limited proteolysis-mass spectrometry in saliva samples to explore structural alterations, comparing the proteome of healthy control and oral squamous cell carcinoma (OSCC) patients with and without lymph node metastasis. Thirty-six proteins with potential structural rearrangements were associated with clinical patient features including transketolase and its interacting partners. Moreover, N-glycosylated peptides contribute to structural rearrangements of potential diagnostic and prognostic markers. Altogether, this approach utilizes saliva proteins to search for targets for diagnosing and prognosing oral cancer and can guide the discovery of potential regulated sites beyond protein-level abundance.
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Affiliation(s)
- Daniela C. Granato
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Carolina M. Carnielli
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Luciana D. Trino
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Ariane F. Busso-Lopes
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Guilherme A. Câmara
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Ana Gabriela C. Normando
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Helder V. R. Filho
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Romênia
R. Domingues
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Sami Yokoo
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Bianca A. Pauletti
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Fabio M. Patroni
- Centro
de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-875, Brazil
| | - Alan R. Santos-Silva
- Departamento
de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas (UNICAMP), Piracicaba, SP 13414-903, Brazil
| | - Márcio A. Lopes
- Departamento
de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas (UNICAMP), Piracicaba, SP 13414-903, Brazil
| | - Thaís Bianca Brandão
- Instituto
do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo 01246-000, Brazil
| | | | - Paulo. S. Lopes-de Oliveira
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Guilherme P. Telles
- Instituto
de Computação, Universidade
Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-852, Brazil
| | - Adriana F. Paes Leme
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
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Fournier C, Fiedler A, Weidele M, Kautz H, Schleheck D. Description of a 'plankton filtration bias' in sequencing-based bacterial community analysis and of an Arduino microcontroller-based flowmeter device that can help to resolve it. PLoS One 2024; 19:e0303937. [PMID: 38805423 PMCID: PMC11132488 DOI: 10.1371/journal.pone.0303937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/03/2024] [Indexed: 05/30/2024] Open
Abstract
Diversity studies of aquatic picoplankton (bacterioplankton) communities using size-class filtration, DNA extraction, PCR and sequencing of phylogenetic markers, require a robust methodological pipeline, since biases have been demonstrated essentially at all levels, including DNA extraction, primer choice and PCR. Even different filtration volumes of the same plankton sample and, thus, different biomass loading of the filters, can distort the sequencing results. In this study, we designed an Arduino microcontroller-based flowmeter that records the decrease of initial (maximal) flowrate as proxy for increasing biomass loading and clogging of filters during plankton filtration. The device was tested using freshwater plankton of Lake Constance, and total DNA was extracted and an 16S rDNA amplicon was sequenced. We confirmed that different filtration volumes used for the same water sample affect the sequencing results. Differences were visible in alpha and beta diversities and across all taxonomic ranks. Taxa most affected were typical freshwater Actinobacteria and Bacteroidetes, increasing up to 38% and decreasing up to 29% in relative abundance, respectively. In another experiment, a lake water sample was filtered undiluted and three-fold diluted, and each filtration was stopped once the flowrate had reduced to 50% of initial flowrate, hence, at the same degree of filter clogging. The three-fold diluted sample required three-fold filtration volumes, while equivalent amounts of total DNA were extracted and differences across all taxonomic ranks were not statistically significant compared to the undiluted controls. In conclusion, this work confirms a volume/biomass-dependent bacterioplankton filtration bias for sequencing-based community analyses and provides an improved procedure for controlling biomass loading during filtrations and recovery of equivalent amounts of DNA from samples independent of the plankton density. The application of the device can also avoid the distorting of sequencing results as caused by the plankton filtration bias.
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Affiliation(s)
- Corentin Fournier
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Alexander Fiedler
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Maximilian Weidele
- Scientific Engineering and Manufacturing Services, University of Konstanz, Konstanz, Germany
| | - Harald Kautz
- Scientific Engineering and Manufacturing Services, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
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5
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Lundtorp-Olsen C, Markvart M, Twetman S, Belstrøm D. Effect of Probiotic Supplements on the Oral Microbiota-A Narrative Review. Pathogens 2024; 13:419. [PMID: 38787271 PMCID: PMC11124442 DOI: 10.3390/pathogens13050419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Data from systematic reviews and meta-analyses show that probiotics positively impact clinical parameters of oral diseases such as gingivitis, dental caries, and periodontitis. However, the working mechanism of probiotics is not fully understood, but is hypothesized to be mediated by direct and indirect interactions with the oral microbiota and the human host. In the present narrative review, we focused on the microbiological effect of probiotic supplements based on data retrieved from randomized clinical trials (RCTs). In addition, we assessed to what extent contemporary molecular methods have been employed in clinical trials in the field of oral probiotics. Multiple RCTs have been performed studying the potential effect of probiotics on gingivitis, dental caries, and periodontitis, as evaluated by microbial endpoints. In general, results are conflicting, with some studies reporting a positive effect, whereas others are not able to record any effect. Major differences in terms of study designs and sample size, as well as delivery route, frequency, and duration of probiotic consumption, hamper comparison across studies. In addition, most RCTs have been performed with a limited sample size using relatively simple methods for microbial identification, such as culturing, qPCR, and DNA-DNA checkerboard, while high-throughput methods such as 16S sequencing have only been employed in a few studies. Currently, state-of-the-art molecular methods such as metagenomics, metatranscriptomics, and metaproteomics have not yet been used in RCTs in the field of probiotics. The present narrative review revealed that the effect of probiotic supplements on the oral microbiota remains largely uncovered. One important reason is that most RCTs are performed without studying the microbiological effect. To facilitate future systematic reviews and meta-analyses, an internationally agreed core outcome set for the reporting of microbial endpoints in clinical trials would be desirable. Such a standardized collection of outcomes would most likely improve the quality of probiotic research in the oral context.
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Affiliation(s)
| | | | | | - Daniel Belstrøm
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (C.L.-O.); (M.M.); (S.T.)
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6
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Smith H, Giulivi C. Starch treatment improves the salivary proteome for subject identification purposes. Forensic Sci Med Pathol 2024; 20:117-128. [PMID: 37084127 PMCID: PMC10944386 DOI: 10.1007/s12024-023-00629-y] [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] [Accepted: 04/04/2023] [Indexed: 04/22/2023]
Abstract
Identification of subjects, including perpetrators, is one of the most crucial goals of forensic science. Saliva is among the most common biological fluids found at crime scenes, containing identifiable components. DNA has been the most prominent identifier to date, but its analysis can be complex due to low DNA yields and issues preserving its integrity at the crime scene. Proteins are emerging as viable candidates for subject identification. Previous work has shown that the salivary proteome of the least-abundant proteins may be helpful for subject identification, but more optimized techniques are needed. Among them is removing the most abundant proteins, such as salivary α-amylase. Starch treatment of saliva samples elicited the removal of this enzyme and that of glycosylated, low-molecular-weight proteins, proteases, and immunoglobulins, resulting in a saliva proteome profile enriched with a subset of proteins, allowing a more reliable and nuanced subject identification.
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Affiliation(s)
- Hannah Smith
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA.
- MIND Institute, University of California at Davis Medical Center, Sacramento, CA, USA.
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7
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Zhang Y, Chen Y, Chen C, Zhu Y, Liu M, Chen J. The enhancement mechanisms of mucin and lactoferrin on α-amylase activity in saliva: Exploring the interactions using QCM-D and molecular docking. Int J Biol Macromol 2024; 257:128710. [PMID: 38101660 DOI: 10.1016/j.ijbiomac.2023.128710] [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: 08/22/2023] [Revised: 11/12/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
α-Amylase activity differs between individuals and is influenced by dietary behavior and salivary constituents, but limited information is available on the relationship between α-amylase activity and saliva components. This study investigated the impact of salivary proteins on α-amylase activity, their various correlations, the effect of mucin (MUC5B and MUC7) and lactoferrin on the enzymatic kinetics of α-amylase, and the mechanisms of these interactions using the quartz crystal microbalance with dissipation (QCM-D) technique and molecular docking. The results showed that α-amylase activity was significantly correlated with the concentrations of MUC5B (R2 = 0.42, p < 0.05), MUC7 (R2 = 0.35, p < 0.05), and lactoferrin (R2 = 0.35, p < 0.05). An in vitro study demonstrated that α-amylase activity could be significantly increased by mucins and lactoferrin by decreasing the Michaelis constant (Km) of α-amylase. Moreover, the results from the QCM-D and molecule docking suggested that mucin and lactoferrin could interact with α-amylase to form stable α-amylase-mucin and α-amylase-lactoferrin complexes through hydrophobic interactions, electrostatic interactions, Van der Waals forces, and hydrogen bonds. In conclusion, these findings indicated that the salivary α-amylase activity depended not only on the α-amylase content, but also could be enhanced by the interactions of mucin/lactoferrin with α-amylase.
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Affiliation(s)
- Yufeng Zhang
- Laboratory of Food Oral Processing, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Yong Chen
- Laboratory of Food Oral Processing, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China.
| | - Chen Chen
- Laboratory of Food Oral Processing, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Yang Zhu
- Laboratory of Food Oral Processing, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Ming Liu
- Fujian Provincial Key Laboratory of Terahertz Functional Devices and Intelligent Sensing, School of Mechanical Engineering and Automation, Fuzhou University - Qishan Campus, Fuzhou, Fujian 350108, China
| | - Jianshe Chen
- Laboratory of Food Oral Processing, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
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8
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López-Solís R, Cortés-Araya K, Medel-Marabolí M, Obreque-Slier E. Different physicochemical interactions between varietal wines and human saliva: Correspondence with astringency. Food Res Int 2024; 178:113964. [PMID: 38309881 DOI: 10.1016/j.foodres.2024.113964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 12/19/2023] [Accepted: 01/02/2024] [Indexed: 02/05/2024]
Abstract
Astringency corresponds to the sensation of dryness and roughness that is experienced in the oral cavity in association with the interaction between salivary proteins and food polyphenols. In this study, the phenolic composition of seven varietal wines, the intensity of astringency they evoke and the physicochemical reactivity of these wines with whole human saliva were evaluated. Phenolic composition of wines was characterized by spectrophotometry and HPLC chromatography. Intensity of astringency was evaluated by trained sensory panels. Saliva from a single volunteer subject was used to assess wine-saliva interactions. To this end, binary mixtures were produced at different v/v wine/saliva ratios and each of them assayed for the ability of the salivary protein to diffuse on a cellulose membrane (diffusion test) and to remain in solution (precipitation test). Physicochemical reactivities between wine components and the protein fraction of saliva were contrasted against the astringency and the phenolic profile of each varietal wine. The study supports the view that astringency depends on physicochemical interactions between two complex matrices -wine and saliva- and not between some of their particular components.
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Affiliation(s)
- Remigio López-Solís
- Program of Cellular and Molecular Biology, Faculty of Medicine-ICBM, University of Chile, Independencia 1027, Santiago, Chile
| | - Katherine Cortés-Araya
- Department of Agro-Industry and Enology, Faculty of Agronomical Sciences,University of Chile, P.O. Box 1004, Santiago, Chile
| | - Marcela Medel-Marabolí
- Department of Agro-Industry and Enology, Faculty of Agronomical Sciences,University of Chile, P.O. Box 1004, Santiago, Chile
| | - Elías Obreque-Slier
- Department of Agro-Industry and Enology, Faculty of Agronomical Sciences,University of Chile, P.O. Box 1004, Santiago, Chile.
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9
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Dongiovanni P, Meroni M, Aiello G, D’Amato A, Cenzato N, Casati S, Damiani G, Fenoglio C, Galimberti D, Grossi E, Prati D, Lamorte G, Bianco C, Valenti L, Soggiu A, Zapperi S, La Porta CAM, Del Fabbro M, Tartaglia GM. Salivary proteomic profile of young healthy subjects. Front Mol Biosci 2023; 10:1327233. [PMID: 38099196 PMCID: PMC10720708 DOI: 10.3389/fmolb.2023.1327233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Background: The incidence of noncommunicable diseases (NCDs) has been rapidly ramped up worldwide. Hence, there is an urgent need to non-invasively detect NCDs possibly by exploiting saliva as a 'liquid biopsy' to identify biomarkers of the health status. Since, the absence of standardized procedures of collection/analysis and the lack of normal ranges makes the use of saliva still tricky, our purpose was to outline a salivary proteomic profile which features healthy individuals. Methods: We collected saliva samples from 19 young blood donors as reference population and the proteomic profile was investigated through mass-spectrometry. Results: We identified 1,004 proteins of whose 243 proteins were shared by all subjects. By applying a data clustering approach, we found a set of six most representative proteins across all subjects including Coronin-1A, F-actin-capping protein subunit alpha, Immunoglobulin J chain, Prosaposin, 78 kDa glucose-regulated protein and Heat shock 70 kDa protein 1A and 1B. Conclusion: All of these proteins are involved in immune system activation, cellular stress responses, proliferation, and invasion thus suggesting their use as biomarkers in patients with NCDs.
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Affiliation(s)
- P. Dongiovanni
- Medicine and Metabolic Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - M. Meroni
- Medicine and Metabolic Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Gilda Aiello
- Department of Human Science and Quality of Life Promotion, Telematic University San Raffaele, Rome, Italy
| | - A. D’Amato
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - N. Cenzato
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - S. Casati
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - G. Damiani
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - C. Fenoglio
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - D. Galimberti
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- Neurodegenerative Diseases Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - E. Grossi
- Villa Santa Maria Foundation, Tavernerio, Italy
| | - D. Prati
- Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - G. Lamorte
- Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - C. Bianco
- Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - L. Valenti
- Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - A. Soggiu
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - S. Zapperi
- Department of Physics, Center for Complexity and Biosystems, University of Milan, Milan, Italy
| | - C. A. M. La Porta
- Department of Environmental Science and Policy, Center for Complexity and Biosystems, University of Milan, Milan, Italy
| | - M. Del Fabbro
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- SC Maxillo-Facial Surgery and Dentistry, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - G. M. Tartaglia
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- SC Maxillo-Facial Surgery and Dentistry, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
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10
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Klaes S, Madan S, Deobald D, Cooper M, Adrian L. GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry. Int J Mol Sci 2023; 24:15692. [PMID: 37958676 PMCID: PMC10649880 DOI: 10.3390/ijms242115692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Profiling bacterial populations in mixed communities is a common task in microbiology. Sequencing of 16S small subunit ribosomal-RNA (16S rRNA) gene amplicons is a widely accepted and functional approach but relies on amplification primers and cannot quantify isotope incorporation. Tandem mass spectrometry proteotyping is an effective alternative for taxonomically profiling microorganisms. We suggest that targeted proteotyping approaches can complement traditional population analyses. Therefore, we describe an approach to assess bacterial community compositions at the family level using the taxonomic marker protein GroEL, which is ubiquitously found in bacteria, except a few obligate intracellular species. We refer to our method as GroEL-proteotyping. GroEL-proteotyping is based on high-resolution tandem mass spectrometry of GroEL peptides and identification of GroEL-derived taxa via a Galaxy workflow and a subsequent Python-based analysis script. Its advantage is that it can be performed with a curated and extendable sample-independent database and that GroEL can be pre-separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to reduce sample complexity, improving GroEL identification while simultaneously decreasing the instrument time. GroEL-proteotyping was validated by employing it on a comprehensive raw dataset obtained through a metaproteome approach from synthetic microbial communities as well as real human gut samples. Our data show that GroEL-proteotyping enables fast and straightforward profiling of highly abundant taxa in bacterial communities at reasonable taxonomic resolution.
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Affiliation(s)
- Simon Klaes
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty III Process Sciences, Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Shobhit Madan
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty of Engineering, Ansbach University of Applied Sciences, 91522 Ansbach, Germany
| | - Darja Deobald
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
| | - Myriel Cooper
- Faculty III Process Sciences, Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, 10587 Berlin, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty III Process Sciences, Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, 13355 Berlin, Germany
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11
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Nakayasu ES, Gritsenko MA, Kim YM, Kyle JE, Stratton KG, Nicora CD, Munoz N, Navarro KM, Claborne D, Gao Y, Weitz KK, Paurus VL, Bloodsworth KJ, Allen KA, Bramer LM, Montes F, Clark KA, Tietje G, Teeguarden J, Burnum-Johnson KE. Elucidating regulatory processes of intense physical activity by multi-omics analysis. Mil Med Res 2023; 10:48. [PMID: 37853489 PMCID: PMC10583322 DOI: 10.1186/s40779-023-00477-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/28/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Physiological and biochemical processes across tissues of the body are regulated in response to the high demands of intense physical activity in several occupations, such as firefighting, law enforcement, military, and sports. A better understanding of such processes can ultimately help improve human performance and prevent illnesses in the work environment. METHODS To study regulatory processes in intense physical activity simulating real-life conditions, we performed a multi-omics analysis of three biofluids (blood plasma, urine, and saliva) collected from 11 wildland firefighters before and after a 45 min, intense exercise regimen. Omics profiles post- versus pre-exercise were compared by Student's t-test followed by pathway analysis and comparison between the different omics modalities. RESULTS Our multi-omics analysis identified and quantified 3835 proteins, 730 lipids and 182 metabolites combining the 3 different types of samples. The blood plasma analysis revealed signatures of tissue damage and acute repair response accompanied by enhanced carbon metabolism to meet energy demands. The urine analysis showed a strong, concomitant regulation of 6 out of 8 identified proteins from the renin-angiotensin system supporting increased excretion of catabolites, reabsorption of nutrients and maintenance of fluid balance. In saliva, we observed a decrease in 3 pro-inflammatory cytokines and an increase in 8 antimicrobial peptides. A systematic literature review identified 6 papers that support an altered susceptibility to respiratory infection. CONCLUSION This study shows simultaneous regulatory signatures in biofluids indicative of homeostatic maintenance during intense physical activity with possible effects on increased infection susceptibility, suggesting that caution against respiratory diseases could benefit workers on highly physical demanding jobs.
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Affiliation(s)
- Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA.
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Kelly G Stratton
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Nathalie Munoz
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Kathleen M Navarro
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Western States Division, Denver, CO, 80204, USA
| | - Daniel Claborne
- Computational Analytics Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Vanessa L Paurus
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Kent J Bloodsworth
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Kelsey A Allen
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Fernando Montes
- Los Angeles County Fire Department, Los Angeles, CA, 90063, USA
| | - Kathleen A Clark
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Respiratory Health Division, Morgantown, WV, 26505, USA
| | - Grant Tietje
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Justin Teeguarden
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA.
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, 97331, USA.
| | - Kristin E Burnum-Johnson
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA.
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12
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Romano F, Franco F, Corana M, Abbadessa G, Di Scipio F, Pergolizzi B, Castrignano C, Aimetti M, Berta GN. Cystatin SN (CST1) as a Novel Salivary Biomarker of Periodontitis. Int J Mol Sci 2023; 24:13834. [PMID: 37762137 PMCID: PMC10530756 DOI: 10.3390/ijms241813834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Identification of biomarkers could help in assessing periodontal health status and monitoring treatment outcomes. Therefore, the aim of this cross-sectional study was to identify potential innovative salivary biomarkers for the diagnosis of periodontitis using an untargeted proteomic approach. Forty-five healthy non-smoker participants diagnosed as having periodontally healthy conditions (H), severe periodontitis (P), and healthy but reduced periodontium after active periodontal treatment (T) were consecutively enrolled (15 per each group) in the study. A higher number of spots were identified in the proteome of unstimulated whole saliva collected from H and T subjects compared with P group, mainly within the range of 8-40 kDa. Protein spots of interest were analysed by MALDI-TOF-MS, allowing the identification of cystatin SN (CST1) isoform, as confirmed by Western blot. CST1 was markedly expressed in the H group, while it was absent in most P samples (p < 0.001). Interestingly, a distinct CST1 expression was observed in saliva from T patients. CST1 was negatively correlated with the percentage of pathological sites (p < 0.001) and was effective in discriminating active periodontitis from healthy periodontal status (whether H or T). Therefore, salivary CST1 may be a promising non-invasive biomarker for periodontal disease diagnosis and monitoring.
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Affiliation(s)
- Federica Romano
- Department of Surgical Sciences, C.I.R. Dental School, Section of Periodontology, University of Turin, 10126 Turin, Italy; (F.R.); (M.C.); (F.D.S.); (M.A.)
| | - Francesco Franco
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.F.); (G.A.); (B.P.); (C.C.)
| | - Matteo Corana
- Department of Surgical Sciences, C.I.R. Dental School, Section of Periodontology, University of Turin, 10126 Turin, Italy; (F.R.); (M.C.); (F.D.S.); (M.A.)
| | - Giuliana Abbadessa
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.F.); (G.A.); (B.P.); (C.C.)
| | - Federica Di Scipio
- Department of Surgical Sciences, C.I.R. Dental School, Section of Periodontology, University of Turin, 10126 Turin, Italy; (F.R.); (M.C.); (F.D.S.); (M.A.)
| | - Barbara Pergolizzi
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.F.); (G.A.); (B.P.); (C.C.)
| | - Chiara Castrignano
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.F.); (G.A.); (B.P.); (C.C.)
| | - Mario Aimetti
- Department of Surgical Sciences, C.I.R. Dental School, Section of Periodontology, University of Turin, 10126 Turin, Italy; (F.R.); (M.C.); (F.D.S.); (M.A.)
| | - Giovanni N. Berta
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (F.F.); (G.A.); (B.P.); (C.C.)
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13
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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: 0] [Impact Index Per Article: 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.
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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
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14
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Guadalupi G, Contini C, Iavarone F, Castagnola M, Messana I, Faa G, Onali S, Chessa L, Vitorino R, Amado F, Diaz G, Manconi B, Cabras T, Olianas A. Combined Salivary Proteome Profiling and Machine Learning Analysis Provides Insight into Molecular Signature for Autoimmune Liver Diseases Classification. Int J Mol Sci 2023; 24:12207. [PMID: 37569584 PMCID: PMC10418803 DOI: 10.3390/ijms241512207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC) are autoimmune liver diseases that target the liver and have a wide spectrum of presentation. A global overview of quantitative variations on the salivary proteome in presence of these two pathologies is investigated in this study. The acid-insoluble salivary fraction of AIH and PBC patients, and healthy controls (HCs), was analyzed using a gel-based bottom-up proteomic approach combined with a robust machine learning statistical analysis of the dataset. The abundance of Arginase, Junction plakoglobin, Desmoplakin, Hexokinase-3 and Desmocollin-1 decreased, while that of BPI fold-containing family A member 2 increased in AIHp compared to HCs; the abundance of Gelsolin, CD14, Tumor-associated calcium signal transducer 2, Clusterin, Heterogeneous nuclear ribonucleoproteins A2/B1, Cofilin-1 and BPI fold-containing family B member 2 increased in PBCp compared to HCs. The abundance of Hornerin decreased in both AIHp and PBCp with respect to HCs and provided an area under the ROC curve of 0.939. Machine learning analysis confirmed the feasibility of the salivary proteome to discriminate groups of subjects based on AIH or PBC occurrence as previously suggested by our group. The topology-based functional enrichment analysis performed on these potential salivary biomarkers highlights an enrichment of terms mostly related to the immune system, but also with a strong involvement in liver fibrosis process and with antimicrobial activity.
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Affiliation(s)
- Giulia Guadalupi
- Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, 09124 Cagliari, Italy; (G.G.); (C.C.); (T.C.); (A.O.)
| | - Cristina Contini
- Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, 09124 Cagliari, Italy; (G.G.); (C.C.); (T.C.); (A.O.)
| | - Federica Iavarone
- Fondazione Policlinico Universitario IRCCS “A. Gemelli”, 00168 Rome, Italy;
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, 00168 Rome, Italy;
| | - Irene Messana
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, Consiglio Nazionale delle Ricerche, 00168 Rome, Italy;
| | - Gavino Faa
- Division of Pathology, Department of Medical Sciences and Public Health, University Hospital, 09124 Cagliari, Italy;
| | - Simona Onali
- Liver Unit, University Hospital of Cagliari, 09124 Cagliari, Italy; (S.O.); (L.C.)
| | - Luchino Chessa
- Liver Unit, University Hospital of Cagliari, 09124 Cagliari, Italy; (S.O.); (L.C.)
| | - Rui Vitorino
- iBiMED, Department of Medical Science, University of Aveiro, 3810-193 Aveiro, Portugal;
- UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, 4200-319 Porto, Portugal
| | - Francisco Amado
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Giacomo Diaz
- Dipartimento di Scienze Biomediche, Università di Cagliari, 09124 Cagliari, Italy;
| | - Barbara Manconi
- Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, 09124 Cagliari, Italy; (G.G.); (C.C.); (T.C.); (A.O.)
| | - Tiziana Cabras
- Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, 09124 Cagliari, Italy; (G.G.); (C.C.); (T.C.); (A.O.)
| | - Alessandra Olianas
- Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, 09124 Cagliari, Italy; (G.G.); (C.C.); (T.C.); (A.O.)
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15
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Umapathy VR, Natarajan PM, Swamikannu B. Review Insights on Salivary Proteomics Biomarkers in Oral Cancer Detection and Diagnosis. Molecules 2023; 28:5283. [PMID: 37446943 PMCID: PMC10343386 DOI: 10.3390/molecules28135283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/02/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Early detection is crucial for the treatment and prognosis of oral cancer, a potentially lethal condition. Tumor markers are abnormal biological byproducts produced by malignant cells that may be found and analyzed in a variety of bodily fluids, including saliva. Early detection and appropriate treatment can increase cure rates to 80-90% and considerably improve quality of life by reducing the need for costly, incapacitating medicines. Salivary diagnostics has drawn the interest of many researchers and has been proven to be an effective tool for both medication monitoring and the diagnosis of several systemic diseases. Since researchers are now searching for biomarkers in saliva, an accessible bodily fluid, for noninvasive diagnosis of oral cancer, measuring tumor markers in saliva is an interesting alternative to blood testing for early identification, post-treatment monitoring, and monitoring high-risk lesions. New molecular markers for oral cancer detection, treatment, and prognosis have been found as a result of developments in the fields of molecular biology and salivary proteomics. The numerous salivary tumor biomarkers and how they relate to oral cancer and pre-cancer are covered in this article. We are optimistic that salivary protein biomarkers may one day be discovered for the clinical detection of oral cancer because of the rapid advancement of proteomic technology.
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Affiliation(s)
- Vidhya Rekha Umapathy
- Department of Public Health Dentistry, Thai Moogambigai Dental College and Hospital, Dr. M.G.R. Educational and Research Institute, Chennai 600107, Tamil Nadu, India
| | - Prabhu Manickam Natarajan
- Department of Clinical Sciences, Centre of Medical and Bio-Allied Health Sciences and Research, Ajman University, Ajman P.O. Box 346, United Arab Emirates
| | - Bhuminathan Swamikannu
- Department of Prosthodontics, Sree Balaji Dental College and Hospital, BIHER University, Pallikaranai, Chennai 600100, Tamil Nadu, India;
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16
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van Leeuwen SJM, Proctor GB, Staes A, Laheij AMGA, Potting CMJ, Brennan MT, von Bültzingslöwen I, Rozema FR, Hazenberg MD, Blijlevens NMA, Raber-Durlacher JE, Huysmans MCDNJM. The salivary proteome in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients: a labelled and label-free proteomics approach. BMC Oral Health 2023; 23:460. [PMID: 37420206 PMCID: PMC10329372 DOI: 10.1186/s12903-023-03190-w] [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: 12/20/2022] [Accepted: 06/30/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Oral mucositis is a frequently seen complication in the first weeks after hematopoietic stem cell transplantation recipients which can severely affects patients quality of life. In this study, a labelled and label-free proteomics approach were used to identify differences between the salivary proteomes of autologous hematopoietic stem cell transplantation (ASCT) recipients developing ulcerative oral mucositis (ULC-OM; WHO score ≥ 2) or not (NON-OM). METHODS In the TMT-labelled analysis we pooled saliva samples from 5 ULC-OM patients at each of 5 timepoints: baseline, 1, 2, 3 weeks and 3 months after ASCT and compared these with pooled samples from 5 NON-OM patients. For the label-free analysis we analyzed saliva samples from 9 ULC-OM and 10 NON-OM patients at 6 different timepoints (including 12 months after ASCT) with Data-Independent Acquisition (DIA). As spectral library, all samples were grouped (ULC-OM vs NON-OM) and analyzed with Data Dependent Analysis (DDA). PCA plots and a volcano plot were generated in RStudio and differently regulated proteins were analyzed using GO analysis with g:Profiler. RESULTS A different clustering of ULC-OM pools was found at baseline, weeks 2 and 3 after ASCT with TMT-labelled analysis. Using label-free analysis, week 1-3 samples clustered distinctly from the other timepoints. Unique and up-regulated proteins in the NON-OM group (DDA analysis) were involved in immune system-related processes, while those proteins in the ULC-OM group were intracellular proteins indicating cell lysis. CONCLUSIONS The salivary proteome in ASCT recipients has a tissue protective or tissue-damage signature, that corresponded with the absence or presence of ulcerative oral mucositis, respectively. TRIAL REGISTRATION The study is registered in the national trial register (NTR5760; automatically added to the International Clinical Trial Registry Platform).
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Affiliation(s)
- S J M van Leeuwen
- Department of Dentistry, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - G B Proctor
- Centre for Host Microbiome Interactions, King's College London Dental Institute, London, UK
| | - A Staes
- VIB Proteomics Core, VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - A M G A Laheij
- Department of Oral Medicine, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University, Amsterdam, The Netherlands
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University, Amsterdam, The Netherlands
- Department of Oral and Maxillofacial Surgery, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - C M J Potting
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M T Brennan
- Department of Oral Medicine/Oral and Maxillofacial Surgery, Atrium Health Carolinas Medical Centre, NC, Charlotte, USA
- Department of Otolaryngology/Head and Neck Surgery, Wake Forest University School of Medicine, NC, Winston-Salem, USA
| | - I von Bültzingslöwen
- Department of Oral Microbiology and Immunology, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - F R Rozema
- Department of Oral Medicine, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University, Amsterdam, The Netherlands
- Department of Oral and Maxillofacial Surgery, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - M D Hazenberg
- Department of Hematology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Hematopoiesis, Sanquin Research, Amsterdam, The Netherlands
| | - N M A Blijlevens
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J E Raber-Durlacher
- Department of Oral Medicine, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University, Amsterdam, The Netherlands
- Department of Oral and Maxillofacial Surgery, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - M C D N J M Huysmans
- Department of Dentistry, Radboud University Medical Center, Nijmegen, The Netherlands
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17
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Morzel M, Ramsamy S, Le Feunteun S. Feasibility of using a realistic food bolus for semi-dynamic in vitro gastric digestion of hard cheese with pH-stat monitoring of protein hydrolysis. Food Res Int 2023; 169:112818. [PMID: 37254396 DOI: 10.1016/j.foodres.2023.112818] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/31/2023] [Accepted: 04/11/2023] [Indexed: 06/01/2023]
Abstract
Oral processing of solid foods leads to boluses made of a human saliva and particles distributed in the size range ∼ 0 to 5 mm. However, studies on the release of nutrients from realistic solid food boluses during digestion are scarce because such mechanisms are difficult to investigate in vivo, and in vitro experiments generally recommend to extensively mince solid foods during the oral stage. Similarly, it has previously been shown that the peptic hydrolysis of protein solutions during in vitro gastric digestion can be monitored by acid titration in both static and dynamic pH conditions, but such approach has never been evaluated in the presence of particles of several millimetres in size. The first objective of the study was therefore to test the feasibility of using a realistic food bolus for gastric digestion studies with a pH-stat monitoring of proteolysis, using Emmental cheese as a solid food and with consideration of gastric acidifying kinetics. Degree of hydrolysis (DH) of proteins was monitored from two series of experiments performed in the presence and absence of pepsin. Other DH measurements, estimated from an independent approach based on the amount of free NH2 groups (OPA method) contained by peptides released in the supernatant (UV absorbance) validated the pH-stat results. A second objective of this work was to test the possible influence of human saliva on gastric proteolysis (in comparison with a water-based bolus). Results showed that saliva slightly delayed initiation of proteolysis, which could be explained by the slightly higher initial pH of the saliva-based bolus, but had no statistical effects on pepsin activity. We conclude that acid titration with a pH-stat system can be a valuable approach to monitor the gastric in vitro proteolysis of realistic solid food boluses in dynamic pH conditions.
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18
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Wang X, Yue L, Zhang F, Tang Z, Chen Z, Li Z. A novel strategy for quantification of α2,3- and α2,6-linked sialic acids in sialylated glycoproteins. Carbohydr Res 2023; 531:108892. [PMID: 37429229 DOI: 10.1016/j.carres.2023.108892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/24/2023] [Accepted: 06/28/2023] [Indexed: 07/12/2023]
Abstract
Sialic acid, a monosaccharide containing nine carbon atoms, is widely distributed in eukaryotic cells. The bound sialic acids are mainly present at the glycan ends of glycoconjugates via α2-3 or α2-6 glycosidic bonds, and alterations in their expression levels and linkage types are associated with the progress of many diseases and tumors. The present study provides a new strategy for quantification of α2,3- and α2,6-linked sialic acids in sialylated glycoproteins. In fact, quantification of α2,3-linked sialic acids were based on the difference of the bound sialic acids in the sample before and after treatment with α2-3 neuraminidase, whereas the α2,6-linked sialic acids were equal to the bound sialic acids in the α2-3 neuraminidase-treated sample. Subsequently, α2,3/6-linked sialic acids in salivary glycoproteins from healthy volunteers and diabetic patients were quantified in accordance with this method. This work provides an accurate method for the quantification of α2,3- and α2,6-linked sialic acids in the sialoglycoproteins, which is more instructive for understanding the biological roles of α2,3/6-linked sialic acid in sialoglycoproteins.
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Affiliation(s)
- Xilong Wang
- College of Life Sciences and Technology, Longdong University, Qingyang, Gansu, China; Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Qingyang, Gansu, China.
| | - Lixin Yue
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Fan Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Zhen Tang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Zhuo Chen
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
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Raksakmanut R, Thanyasrisung P, Sritangsirikul S, Kitsahawong K, Seminario A, Pitiphat W, Matangkasombut O. Prediction of Future Caries in 1-Year-Old Children via the Salivary Microbiome. J Dent Res 2023; 102:626-635. [PMID: 36919874 PMCID: PMC10399075 DOI: 10.1177/00220345231152802] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Dental caries is the most common chronic disease in children that causes negative effects on their health, development, and well-being. Early preventive interventions are key to reduce early childhood caries prevalence. An efficient strategy is to provide risk-based targeted prevention; however, this requires an accurate caries risk predictor, which is still lacking for infants before caries onset. We aimed to develop a caries prediction model based on the salivary microbiome of caries-free 1-y-old children. Using a nested case-control design within a prospective cohort study, we selected 30 children based on their caries status at 1-y follow-up (at 2 y old): 10 children who remained caries-free, 10 who developed noncavitated caries, and 10 who developed cavitated caries. Saliva samples collected at baseline before caries onset were analyzed through 16S rRNA gene sequencing. The results of β diversity analysis showed a significant difference in salivary microbiome composition between children who remained caries-free and those who developed cavitated caries at 2 y old (analysis of similarities, Benjamini-Hochberg corrected, P = 0.042). The relative abundance of Prevotella nanceiensis, Leptotrichia sp. HMT 215, Prevotella melaninogenica, and Campylobacter concisus in children who remained caries-free was significantly higher than in children who developed cavitated caries (Wilcoxon rank sum test, P = 0.024, 0.040, 0.049, and 0.049, respectively). These taxa were also identified as biomarkers for children who remained caries-free (linear discriminant analysis effect size, linear discriminant analysis score = 3.69, 3.74, 3.53, and 3.46). A machine learning model based on these 4 species distinguished between 1-y-old children who did and did not develop cavitated caries at 2 y old, with an accuracy of 80%, sensitivity of 80%, and specificity of 80% (area under the curve, 0.8; 95% CI, 44.4 to 97.5). Our findings suggest that these salivary microbial biomarkers could assist in predicting future caries in caries-free 1-y-old children and, upon validation, are promising for development into an adjunctive tool for caries risk prediction for prevention and monitoring.
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Affiliation(s)
- R. Raksakmanut
- Graduate Program in Oral Biology and Center of Excellence on Oral Microbiology and Immunology, Faculty of Dentistry, Chulalongkorn University, Wang-Mai, Pathumwan, Bangkok, Thailand
| | - P. Thanyasrisung
- Department of Microbiology and Center of Excellence on Oral Microbiology and Immunology, Faculty of Dentistry, Chulalongkorn University, Wang-Mai, Pathumwan, Bangkok, Thailand
| | - S. Sritangsirikul
- Department of Pediatric Dentistry, Faculty of Dentistry, Chulalongkorn University, Wang-Mai, Pathumwan, Bangkok, Thailand
- PhD Program in Oral Sciences, Faculty of Dentistry, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - K. Kitsahawong
- Division of Pediatric Dentistry, Department of Preventive Dentistry, Faculty of Dentistry, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - A.L. Seminario
- Department of Pediatric Dentistry, School of Dentistry, University of Washington, WA, USA
| | - W. Pitiphat
- Division of Dental Public Health, Department of Preventive Dentistry, Faculty of Dentistry, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - O. Matangkasombut
- Department of Microbiology and Center of Excellence on Oral Microbiology and Immunology, Faculty of Dentistry, Chulalongkorn University, Wang-Mai, Pathumwan, Bangkok, Thailand
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Laksi, Bangkok, Thailand
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20
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Marjit S, Bhattacharyya T, Chatterjee B, Sarkar R. Simulated annealing aided genetic algorithm for gene selection from microarray data. Comput Biol Med 2023; 158:106854. [PMID: 37023541 DOI: 10.1016/j.compbiomed.2023.106854] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/26/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023]
Abstract
In recent times, microarray gene expression datasets have gained significant popularity due to their usefulness to identify different types of cancer directly through bio-markers. These datasets possess a high gene-to-sample ratio and high dimensionality, with only a few genes functioning as bio-markers. Consequently, a significant amount of data is redundant, and it is essential to filter out important genes carefully. In this paper, we propose the Simulated Annealing aided Genetic Algorithm (SAGA), a meta-heuristic approach to identify informative genes from high-dimensional datasets. SAGA utilizes a two-way mutation-based Simulated Annealing (SA) as well as Genetic Algorithm (GA) to ensure a good trade-off between exploitation and exploration of the search space, respectively. The naive version of GA often gets stuck in a local optimum and depends on the initial population, leading to premature convergence. To address this, we have blended a clustering-based population generation with SA to distribute the initial population of GA over the entire feature space. To further enhance the performance, we reduce the initial search space by a score-based filter approach called the Mutually Informed Correlation Coefficient (MICC). The proposed method is evaluated on 6 microarray and 6 omics datasets. Comparison of SAGA with contemporary algorithms has shown that SAGA performs much better than its peers. Our code is available at https://github.com/shyammarjit/SAGA.
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21
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Schwartz M, Boichot V, Fraichard S, Muradova M, Senet P, Nicolai A, Lirussi F, Bas M, Canon F, Heydel JM, Neiers F. Role of Insect and Mammal Glutathione Transferases in Chemoperception. Biomolecules 2023; 13:biom13020322. [PMID: 36830691 PMCID: PMC9953322 DOI: 10.3390/biom13020322] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Glutathione transferases (GSTs) are ubiquitous key enzymes with different activities as transferases or isomerases. As key detoxifying enzymes, GSTs are expressed in the chemosensory organs. They fulfill an essential protective role because the chemosensory organs are located in the main entry paths of exogenous compounds within the body. In addition to this protective function, they modulate the perception process by metabolizing exogenous molecules, including tastants and odorants. Chemosensory detection involves the interaction of chemosensory molecules with receptors. GST contributes to signal termination by metabolizing these molecules. By reducing the concentration of chemosensory molecules before receptor binding, GST modulates receptor activation and, therefore, the perception of these molecules. The balance of chemoperception by GSTs has been shown in insects as well as in mammals, although their chemosensory systems are not evolutionarily connected. This review will provide knowledge supporting the involvement of GSTs in chemoperception, describing their localization in these systems as well as their enzymatic capacity toward odorants, sapid molecules, and pheromones in insects and mammals. Their different roles in chemosensory organs will be discussed in light of the evolutionary advantage of the coupling of the detoxification system and chemosensory system through GSTs.
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Affiliation(s)
- Mathieu Schwartz
- Laboratory: Flavour Perception: Molecular Mechanims (Flavours), INRAE, CNRS, Institut Agro, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Valentin Boichot
- Laboratory: Flavour Perception: Molecular Mechanims (Flavours), INRAE, CNRS, Institut Agro, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Stéphane Fraichard
- Laboratory: Flavour Perception: Molecular Mechanims (Flavours), INRAE, CNRS, Institut Agro, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Mariam Muradova
- Laboratory: Flavour Perception: Molecular Mechanims (Flavours), INRAE, CNRS, Institut Agro, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Patrick Senet
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université de Bourgogne Franche-Comté, 21078 Dijon, France
| | - Adrien Nicolai
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université de Bourgogne Franche-Comté, 21078 Dijon, France
| | - Frederic Lirussi
- UMR 1231, Lipides Nutrition Cancer, INSERM, 21000 Dijon, France
- UFR des Sciences de Santé, Université de Bourgogne Franche-Comté, 25000 Besançon, France
- Plateforme PACE, Laboratoire de Pharmacologie-Toxicologie, Centre Hospitalo-Universitaire Besançon, 25000 Besançon, France
| | - Mathilde Bas
- Laboratory: Flavour Perception: Molecular Mechanims (Flavours), INRAE, CNRS, Institut Agro, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Francis Canon
- Laboratory: Flavour Perception: Molecular Mechanims (Flavours), INRAE, CNRS, Institut Agro, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Jean-Marie Heydel
- Laboratory: Flavour Perception: Molecular Mechanims (Flavours), INRAE, CNRS, Institut Agro, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Fabrice Neiers
- Laboratory: Flavour Perception: Molecular Mechanims (Flavours), INRAE, CNRS, Institut Agro, Université de Bourgogne Franche-Comté, 21000 Dijon, France
- Correspondence:
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22
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Qualitative and Quantitative Mass Spectrometry in Salivary Metabolomics and Proteomics. Metabolites 2023; 13:metabo13020155. [PMID: 36837774 PMCID: PMC9964739 DOI: 10.3390/metabo13020155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
The metabolomics and proteomics analysis of saliva, an excellent biofluid that is a rich source of biological compounds, allows for the safe and frequent screening of drugs, their metabolites, and molecular biomarkers of various diseases. One of the most frequently used analytical methods in saliva analysis is liquid chromatography coupled with mass spectrometry (LC-MS) and tandem mass spectrometry. The low ionisation efficiency of some compounds and a complex matrix makes their identification by MS difficult. Furthermore, quantitative analysis by LC-MS frequently cannot be performed without isotopically labelled standards, which usually have to be specially synthesised. This review presented reports on qualitative and quantitative approaches in salivary metabolomics and proteomics. The purpose of this manuscript was to present the challenges, advances, and future prospects of mass spectrometry, both in the analysis of salivary metabolites and proteins. The presented review should appeal to those interested in the recent advances and trends in qualitative and quantitative mass spectrometry in salivary metabolomics and proteomics, which may facilitate a diagnostic accuracy, the evaluation of treatment efficacy, the early diagnosis of disease, and a forensic investigation of some unapproved drugs for any medical or dietary administration.
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23
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Top-Down Proteomics Detection of Potential Salivary Biomarkers for Autoimmune Liver Diseases Classification. Int J Mol Sci 2023; 24:ijms24020959. [PMID: 36674470 PMCID: PMC9866740 DOI: 10.3390/ijms24020959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023] Open
Abstract
(1) Autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC) are autoimmune liver diseases characterized by chronic hepatic inflammation and progressive liver fibrosis. The possible use of saliva as a diagnostic tool has been explored in several oral and systemic diseases. The use of proteomics for personalized medicine is a rapidly emerging field. (2) Salivary proteomic data of 36 healthy controls (HCs), 36 AIH and 36 PBC patients, obtained by liquid chromatography/mass spectrometry top-down pipeline, were analyzed by multiple Mann-Whitney test, Kendall correlation, Random Forest (RF) analysis and Linear Discriminant Analysis (LDA); (3) Mann-Whitney tests provided indications on the panel of differentially expressed salivary proteins and peptides, namely cystatin A, statherin, histatin 3, histatin 5 and histatin 6, which were elevated in AIH patients with respect to both HCs and PBC patients, while S100A12, S100A9 short, cystatin S1, S2, SN and C showed varied levels in PBC with respect to HCs and/or AIH patients. RF analysis evidenced a panel of salivary proteins/peptides able to classify with good accuracy PBC vs. HCs (83.3%), AIH vs. HCs (79.9%) and PBC vs. AIH (80.2%); (4) RF appears to be an attractive machine-learning tool suited for classification of AIH and PBC based on their different salivary proteomic profiles.
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24
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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.
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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.
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25
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Barlin M, Erdmann-Gilmore P, Mudd JL, Zhang Q, Seymour RW, Guo Z, Miessner JR, Goedegebuure SP, Bi Y, Osorio OA, Alexander-Brett J, Li S, Ma CX, Fields RC, Townsend RR, Held JM. Proteins in Tumor-Derived Plasma Extracellular Vesicles Indicate Tumor Origin. Mol Cell Proteomics 2023; 22:100476. [PMID: 36470535 PMCID: PMC9801135 DOI: 10.1016/j.mcpro.2022.100476] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/12/2022] [Accepted: 11/28/2022] [Indexed: 12/09/2022] Open
Abstract
Cancer-derived extracellular vesicles (EVs) promote tumorigenesis, premetastatic niche formation, and metastasis via their protein cargo. However, the proteins packaged by patient tumors into EVs cannot be determined in vivo because of the presence of EVs derived from other tissues. We therefore developed a cross-species proteomic method to quantify the human tumor-derived proteome of plasma EVs produced by patient-derived xenografts of four cancer types. Proteomic profiling revealed individualized packaging of novel protein cargo, and machine learning accurately classified the type of the underlying tumor.
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Affiliation(s)
- Meltem Barlin
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Petra Erdmann-Gilmore
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Jacqueline L Mudd
- Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Surgery, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Qiang Zhang
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Robert W Seymour
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Zhanfang Guo
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Julia R Miessner
- Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Surgery, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - S Peter Goedegebuure
- Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Surgery, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Ye Bi
- Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Surgery, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Omar A Osorio
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Jennifer Alexander-Brett
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Shunqiang Li
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Cynthia X Ma
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Ryan C Fields
- Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Surgery, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - R Reid Townsend
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Jason M Held
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Anesthesiology, Washington University School of Medicine in St Louis, St Louis, Missouri, USA.
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Intraglandular mesenchymal stem cell treatment induces changes in the salivary proteome of irradiated patients. COMMUNICATIONS MEDICINE 2022; 2:160. [PMID: 36496530 PMCID: PMC9735277 DOI: 10.1038/s43856-022-00223-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Hyposalivation and xerostomia (dry mouth), are the leading site-effects to treatment of head and neck cancer. Currently, there are no effective therapies to alleviate radiation-induced hyposalivation. Adipose tissue-derived mesenchymal stem/stromal cells (AT-MSCs) have shown potential for restoring salivary gland function. However, the mode of action is unknown. The purpose of the present study was therefore to characterize the effect of AT-MSC therapy on the salivary proteome in previously irradiated head and neck cancer patients. METHODS Whole saliva was collected from patients with radiation-induced salivary gland hypofunction (n = 8) at baseline, and 120 days after AT-MSC treatment, and from healthy controls (n = 10). The salivary proteome was characterized with mass spectrometry based proteomics, and data was compared within the AT-MSC group (baseline versus day 120) and between AT-MSC group and healthy controls. Significance levels between groups were determined by using double-sided t-test, and visualized by means of principal component analysis, volcano plots and cluster analysis. RESULTS Here we show that 140 human proteins are significantly differentially expressed in saliva from patients with radiation-induced hypofunction versus healthy controls. AT-MSC treatment induce a significant impact on the salivary proteome, as 99 proteins are differentially expressed at baseline vs. 120 days after treatment. However, AT-MSC treatment does not restore healthy conditions, as 212 proteins are significantly differentially expressed in saliva 120 days after AT-MSCs treatment, as compared to healthy controls. CONCLUSION The results indicate an increase in proteins related to tissue regeneration in AT-MSCs treated patients. Our study demonstrates the impact of AT-MSCs on the salivary proteome, thereby providing insight into the potential mode of action of this novel treatment approach.
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McNicholas K, François M, Liu JW, Doecke JD, Hecker J, Faunt J, Maddison J, Johns S, Pukala TL, Rush RA, Leifert WR. Salivary inflammatory biomarkers are predictive of mild cognitive impairment and Alzheimer's disease in a feasibility study. Front Aging Neurosci 2022; 14:1019296. [PMID: 36438010 PMCID: PMC9685799 DOI: 10.3389/fnagi.2022.1019296] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/26/2022] [Indexed: 09/10/2023] Open
Abstract
Alzheimer's disease (AD) is an insidious disease. Its distinctive pathology forms over a considerable length of time without symptoms. There is a need to detect this disease, before even subtle changes occur in cognition. Hallmark AD biomarkers, tau and amyloid-β, have shown promising results in CSF and blood. However, detecting early changes in these biomarkers and others will involve screening a wide group of healthy, asymptomatic individuals. Saliva is a feasible alternative. Sample collection is economical, non-invasive and saliva is an abundant source of proteins including tau and amyloid-β. This work sought to extend an earlier promising untargeted mass spectrometry study in saliva from individuals with mild cognitive impairment (MCI) or AD with age- and gender-matched cognitively normal from the South Australian Neurodegenerative Disease cohort. Five proteins, with key roles in inflammation, were chosen from this study and measured by ELISA from individuals with AD (n = 16), MCI (n = 15) and cognitively normal (n = 29). The concentrations of Cystatin-C, Interleukin-1 receptor antagonist, Stratifin, Matrix metalloproteinase 9 and Haptoglobin proteins had altered abundance in saliva from AD and MCI, consistent with the earlier study. Receiver operating characteristic analysis showed that combinations of these proteins demonstrated excellent diagnostic accuracy for distinguishing both MCI (area under curve = 0.97) and AD (area under curve = 0.97) from cognitively normal. These results provide evidence for saliva being a valuable source of biomarkers for early detection of cognitive impairment in individuals on the AD continuum and potentially other neurodegenerative diseases.
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Affiliation(s)
- Kym McNicholas
- Molecular Diagnostic Solutions Group, Human Health Program, CSIRO Health and Biosecurity, Adelaide, SA, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Maxime François
- Molecular Diagnostic Solutions Group, Human Health Program, CSIRO Health and Biosecurity, Adelaide, SA, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Jian-Wei Liu
- CSIRO Land and Water, Black Mountain Research and Innovation Park, Canberra, ACT, Australia
| | - James D. Doecke
- Australian e-Health Research Centre, CSIRO, Herston, QLD, Australia
| | - Jane Hecker
- Department of Internal Medicine, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Jeff Faunt
- Department of General Medicine, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - John Maddison
- Aged Care Rehabilitation and Palliative Care, SA Health, Modbury Hospital, Modbury, SA, Australia
| | - Sally Johns
- Aged Care Rehabilitation and Palliative Care, SA Health, Modbury Hospital, Modbury, SA, Australia
| | - Tara L. Pukala
- School of Physical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | | | - Wayne R. Leifert
- Molecular Diagnostic Solutions Group, Human Health Program, CSIRO Health and Biosecurity, Adelaide, SA, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
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28
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Liu Y, Qv W, Ma Y, Zhang Y, Ding C, Chu M, Chen F. The interplay between oral microbes and immune responses. Front Microbiol 2022. [DOI: 10.3389/fmicb.2022.1009018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oral microbes play a critical role in maintaining oral homeostasis. Microbial dysbiosis promotes disease pathogenesis through several mechanisms. Recent studies have revealed that microbial imbalance and sustained inflammation are involved in disease progression. The adverse interaction triggered by a host immune response to microorganisms can lead to oral and systemic diseases. Here, we reviewed how oral microbes communicate with hosts during the development of local and distant inflammation. Elucidation of these processes may reveal future directions in this field and the potential targets of novel biological therapies for oral and systemic diseases.
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29
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Jiang X, Zhang Y, Wang H, Wang Z, Hu S, Cao C, Xiao H. In-Depth Metaproteomics Analysis of Oral Microbiome for Lung Cancer. Research (Wash D C) 2022; 2022:9781578. [PMID: 36320634 PMCID: PMC9590273 DOI: 10.34133/2022/9781578] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/22/2022] [Indexed: 11/12/2022] Open
Abstract
The human oral microbiome correlates with numerous diseases, including lung cancer. Identifying the functional changes by metaproteomics helps understand the disease-related dysbiosis, yet characterizing low-abundant bacteria is challenging. Here, we developed a free-flow isoelectric focusing electrophoresis-mass spectrometry- (FFIEF-MS-) based metaproteomics strategy to reduce host interferences and enrich low-abundant bacteria for in-depth interpretation of the oral microbiome. With our method, the number of interfering peptides decreased by 52.87%, whereas the bacterial peptides and species increased by 94.97% and 44.90%, respectively, compared to the conventional metaproteomics approach. We identified 3647 bacterial proteins, which is the most comprehensive oral metaproteomics study to date. Lung cancer-associated bacteria were validated among an independent cohort. The imbalanced Fusobacterium nucleatum and Prevotella histicola and their dysregulated functions in inhibiting immune response and maintaining cell redox homeostasis were revealed. The FFIEF-MS may serve as a valuable strategy to study the mechanisms between human diseases and microbiomes with broader applications.
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Affiliation(s)
- Xiaoteng Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shen Hu
- School of Dentistry and Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles 90095, USA
| | - Chengxi Cao
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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30
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Zhang T, Duong P, Dayuha R, Collins CJ, Beckman E, Thies J, Chang I, Lam C, Sun A, Scott AI, Thompson J, Singh A, Khaledi H, Gelb MH, Hahn SH. A rapid and non-invasive proteomic analysis using DBS and buccal swab for multiplexed second-tier screening of Pompe disease and Mucopolysaccharidosis type I. Mol Genet Metab 2022; 136:296-305. [PMID: 35787971 PMCID: PMC10387444 DOI: 10.1016/j.ymgme.2022.06.006] [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: 04/26/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 11/19/2022]
Abstract
PURPOSE Current newborn screening programs for Pompe disease (PD) and mucopolysaccharidosis type I (MPS I) suffer from a high false positive rate and long turnaround time for clinical follow up. This study aimed to develop a novel proteomics-based assay for rapid and accurate second-tier screening of PD and MPS I. A fast turnaround assay would enable the identification of severe cases who need immediate clinical follow up and treatment. METHODS We developed an immunocapture coupled with mass spectrometry-based proteomics (Immuno-SRM) assay to quantify GAA and IDUA proteins in dried blood spots (DBS) and buccal swabs. Sensitivity, linearity, reproducibility, and protein concentration range in healthy control samples were determined. Clinical performance was evaluated in known PD and MPS I patients as well as pseudodeficiency and carrier cases. RESULTS Using three 3.2 mm punches (~13.1 μL of blood) of DBS, the assay showed reproducible and sensitive quantification of GAA and IDUA. Both proteins can also be quantified in buccal swabs with high reproducibility and sensitivity. Infantile onset Pompe disease (IOPD) and severe MPS I cases are readily identifiable due to the absence of GAA and IDUA, respectively. In addition, late onset Pompe disease (LOPD) and attenuated MPS I patients showed much reduced levels of the target protein. By contrast, pseudodeficiency and carrier cases exhibited significant higher target protein levels compared to true patients. CONCLUSION Direct quantification of endogenous GAA and IDUA peptides in DBS by Immuno-SRM can be used for second-tier screening to rapidly identify severe PD and MPS I patients with a turnaround time of <1 week. Such patients could benefit from immediate clinical follow up and possibly earlier treatment.
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Affiliation(s)
- Tong Zhang
- Seattle Children's Research Institute, Seattle, WA, United States of America
| | - Phi Duong
- Seattle Children's Research Institute, Seattle, WA, United States of America
| | - Remwilyn Dayuha
- Seattle Children's Research Institute, Seattle, WA, United States of America
| | | | - Erika Beckman
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, United States of America
| | - Jenny Thies
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, United States of America
| | - Irene Chang
- Biochemical Genetics Clinic, Seattle Children's Hospital, Seattle, WA, United States of America; Department of Pediatrics, Division of Genetic Medicine, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Christina Lam
- Biochemical Genetics Clinic, Seattle Children's Hospital, Seattle, WA, United States of America; Department of Pediatrics, Division of Genetic Medicine, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Angela Sun
- Biochemical Genetics Clinic, Seattle Children's Hospital, Seattle, WA, United States of America; Department of Pediatrics, Division of Genetic Medicine, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Anna I Scott
- Department of Laboratory, Seattle Children's Hospital, Seattle, WA, United States of America
| | - John Thompson
- WA State Department of Health, Seattle, WA, United States of America
| | - Aranjeet Singh
- WA State Department of Health, Seattle, WA, United States of America
| | - Hamid Khaledi
- Department of Chemistry, University of Washington, Seattle, WA, United States of America
| | - Michael H Gelb
- Department of Chemistry, University of Washington, Seattle, WA, United States of America
| | - Si Houn Hahn
- Seattle Children's Research Institute, Seattle, WA, United States of America; Biochemical Genetics Clinic, Seattle Children's Hospital, Seattle, WA, United States of America; Department of Pediatrics, Division of Genetic Medicine, University of Washington School of Medicine, Seattle, WA, United States of America.
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31
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Grant MM, Taylor JJ, Jaedicke K, Creese A, Gowland C, Burke B, Doudin K, Patel U, Weston P, Milward M, Bissett SM, Cooper HJ, Kooijman G, Rmaile A, de Jager M, Preshaw PM, Chapple ILC. Discovery, validation, and diagnostic ability of multiple protein-based biomarkers in saliva and gingival crevicular fluid to distinguish between health and periodontal diseases. J Clin Periodontol 2022; 49:622-632. [PMID: 35451104 PMCID: PMC9324935 DOI: 10.1111/jcpe.13630] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 03/25/2022] [Accepted: 04/08/2022] [Indexed: 12/25/2022]
Abstract
Aim To discover and validate differential protein biomarker expression in saliva and gingival crevicular fluid (GCF) to discriminate objectively between periodontal health and plaque‐induced periodontal disease states. Materials and Methods One‐hundred and ninety participants were recruited from two centres (Birmingham and Newcastle upon Tyne, UK) comprising healthy, gingivitis, periodontitis, and edentulous donors. Samples from the Birmingham cohort were analysed by quantitative mass spectrometry proteomics for biomarker discovery. Shortlisted candidate proteins were then verified by enzyme‐linked immunosorbent assay in both cohorts. Leave‐one‐out cross validation logistic regression analysis was used to identify the best performing biomarker panels. Results Ninety‐five proteins were identified in both GCF and saliva samples, and 15 candidate proteins were selected based upon differences discovered between the donor groups. The best performing panels to distinguish between: health or gingivitis and periodontitis contained matrix metalloproteinase‐9 (MMP9), S100A8, alpha‐1‐acid glycoprotein (A1AGP), pyruvate kinase, and age (area under the curve [AUC] 0.970); health and gingivitis contained MMP9, S100A8, A1AGP, and pyruvate kinase, but not age (AUC 0.768); and mild to moderate and advanced periodontitis contained MMP9, S100A8, A1AGP, pyruvate kinase, and age (AUC 0.789). Conclusions Biomarker panels containing four proteins with and without age as a further parameter can distinguish between periodontal health and disease states.
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Affiliation(s)
- Melissa M Grant
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham and Birmingham Dental Hospital (Birmingham Community Healthcare Trust), Birmingham, UK
| | - John J Taylor
- School of Dental Sciences and Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katrin Jaedicke
- School of Dental Sciences and Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Creese
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham and Birmingham Dental Hospital (Birmingham Community Healthcare Trust), Birmingham, UK.,School of Biosciences, University of Birmingham, Birmingham, UK
| | - Catherine Gowland
- School of Dental Sciences and Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Bernard Burke
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham and Birmingham Dental Hospital (Birmingham Community Healthcare Trust), Birmingham, UK.,Centre for Sport, Exercise and Life Sciences, Coventry University, 20 Whitefriars Street, Coventry, UK
| | - Khawla Doudin
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham and Birmingham Dental Hospital (Birmingham Community Healthcare Trust), Birmingham, UK
| | - Upen Patel
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham and Birmingham Dental Hospital (Birmingham Community Healthcare Trust), Birmingham, UK
| | - Paul Weston
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham and Birmingham Dental Hospital (Birmingham Community Healthcare Trust), Birmingham, UK
| | - Michael Milward
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham and Birmingham Dental Hospital (Birmingham Community Healthcare Trust), Birmingham, UK
| | - Susan M Bissett
- School of Dental Sciences and Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Amir Rmaile
- Philips Research, Eindhoven, The Netherlands
| | | | | | - Iain L C Chapple
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham and Birmingham Dental Hospital (Birmingham Community Healthcare Trust), Birmingham, UK
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32
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Liu S, Wang H, Jiang X, Ji Y, Wang Z, Zhang Y, Wang P, Xiao H. Integrated N-glycoproteomics Analysis of Human Saliva for Lung Cancer. J Proteome Res 2022; 21:1589-1602. [PMID: 35715216 DOI: 10.1021/acs.jproteome.1c00701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aberrant protein N-glycosylation is a cancer hallmark, which has great potential for cancer detection. However, large-scale and in-depth analysis of N-glycosylation remains challenging because of its high heterogeneity, complexity, and low abundance. Human saliva is an attractive diagnostic body fluid, while few efforts explored its N-glycoproteome for lung cancer. Here, we utilized a zwitterionic-hydrophilic interaction chromatography-based strategy to specifically enrich salivary glycopeptides. Through quantitative proteomics analysis, 1492 and 1234 intact N-glycopeptides were confidently identified from pooled saliva samples of 10 subjects in the nonsmall-cell lung cancer group and 10 subjects in the normal control group. Accordingly, 575 and 404 N-glycosites were revealed for the lung cancer group and normal control group. In particular, 154 N-glycosites and 259 site-specific glycoforms were significantly dysregulated in the lung cancer group. Several N-glycosites located at the same glycoprotein and glycans attached to the same N-glycosites were observed with differential expressions, including haptoglobin, Mucin-5B, lactotransferrin, and α-1-acid glycoprotein 1. These N-glycoproteins were mainly related to inflammatory responses, infectious diseases, and cancers. Our study achieved comprehensive characterization of salivary N-glycoproteome, and dysregulated site-specific glycoforms hold promise for noninvasive detection of lung cancer.
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Affiliation(s)
- Sha Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoteng Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yin Ji
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Pharmaceutical Co., Ltd., Nanjing 210042, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Peng Wang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Pharmaceutical Co., Ltd., Nanjing 210042, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Moussa DG, Ahmad P, Mansour TA, Siqueira WL. Current State and Challenges of the Global Outcomes of Dental Caries Research in the Meta-Omics Era. Front Cell Infect Microbiol 2022; 12:887907. [PMID: 35782115 PMCID: PMC9247192 DOI: 10.3389/fcimb.2022.887907] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/04/2022] [Indexed: 12/20/2022] Open
Abstract
Despite significant healthcare advances in the 21st century, the exact etiology of dental caries remains unsolved. The past two decades have witnessed a tremendous growth in our understanding of dental caries amid the advent of revolutionary omics technologies. Accordingly, a consensus has been reached that dental caries is a community-scale metabolic disorder, and its etiology is beyond a single causative organism. This conclusion was based on a variety of microbiome studies following the flow of information along the central dogma of biology from genomic data to the end products of metabolism. These studies were facilitated by the unprecedented growth of the next- generation sequencing tools and omics techniques, such as metagenomics and metatranscriptomics, to estimate the community composition of oral microbiome and its functional potential. Furthermore, the rapidly evolving proteomics and metabolomics platforms, including nuclear magnetic resonance spectroscopy and/or mass spectrometry coupled with chromatography, have enabled precise quantification of the translational outcomes. Although the majority supports ‘conserved functional changes’ as indicators of dysbiosis, it remains unclear how caries dynamics impact the microbiota functions and vice versa, over the course of disease onset and progression. What compounds the situation is the host-microbiota crosstalk. Genome-wide association studies have been undertaken to elucidate the interaction of host genetic variation with the microbiome. However, these studies are challenged by the complex interaction of host genetics and environmental factors. All these complementary approaches need to be orchestrated to capture the key players in this multifactorial disease. Herein, we critically review the milestones in caries research focusing on the state-of-art singular and integrative omics studies, supplemented with a bibliographic network analysis to address the oral microbiome, the host factors, and their interactions. Additionally, we highlight gaps in the dental literature and shed light on critical future research questions and study designs that could unravel the complexities of dental caries, the most globally widespread disease.
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Affiliation(s)
- Dina G. Moussa
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paras Ahmad
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Tamer A. Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States
- Department of Clinical Pathology, School of Medicine, Mansoura University, Mansoura, Egypt
| | - Walter L. Siqueira
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Walter L. Siqueira,
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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.
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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
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35
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Mass Spectrometry Approaches for SARS-CoV-2 Detection: Harnessing for Application in Food and Environmental Samples. Viruses 2022; 14:v14050872. [PMID: 35632614 PMCID: PMC9144875 DOI: 10.3390/v14050872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
The public health crisis caused by the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in 2019 has drastically changed our lifestyle in virtually all contexts around the world. SARS-CoV-2 is mainly airborne, transmitted by the salivary droplets produced when infected people cough or sneeze. In addition, diarrhea symptoms and the detection of SARS-CoV-2 in feces suggest a fecal–oral route of contagion. Currently, the high demand for SARS-CoV-2 diagnosis has surpassed the availability of PCR and immunodetection probes and has prompted the development of other diagnostic alternatives. In this context, mass spectrometry (MS) represents a mature, robust alternative platform for detection of SARS-CoV-2 and other human viruses. This possibility has raised great interest worldwide. Therefore, it is time for the global application of MS as a feasible option for detecting SARS-CoV-2, not only in human fluids, but also in other matrices such as foods and wastewater. This review covers the most relevant established methods for MS-based SARS-CoV-2 detection and discusses the future application of these tools in different matrices. Significance: The Coronavirus Disease 2019 (COVID-19) pandemic highlighted the pros and cons of currently available PCR and immunodetection tools. The great concern over the infective potential of SARS-CoV-2 viral particles that can persist for several hours on different surfaces under various conditions further evidenced the need for reliable alternatives and high-throughput methods to meet the needs for mass detection of SARS-CoV-2. In this context, MS-based proteomics emerging from fundamental studies in life science can offer a robust option for SARS-CoV-2 detection in human fluids and other matrices. In addition, the substantial efforts towards detecting SARS-CoV-2 in clinal samples, position MS to support the detection of this virus in different matrices such as the surfaces of the packing food process, frozen foods, and wastewaters. Proteomics and mass spectrometry are, therefore, well positioned to play a role in the epidemiological control of COVID-19 and other future diseases. We are currently witnessing the opportunity to generate technologies to overcome prolonged pandemics for the first time in human history.
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36
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Sato H, Nakajima D, Ishikawa M, Konno R, Nakamura R, Ohara O, Kawashima Y. Evaluation of the Suitability of Dried Saliva Spots for In-Depth Proteome Analyses for Clinical Applications. J Proteome Res 2022; 21:1340-1348. [PMID: 35446574 DOI: 10.1021/acs.jproteome.2c00099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previously, we performed nontargeted proteome analysis using dried blood spots (DBSs) that are widely used in newborn screening for the clinical diagnosis of congenital genetic diseases and immunodeficiency. We have developed an efficient and simple pretreatment method for DBSs that can detect more than 1000 proteins. To complement proteins that are difficult to detect via DBS analysis with less invasive alternative body fluids, we conducted this study to investigate the proteins detected from dried saliva spots (DSSs) using single-shot LC-MS/MS, which is practical in clinical settings. We also clarified whether DSSs have the same advantages as DBSs, and we investigated the influence of saliva collection conditions and the storage environment on their protein profile. As a result, we detected approximately 5000 proteins in DSSs and whole saliva, and we concluded that they were sufficient to complement the proteins lacking in the blood analysis. DSSs could be used as an alternative tool to DBSs for detecting the presence of causative proteins.
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Affiliation(s)
- Hironori Sato
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.,Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-8677, Japan
| | - Daisuke Nakajima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Ren Nakamura
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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37
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Uchida H, Ovitt CE. Novel impacts of saliva with regard to oral health. J Prosthet Dent 2022; 127:383-391. [PMID: 34140141 PMCID: PMC8669010 DOI: 10.1016/j.prosdent.2021.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022]
Abstract
The maintenance of balanced oral homeostasis depends on saliva. A readily available and molecularly rich source of biological fluid, saliva fulfills many functions in the oral cavity, including lubrication, pH buffering, and tooth mineralization. Saliva composition and flow can be modulated by different factors, including circadian rhythm, diet, age, drugs, and disease. Recent events have revealed that saliva plays a central role in the dissemination and detection of the SARS-CoV-2 coronavirus. A working knowledge of saliva function and physiology is essential for dental health professionals.
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Affiliation(s)
- Hitoshi Uchida
- Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY
| | - Catherine E. Ovitt
- Department of Biomedical Genetics, Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY
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38
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Lazari LC, Zerbinati RM, Rosa-Fernandes L, Santiago VF, Rosa KF, Angeli CB, Schwab G, Palmieri M, Sarmento DJS, Marinho CRF, Almeida JD, To K, Giannecchini S, Wrenger C, Sabino EC, Martinho H, Lindoso JAL, Durigon EL, Braz-Silva PH, Palmisano G. MALDI-TOF mass spectrometry of saliva samples as a prognostic tool for COVID-19. J Oral Microbiol 2022; 14:2043651. [PMID: 35251522 PMCID: PMC8890567 DOI: 10.1080/20002297.2022.2043651] [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] [Indexed: 11/02/2022] Open
Abstract
Background Methods Results Conclusion
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Affiliation(s)
- Lucas C. Lazari
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Rodrigo M. Zerbinati
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Veronica Feijoli Santiago
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Klaise F. Rosa
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Claudia B. Angeli
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Gabriela Schwab
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Michelle Palmieri
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Dmitry J. S. Sarmento
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Claudio R. F. Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Janete Dias Almeida
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University, São José dos Campos, Brazil
| | - Kelvin To
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, Li KaShing Faculty of Medicine of the University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Ester C. Sabino
- Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Herculano Martinho
- Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC, Santo André, Brazil
| | - José A. L. Lindoso
- Institute of Infectious Diseases Emílio Ribas, São Paulo, Brazil
- Laboratory of Protozoology (LIM-49-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
- Department of Infectious Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Edison L. Durigon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, ICB, University of São Paulo, São Paulo, Brazil
| | - Paulo H. Braz-Silva
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
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Nalpas N, Hoyles L, Anselm V, Ganief T, Martinez-Gili L, Grau C, Droste-Borel I, Davidovic L, Altafaj X, Dumas ME, Macek B. An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome. Gut Microbes 2022; 13:1994836. [PMID: 34763597 PMCID: PMC8726736 DOI: 10.1080/19490976.2021.1994836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Intestinal microbiota plays a key role in shaping host homeostasis by regulating metabolism, immune responses and behavior. Its dysregulation has been associated with metabolic, immune and neuropsychiatric disorders and is accompanied by changes in bacterial metabolic regulation. Although proteomics is well suited for analysis of individual microbes, metaproteomics of fecal samples is challenging due to the physical structure of the sample, presence of contaminating host proteins and coexistence of hundreds of taxa. Furthermore, there is a lack of consensus regarding preparation of fecal samples, as well as downstream bioinformatic analyses following metaproteomics data acquisition. Here we assess sample preparation and data analysis strategies applied to mouse feces in a typical mass spectrometry-based metaproteomic experiment. We show that subtle changes in sample preparation protocols may influence interpretation of biological findings. Two-step database search strategies led to significant underestimation of false positive protein identifications. Unipept software provided the highest sensitivity and specificity in taxonomic annotation of the identified peptides of unknown origin. Comparison of matching metaproteome and metagenome data revealed a positive correlation between protein and gene abundances. Notably, nearly all functional categories of detected protein groups were differentially abundant in the metaproteome compared to what would be expected from the metagenome, highlighting the need to perform metaproteomics when studying complex microbiome samples.
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Affiliation(s)
- Nicolas Nalpas
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany
| | - Lesley Hoyles
- Biomolecular Medicine Section, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK,Department of Biosciences, Nottingham Trent University, Nottingham, UK
| | - Viktoria Anselm
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany
| | - Tariq Ganief
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany
| | - Laura Martinez-Gili
- Biomolecular Medicine Section, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Cristina Grau
- Pharmacology unit, Bellvitge Biomedical Research Institute, University of Barcelona, Barcelona, Spain
| | | | | | - Xavier Altafaj
- Pharmacology unit, Bellvitge Biomedical Research Institute, University of Barcelona, Barcelona, Spain,Neurophysiology Unit, University of Barcelona – Idibaps, Barcelona, Spain
| | - Marc-Emmanuel Dumas
- Biomolecular Medicine Section, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK,Genomic and Environmental Medicine, National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, UK,European Genomic Institute for Diabetes, Inserm Umr 1283, Cnrs Umr 8199, Institut Pasteur De Lille, Lille University Hospital, University of Lille, Lille, France
| | - Boris Macek
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany,CONTACT Boris Macek Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, Auf Der Morgenstelle 15, Tuebingen72076, Germany
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40
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Zhang T, Du Y, Wu Q, Li H, Nguyen T, Gidley G, Duran V, Goldman D, Petri M, Mohan C. Salivary anti-nuclear antibody (ANA) mirrors serum ANA in systemic lupus erythematosus. Arthritis Res Ther 2022; 24:3. [PMID: 34980255 PMCID: PMC8721993 DOI: 10.1186/s13075-021-02694-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 12/07/2021] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVES To assay salivary anti-nuclear antibody (ANA) and its isotypes in patients with systemic lupus erythematosus (SLE) and to investigate relevant clinical associations. METHODS Saliva samples were collected from SLE patients and assayed for salivary ANA using immunofluorescence (IF). Isotypes of salivary ANA, including IgG-ANA, IgA-ANA, and IgM-ANA, were quantified using enzyme-linked immunosorbent assay. The correlations between clinical parameters and levels of salivary ANA and isotypes were evaluated. RESULTS Salivary ANA IF intensities were significantly higher in SLE patients than in healthy controls, irrespective of SLE patient disease activity, and strongly correlated with serum ANA titers. Salivary ANA was detected in 67.14% of SLE patients and 10.00% of healthy controls (p < 0.001). Among ANA-positive samples, 80.85% exhibited a nuclear ANA pattern, and 42.55% exhibited a cytoplasmic ANA pattern. Salivary IgG-ANA, IgA-ANA, and IgM-ANA levels, as assayed by ELISA, were significantly increased in both active and less active SLE patients compared with healthy controls, and levels of each isotype were significantly correlated with serum ANA titer. Salivary IgM-ANA levels correlated with the physician global assessment (PGA), SLE disease activity index (SLEDAI), and negatively with serum C3 and C4. Salivary IgG-ANA also correlated with erythrocyte sedimentation rate (ESR), SLEDAI, and negatively with serum C3. CONCLUSION Salivary ANA levels correlate with serum ANA titer, and salivary IgM-ANA and IgG-ANA correlate variably with PGA, SLEDAI, ESR and complement levels. These findings underscore the potential of using salivary ANA and ANA isotypes as surrogates for serum ANA, particularly for future point-of-care applications since saliva is easier to obtain than blood.
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Affiliation(s)
- Ting Zhang
- Biomedical Engineering Department, University of Houston, 3517 Cullen Blvd, Room 2027, TX, Houston, USA.,Present affiliation: The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Du
- Biomedical Engineering Department, University of Houston, 3517 Cullen Blvd, Room 2027, TX, Houston, USA
| | - Qingqing Wu
- Biomedical Engineering Department, University of Houston, 3517 Cullen Blvd, Room 2027, TX, Houston, USA
| | - Hao Li
- Biomedical Engineering Department, University of Houston, 3517 Cullen Blvd, Room 2027, TX, Houston, USA
| | - Thao Nguyen
- Biomedical Engineering Department, University of Houston, 3517 Cullen Blvd, Room 2027, TX, Houston, USA
| | - Gabriel Gidley
- Biomedical Engineering Department, University of Houston, 3517 Cullen Blvd, Room 2027, TX, Houston, USA
| | - Valeria Duran
- Biomedical Engineering Department, University of Houston, 3517 Cullen Blvd, Room 2027, TX, Houston, USA
| | - Daniel Goldman
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chandra Mohan
- Biomedical Engineering Department, University of Houston, 3517 Cullen Blvd, Room 2027, TX, Houston, USA.
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41
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Razzaque MS. Salivary phosphate as a biomarker for human diseases. FASEB Bioadv 2022; 4:102-108. [PMID: 35141474 PMCID: PMC8814558 DOI: 10.1096/fba.2021-00104] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/20/2022] Open
Affiliation(s)
- Mohammed S. Razzaque
- Department of Pathology Lake Erie College of Osteopathic Medicine Erie Pennsylvania USA
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42
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Halder A, Verma A, Biswas D, Srivastava S. Recent advances in mass-spectrometry based proteomics software, tools and databases. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 39:69-79. [PMID: 34906327 DOI: 10.1016/j.ddtec.2021.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/08/2021] [Accepted: 06/21/2021] [Indexed: 01/12/2023]
Abstract
The field of proteomics immensely depends on data generation and data analysis which are thoroughly supported by software and databases. There has been a massive advancement in mass spectrometry-based proteomics over the last 10 years which has compelled the scientific community to upgrade or develop algorithms, tools, and repository databases in the field of proteomics. Several standalone software, and comprehensive databases have aided the establishment of integrated omics pipeline and meta-analysis workflow which has contributed to understand the disease pathobiology, biomarker discovery and predicting new therapeutic modalities. For shotgun proteomics where Data Dependent Acquisition is performed, several user-friendly software are developed that can analyse the pre-processed data to provide mechanistic insights of the disease. Likewise, in Data Independent Acquisition, pipelines are emerged which can accomplish the task from building the spectral library to identify the therapeutic targets. Furthermore, in the age of big data analysis the implications of machine learning and cloud computing are appending robustness, rapidness and in-depth proteomics data analysis. The current review talks about the recent advancement, and development of software, tools, and database in the field of mass-spectrometry based proteomics.
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Affiliation(s)
- Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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43
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Saibaba G, Rajesh D, Muthukumar S, Sathiyanarayanan G, Aarthy AP, Archunan G. Salivary Proteome Profile of Women during Fertile Phase of Menstrual Cycle as Characterized by Mass Spectrometry. Gynecol Minim Invasive Ther 2021; 10:226-234. [PMID: 34909380 PMCID: PMC8613494 DOI: 10.4103/gmit.gmit_78_20] [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: 09/14/2020] [Revised: 03/18/2021] [Accepted: 04/15/2021] [Indexed: 01/11/2023] Open
Abstract
Objectives: Ovulation is such a critical physiological process that its noninvasive detection based on salivary constituents has several advantages in humans. Hence, the present study is proposed to identify the ovulatory-specific proteins in saliva in order to detect ovulation phase. Materials and Methods: Samples were collected from women volunteers. The procedure adopted was approved by the Institutional Human Ethical Committee (DM/2014/101/38), Bharathidasan University. The saliva samples were collected from thirty healthy female volunteers, with a prior written consent. One-way analysis of variance was used to calculate protein concentration and band intensity using SPSS 16 software (SPSS Inc., Cary, NC, USA). The salivary protein expression pattern during different phases of menstrual cycle was analyzed using gel-based high resolution-liquid chromatography-mass spectrometry/mass spectrometry and matrix-assisted laser desorption ionization-time of flight/time of flight. Further, bioinformatics tools were adopted to annotate the proteins identified at various phases of menstrual cycle. Results: As many as 530 proteins showed up in the saliva during ovulatory phase, whereas there were only 251 proteins identified during postovulatory phase. The functional annotation of salivary proteins revealed that the proteins got assigned to the class of “extracellular proteins” which are concerned with regulatory functions. The 16 unique and/or differentially expressed protein spots appeared during ovulatory phase, among which Cystatin-S, Prolactin-inducible protein, Cystatin-A, Cystatin-SN, BPI fold-containing family A member 2, Alpha-tubulin N-acetyltransferase 1, Carbonic anhydrase-6, Protein LEG1 homolog, Hemoglobin subunit beta, and Pancreatic alpha-amylase were identified. Conclusion: Total salivary proteome profile has been listed with respect to various phases of menstrual cycle. Among the protein listed, Cystatin-S offers a biomarker protein and/or indicator of ovulatory phase. However, extensive validation is required before arriving to a candidate bio-marker protein.
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Affiliation(s)
- Ganesan Saibaba
- Department of Animal Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India.,Department of Animal Science, Agricultural Research Organization, Volcani Center, Rishon LeTsiyon-7528809, Israel
| | - Durairaj Rajesh
- Department of Animal Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India.,Department of Molecular Biology and Chemical Communication, Research Institute in Semiochemistry and Applied Ethology (IRSEA), 84400 Apt, France
| | - Subramanian Muthukumar
- Department of Biotechnology, School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Thanjavur, Tamil Nadu, India
| | | | - Archunan Priya Aarthy
- Division of Obstetrics and Gynecology, Rabindra Nath Tagore Medical College, Udaipur- 313001, Rajasthan, India
| | - Govindaraju Archunan
- Department of Animal Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
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Boix-Amorós A, Piras E, Bu K, Wallach D, Stapylton M, Fernández-Sesma A, Malaspina D, Clemente JC. Viral Inactivation Impacts Microbiome Estimates in a Tissue-Specific Manner. mSystems 2021; 6:e0067421. [PMID: 34609165 PMCID: PMC8547476 DOI: 10.1128/msystems.00674-21] [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: 06/02/2021] [Accepted: 09/08/2021] [Indexed: 11/20/2022] Open
Abstract
The global emergence of novel pathogenic viruses presents an important challenge for research, as high biosafety levels are required to process samples. While inactivation of infectious agents facilitates the use of less stringent safety conditions, its effect on other biological entities of interest present in the sample is generally unknown. Here, we analyzed the effect of five inactivation methods (heat, ethanol, formaldehyde, psoralen, and TRIzol) on microbiome composition and diversity in samples collected from four different body sites (gut, nasal, oral, and skin) and compared them against untreated samples from the same tissues. We performed 16S rRNA gene sequencing and estimated abundance and diversity of bacterial taxa present in all samples. Nasal and skin samples were the most affected by inactivation, with ethanol and TRIzol inducing the largest changes in composition, and heat, formaldehyde, TRIzol, and psoralen inducing the largest changes in diversity. Oral and stool microbiomes were more robust to inactivation, with no significant changes in diversity and only moderate changes in composition. Firmicutes was the taxonomic group least affected by inactivation, while Bacteroidetes had a notable enrichment in nasal samples and moderate enrichment in fecal and oral samples. Actinobacteria were more notably depleted in fecal and skin samples, and Proteobacteria exhibited a more variable behavior depending on sample type and inactivation method. Overall, our results demonstrate that inactivation methods can alter the microbiome in a tissue-specific manner and that careful consideration should be given to the choice of method based on the sample type under study. IMPORTANCE Understanding how viral infections impact and are modulated by the microbiome is an important problem in basic research but is also of high clinical relevance under the current pandemic. To facilitate the study of interactions between microbial communities and pathogenic viruses under safe conditions, the infectious agent is generally inactivated prior to processing samples. The effect of this inactivation process in the microbiome is, however, unknown. Further, it is unclear whether biases introduced by inactivation methods are dependent on the sample type under study. Estimating the magnitude and nature of the changes induced by different methods in samples collected from various body sites thus provides important information for current and future studies that require inactivation of pathogenic agents.
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Affiliation(s)
- Alba Boix-Amorós
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Enrica Piras
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kevin Bu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Wallach
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Matthew Stapylton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana Fernández-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai. New York, New York, USA
| | - Dolores Malaspina
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai. New York, New York, USA
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Tierney BT, Szymanski E, Henriksen JR, Kostic AD, Patel CJ. Using Cartesian Doubt To Build a Sequencing-Based View of Microbiology. mSystems 2021; 6:e0057421. [PMID: 34636670 PMCID: PMC8510522 DOI: 10.1128/msystems.00574-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/23/2021] [Indexed: 12/13/2022] Open
Abstract
The technological leap of DNA sequencing generated a tension between modern metagenomics and historical microbiology. We are forcibly harmonizing the output of a modern tool with centuries of experimental knowledge derived from culture-based microbiology. As a thought experiment, we borrow the notion of Cartesian doubt from philosopher Rene Descartes, who used doubt to build a philosophical framework from his incorrigible statement that "I think therefore I am." We aim to cast away preconceived notions and conceptualize microorganisms through the lens of metagenomic sequencing alone. Specifically, we propose funding and building analysis and engineering methods that neither search for nor rely on the assumption of independent genomes bound by lipid barriers containing discrete functional roles and taxonomies. We propose that a view of microbial communities based in sequencing will engender novel insights into metagenomic structure and may capture functional biology not reflected within the current paradigm.
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Affiliation(s)
- Braden T. Tierney
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, Massachusetts, USA
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Erika Szymanski
- Department of English, Colorado State University, Fort Collins, Colorado, USA
| | | | - Aleksandar D. Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, Massachusetts, USA
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Chirag J. Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
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Abstract
Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.
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47
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D'haeseleer P, Collette NM, Lao V, Segelke BW, Branda SS, Franco M. Shotgun Immunoproteomic Approach for the Discovery of Linear B-Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei. Front Immunol 2021; 12:716676. [PMID: 34659206 PMCID: PMC8513525 DOI: 10.3389/fimmu.2021.716676] [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: 05/29/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Peptide-based subunit vaccines are coming to the forefront of current vaccine approaches, with safety and cost-effective production among their top advantages. Peptide vaccine formulations consist of multiple synthetic linear epitopes that together trigger desired immune responses that can result in robust immune memory. The advantages of linear compared to conformational epitopes are their simple structure, ease of synthesis, and ability to stimulate immune responses by means that do not require complex 3D conformation. Prediction of linear epitopes through use of computational tools is fast and cost-effective, but typically of low accuracy, necessitating extensive experimentation to verify results. On the other hand, identification of linear epitopes through experimental screening has been an inefficient process that requires thorough characterization of previously identified full-length protein antigens, or laborious techniques involving genetic manipulation of organisms. In this study, we apply a newly developed generalizable screening method that enables efficient identification of B-cell epitopes in the proteomes of pathogenic bacteria. As a test case, we used this method to identify epitopes in the proteome of Francisella tularensis (Ft), a Select Agent with a well-characterized immunoproteome. Our screen identified many peptides that map to known antigens, including verified and predicted outer membrane proteins and extracellular proteins, validating the utility of this approach. We then used the method to identify seroreactive peptides in the less characterized immunoproteome of Select Agent Burkholderia pseudomallei (Bp). This screen revealed known Bp antigens as well as proteins that have not been previously identified as antigens. Although B-cell epitope prediction tools Bepipred 2.0 and iBCE-EL classified many of our seroreactive peptides as epitopes, they did not score them significantly higher than the non-reactive tryptic peptides in our study, nor did they assign higher scores to seroreactive peptides from known Ft or Bp antigens, highlighting the need for experimental data instead of relying on computational epitope predictions alone. The present workflow is easily adaptable to detecting peptide targets relevant to the immune systems of other mammalian species, including humans (depending upon the availability of convalescent sera from patients), and could aid in accelerating the discovery of B-cell epitopes and development of vaccines to counter emerging biological threats.
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Affiliation(s)
- Patrik D'haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Nicole M Collette
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Victoria Lao
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Brent W Segelke
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Steven S Branda
- Molecular and Microbiology Department, Sandia National Laboratories, Livermore, CA, United States
| | - Magdalena Franco
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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Schwartz M, Neiers F, Charles JP, Heydel JM, Muñoz-González C, Feron G, Canon F. Oral enzymatic detoxification system: Insights obtained from proteome analysis to understand its potential impact on aroma metabolization. Compr Rev Food Sci Food Saf 2021; 20:5516-5547. [PMID: 34653315 DOI: 10.1111/1541-4337.12857] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/02/2021] [Accepted: 09/10/2021] [Indexed: 12/17/2022]
Abstract
The oral cavity is an entry path into the body, enabling the intake of nutrients but also leading to the ingestion of harmful substances. Thus, saliva and oral tissues contain enzyme systems that enable the early neutralization of xenobiotics as soon as they enter the body. Based on recently published oral proteomic data from several research groups, this review identifies and compiles the primary detoxification enzymes (also known as xenobiotic-metabolizing enzymes) present in saliva and the oral epithelium. The functions and the metabolic activity of these enzymes are presented. Then, the activity of these enzymes in saliva, which is an extracellular fluid, is discussed with regard to the salivary parameters. The next part of the review presents research evidencing oral metabolization of aroma compounds and the putative involved enzymes. The last part discusses the potential role of these enzymatic reactions on the perception of aroma compounds in light of recent pieces of evidence of in vivo oral metabolization of aroma compounds affecting their release in mouth and their perception. Thus, this review highlights different enzymes appearing as relevant to explain aroma metabolism in the oral cavity. It also points out that further works are needed to unravel the effect of the oral enzymatic detoxification system on the perception of food flavor in the context of the consumption of complex food matrices, while considering the impact of food oral processing. Thus, it constitutes a basis to explore these biochemical mechanisms and their impact on flavor perception.
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Affiliation(s)
- Mathieu Schwartz
- Centre des Sciences du Goût et de l'Alimentation (CSGA), AgroSup Dijon, CNRS, INRAE, Université de Bourgogne Franche Comté, Dijon, France
| | - Fabrice Neiers
- Centre des Sciences du Goût et de l'Alimentation (CSGA), AgroSup Dijon, CNRS, INRAE, Université de Bourgogne Franche Comté, Dijon, France
| | - Jean-Philippe Charles
- Centre des Sciences du Goût et de l'Alimentation (CSGA), AgroSup Dijon, CNRS, INRAE, Université de Bourgogne Franche Comté, Dijon, France
| | - Jean-Marie Heydel
- Centre des Sciences du Goût et de l'Alimentation (CSGA), AgroSup Dijon, CNRS, INRAE, Université de Bourgogne Franche Comté, Dijon, France
| | - Carolina Muñoz-González
- Instituto de investigación en Ciencias de la Alimentación (CIAL), (CSIC-UAM), C/ Nicolás Cabrera, Madrid, Spain
| | - Gilles Feron
- Centre des Sciences du Goût et de l'Alimentation (CSGA), AgroSup Dijon, CNRS, INRAE, Université de Bourgogne Franche Comté, Dijon, France
| | - Francis Canon
- Centre des Sciences du Goût et de l'Alimentation (CSGA), AgroSup Dijon, CNRS, INRAE, Université de Bourgogne Franche Comté, Dijon, France
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Almhöjd U, Cevik-Aras H, Karlsson N, Chuncheng J, Almståhl A. Stimulated saliva composition in patients with cancer of the head and neck region. BMC Oral Health 2021; 21:509. [PMID: 34627217 PMCID: PMC8501675 DOI: 10.1186/s12903-021-01872-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To analyse over time changes in stimulated whole saliva regarding total protein, Immunoglobulin A (IgA), and mucin type O-glycans (mostly MUC5B and MUC7) in head and neck cancer patients. METHODS 29 dentate patients (20 men and 9 women, 59 ± 8 years) treated with curative radiation therapy and chemotherapy for cancer of the head and neck region were included. The stimulated whole salivary secretion rate was determined and saliva collected at four time-points: at pretreatment, and at 6 months, 1 and 2 years post treatment. The total protein concentration was determined spectrophotometrically by using Bicinchoninic Acid assay and Immunoglobulin A (IgA) by using ELISA technique. Glycosylation pattern of salivary mucins was determined in samples collected pre- and post treatment by using LC/MS electrospray and mucin content quantified using SDS-AgPAGE gels and PAS staining. RESULTS Compared with pretreatment, the total protein concentration was increased already at 6 months post treatment (p < 0.01), and continued to increase up to 2 years post treatment (p < 0.001). During that period no significant changes in IgA concentration was detected. At pretreatment, the output/min of both total protein and IgA was significantly higher than at all time-points post treatment. Saliva from the cancer patients showed a low abundance/no detectable MUC7, while the MUC5B level remained, compared to saliva from a healthy control. The glycomic analysis showed that the percentage of core 2 O-glycans was increased as core 1, 3 and 4 O-glycans were decreased. The level of sialylation was higher at 6 months post treatment, while sulfation was lower. CONCLUSION A decreased output per minute of proteins at decreased salivary secretion rate, as well as reduced sulfation of MUC5B at 6 months post treatment tended to correlate with the patients' experience of sticky saliva and oral dryness. At 2 years post treatment, the decreased amount of IgA combined with a lowered salivary secretion rate indicate a reduced oral defense with increased risk of oral infections.
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Affiliation(s)
- Ulrica Almhöjd
- Department of Cariology, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hulya Cevik-Aras
- Department of Oral Pathology and Medicine, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,NÄL Hospital, Trollhättan, Sweden
| | - Niclas Karlsson
- BioMS, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jin Chuncheng
- BioMS, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Annica Almståhl
- Department of Oral Microbiology and Immunology, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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50
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Chen JW, Wu JH, Chiang WF, Chen YL, Wu WS, Wu LW. Taxonomic and Functional Dysregulation in Salivary Microbiomes During Oral Carcinogenesis. Front Cell Infect Microbiol 2021; 11:663068. [PMID: 34604102 PMCID: PMC8482814 DOI: 10.3389/fcimb.2021.663068] [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: 02/02/2021] [Accepted: 08/23/2021] [Indexed: 01/04/2023] Open
Abstract
Exploring microbial community compositions in humans with healthy versus diseased states is crucial to understand the microbe-host interplay associated with the disease progression. Although the relationship between oral cancer and microbiome was previously established, it remained controversial, and yet the ecological characteristics and their responses to oral carcinogenesis have not been well studied. Here, using the bacterial 16S rRNA gene amplicon sequencing along with the in silico function analysis by PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2), we systematically characterized the compositions and the ecological drivers of saliva microbiome in the cohorts of orally healthy, non-recurrent oral verrucous hyperplasia (a pre-cancer lesion), and oral verrucous hyperplasia–associated oral cancer at taxonomic and function levels, and compared them with the re-analysis of publicly available datasets. Diversity analyses showed that microbiome dysbiosis in saliva was significantly linked to oral health status. As oral health deteriorated, the number of core species declined, and metabolic pathways predicted by PICRUSt2 were dysregulated. Partitioned beta-diversity revealed an extremely high species turnover but low function turnover. Functional beta-diversity in saliva microbiome shifted from turnover to nestedness during oral carcinogenesis, which was not observed at taxonomic levels. Correspondingly, the quantitative analysis of stochasticity ratios showed that drivers of microbial composition and functional gene content of saliva microbiomes were primarily governed by the stochastic processes, yet the driver of functional gene content shifted toward deterministic processes as oral cancer developed. Re-analysis of publicly accessible datasets supported not only the distinctive family taxa of Veillonellaceae and Actinomycetaceae present in normal cohorts but also that Flavobacteriaceae and Peptostreptococcaceae as well as the dysregulated metabolic pathways of nucleotides, amino acids, fatty acids, and cell structure were related to oral cancer. Using predicted functional profiles to elucidate the correlations to the oral health status shows superior performance than using taxonomic data among different studies. These findings advance our understanding of the oral ecosystem in relation to oral carcinogenesis and provide a new direction to the development of microbiome-based tools to study the interplay of the oral microbiome, metabolites, and host health.
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Affiliation(s)
- Jiung-Wen Chen
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Fan Chiang
- Department of Oral & Maxillofacial Surgery, Chi-Mei Medical Center, Liouying, Taiwan.,School of Dentistry, National Yang-Ming University, Taipei, Taiwan
| | - Yuh-Ling Chen
- Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Li-Wha Wu
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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