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Halstenbach T, Topitsch A, Schilling O, Iglhaut G, Nelson K, Fretwurst T. Mass spectrometry-based proteomic applications in dental implants research. Proteomics Clin Appl 2024; 18:e2300019. [PMID: 38342588 DOI: 10.1002/prca.202300019] [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: 07/21/2023] [Revised: 12/07/2023] [Accepted: 12/21/2023] [Indexed: 02/13/2024]
Abstract
Dental implants have been established as successful treatment options for missing teeth with steadily increasing demands. Today, the primary areas of research in dental implantology revolve around osseointegration, soft and hard tissue grafting as well as peri-implantitis diagnostics, prevention, and treatment. This review provides a comprehensive overview of the current literature on the application of MS-based proteomics in dental implant research, highlights how explorative proteomics provided insights into the biology of peri-implant soft and hard tissues and how proteomics facilitated the stratification between healthy and diseased implants, enabling the identification of potential new diagnostic markers. Additionally, this review illuminates technical aspects, and provides recommendations for future study designs based on the current evidence.
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Affiliation(s)
- Tim Halstenbach
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Annika Topitsch
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Gerhard Iglhaut
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Katja Nelson
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Tobias Fretwurst
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
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Silbereisen A, Bao K, Wolski W, Nanni P, Kunz L, Afacan B, Emingil G, Bostanci N. Probing the salivary proteome for prognostic biomarkers in response to non-surgical periodontal therapy. J Clin Periodontol 2024. [PMID: 38660744 DOI: 10.1111/jcpe.13990] [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: 11/09/2023] [Revised: 03/04/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
AIM This prospective study investigated the salivary proteome before and after periodontal therapy. MATERIALS AND METHODS Ten systemically healthy, non-smoking, stage III, grade C periodontitis patients underwent non-surgical periodontal treatment. Full-mouth periodontal parameters were measured, and saliva (n = 30) collected pre- (T0), and one (T1) and six (T6) months post-treatment. The proteome was investigated by label-free quantitative proteomics. Protein expression changes were modelled over time, with significant protein regulation considered at false discovery rate <0.05. RESULTS Treatment significantly reduced bleeding scores, percentages of sites with pocket depth ≥5 mm, plaque and gingival indexes. One thousand seven hundred and thirteen proteins were identified and 838 proteins (human = 757, bacterial = 81) quantified (≥2 peptides). At T1, 80 (T1 vs. T0: 60↑:20↓), and at T6, 118 human proteins (T6 vs. T0: 67↑:51↓) were regulated. The salivary proteome at T6 versus T1 remained stable. Highest protein activity post- versus pre-treatment was observed for cellular movement and inflammatory response. The small proline-rich protein 3 (T1 vs. T0: 5.4-fold↑) and lymphocyte-specific protein 1 (T6 vs. T0: 4.6-fold↓) were the top regulated human proteins. Proteins from Neisseria mucosa and Treponema socranskii (T1 vs. T0: 8.0-fold↓, 4.9-fold↓) were down-regulated. CONCLUSIONS Periodontal treatment reduced clinical disease parameters and these changes were reflected in the salivary proteome. This underscores the potential of utilizing saliva biomarkers as prognostic tools for monitoring treatment outcomes.
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Affiliation(s)
- Angelika Silbereisen
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kai Bao
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Witold Wolski
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Paolo Nanni
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Laura Kunz
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Beral Afacan
- Department of Periodontology, Faculty of Dentistry, Adnan Menderes University, Aydın, Turkey
| | - Gülnur Emingil
- Department of Periodontology, School of Dentistry, Ege University, İzmir, Turkey
| | - Nagihan Bostanci
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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Torres A, Michea MA, Végvári Á, Arce M, Morales A, Lanyon E, Alcota M, Fuentes C, Vernal R, Budini M, Zubarev RA, González FE. Proteomic profile of human gingival crevicular fluid reveals specific biological and molecular processes during clinical progression of periodontitis. J Periodontal Res 2023; 58:1061-1081. [PMID: 37522282 DOI: 10.1111/jre.13169] [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: 03/10/2023] [Revised: 06/23/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023]
Abstract
BACKGROUND AND OBJECTIVE There is no clear understanding of molecular events occurring in the periodontal microenvironment during clinical disease progression. Our aim was to explore qualitative and quantitative differences in gingival crevicular fluid (GCF) protein profiles from patients diagnosed with periodontitis between non-progressive and progressive periodontal sites. METHODS Five systemically healthy patients diagnosed with periodontitis were monitored weekly in their progression of the disease and GCF samples from 10 candidate sites were obtained. Two groups of five sites, matched from an equal number of teeth, were selected from the five patients: Progression (PG) and Non-Progression (NP). Global protein identification was performed with high-throughput proteomic approaches and label-free analysis determined their relative abundances. Proteins were identified by Proteome Discoverer v2.4 and searched against human SwissProt protein databases. Enrichment bioinformatic analyses were performed in STRING-DB and ShinyGO environment. RESULTS 1504 and 1500 proteins were identified in NP and PG respectively. Forty-eight proteins were exclusively identified in PG, while 52 were identified in NP. Moreover, 35 proteins were more abundant in PG and 29 proteins in NP (twofold change, p < .05). The NP group was mainly represented by proteins from "response to biotic stimuli and other organisms," "processes of cell death regulation," "peptidase regulation," "protein ubiquitination," and "ribosomal activity" GO categories. The most represented GO categories of the PG group were "assembly of multiprotein complexes," "catabolic processes," "lipid metabolism," and "binding to hemoglobin and haptoglobin." CONCLUSIONS There are quantitative and qualitative differences in the proteome of GCF from periodontal sites according to the status of clinical progression of periodontitis. Progressive periodontitis sites are characterized by a protein profile associated with catabolic processes, immune response, and response to cellular stress, while stable periodontitis sites show a protein profile mainly related to wound repair and healing processes, cell death regulation, and chaperone-mediated autophagy. Understanding the etiopathogenic role of these profiles in progressive periodontitis may help to develop new diagnostic and therapeutic approaches.
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Affiliation(s)
- Alfredo Torres
- Laboratory of Experimental Immunology & Cancer, Faculty of Dentistry, University of Chile, Santiago, Chile
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - M Angélica Michea
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Marion Arce
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Alicia Morales
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Elías Lanyon
- Laboratory of Experimental Immunology & Cancer, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Marcela Alcota
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Camila Fuentes
- Laboratory of Cancer Immunoregulation, Disciplinary Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Rolando Vernal
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
- Periodontal Biology Laboratory, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Mauricio Budini
- Institute for Research in Dental Sciences, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Roman A Zubarev
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fermín E González
- Laboratory of Experimental Immunology & Cancer, Faculty of Dentistry, University of Chile, Santiago, Chile
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
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da Silva CVF, Bacila Sade Y, Naressi Scapin SM, da Silva-Boghossian CM, de Oliveira Santos E. Comparative proteomics of saliva of healthy and gingivitis individuals from Rio de Janeiro. Proteomics Clin Appl 2023; 17:e2200098. [PMID: 36764829 DOI: 10.1002/prca.202200098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
PURPOSE In this work, we identified human and bacterial proteomes in the saliva from volunteers with gingivitis or healthy. EXPERIMENTAL DESIGN The reported population consisted of 18 volunteers (six with gingivitis and 12 healthy controls). Proteomics characterization was performed using a quantitative mass spectrometry method. RESULTS A total of 74 human and 116 bacterial proteins were identified in saliva. The major functional category that was modified in the human proteome was the immune response, followed by transport and protease inhibition. In the bacterial proteome, most of the proteins identified were from the Fusobacteria phylum, followed by Chlamydiae and Spirochaetes. CONCLUSIONS AND CLINICAL RELEVANCE We observed statistically relevant differences in the data between the groups. The 15 most important human proteins affecting the variation between case and control groups included cystatin S, alpha amylase, lactotransferrin, and negative elongation factor E. We found that bacterial proteins from Porphyromonas gingivalis and Fusobacterium nucleatum subsp. nucleatum related to the red and orange complexes were closely correlated with the occurrence of periodontal diseases.
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Affiliation(s)
- Carlos Vinicius Ferreira da Silva
- Faculdade de Ciências Biológicas e da Saúde, Universidade do Estado do Rio de Janeiro, Campus Zona Oeste (UERJ-ZO), Rio de Janeiro, RJ, Brazil
- Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Youssef Bacila Sade
- Instituto Nacional de Metrologia Qualidade e Tecnologia (INMETRO), Duque de Caxias, RJ, Brazil
| | | | | | - Eidy de Oliveira Santos
- Faculdade de Ciências Biológicas e da Saúde, Universidade do Estado do Rio de Janeiro, Campus Zona Oeste (UERJ-ZO), Rio de Janeiro, RJ, Brazil
- Programa da Pós-graduação em Biomedicina Translacional, Unigranrio-INMETRO-UERJ-ZO, Duque de Caxias, Brazil
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Halstenbach T, Nelson K, Iglhaut G, Schilling O, Fretwurst T. Impact of peri-implantitis on the proteome biology of crevicular fluid: A pilot study. J Periodontol 2023; 94:835-847. [PMID: 36585920 DOI: 10.1002/jper.22-0461] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/22/2022] [Accepted: 12/15/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND The proteome of the peri-implant crevicular fluid (PICF) has not been systematically investigated. The aim of the present study was to reveal the proteome biology of dental implants affected with peri-implantitis. METHODS Patients with at least one diseased implant were included (probing depth ≥6 mm, ≥3 mm peri-implant radiological bone loss). Using sterile paper strips, samples were collected from healthy implants (I), healthy teeth (T) and peri-implantitis affected implants (P). Proteome analysis was performed using liquid chromatography - tandem mass spectrometry (LC-MS/MS) and data independent acquisition, allowing the identification and quantification of human and bacterial proteins as well as semi-specific peptides. RESULTS A total of 38 samples from 14 patients were included in the study; 2332 different human proteins were identified across all samples. No differentially expressed proteins between T and I were found. Comparing P to I, 59 proteins were found upregulated and 31 downregulated in P with significance. Upregulated proteins included proinflammatory proteins such as immunoglobulins, dysferlin, and S100P, as well as antimicrobial proteins, for example, myeloperoxidase or azurocidin. Gene ontology analysis further revealed higher activity of immunological pathways. Proteolytic patterns indicated the activity of inflammatory proteins such as cathepsin G. A total of 334 bacterial proteins were identified and quantified. Peri-implantitis showed elevated proteolytic activity. CONCLUSION I and T share similarities in their proteome, while diseased implants deviate strongly from healthy conditions. The PICF proteome of peri-implantitis affected sites exhibits an inflammatory fingerprint, dominated by neutrophil activity when compared with healthy implants.
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Affiliation(s)
- Tim Halstenbach
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Katja Nelson
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Gerhard Iglhaut
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Tobias Fretwurst
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
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Casarin RCV, Salmon CR, Stolf CS, Paz HES, Rangel TP, Domingues RR, Pauletti BA, Paes-Leme AF, Araújo C, Santamaria MP, Ruiz KS, Monteiro MF. Salivary annexin A1: A candidate biomarker for periodontitis. J Clin Periodontol 2023; 50:942-951. [PMID: 36935103 DOI: 10.1111/jcpe.13803] [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: 05/26/2022] [Revised: 02/03/2023] [Accepted: 02/28/2023] [Indexed: 03/20/2023]
Abstract
AIM To compare the salivary proteomic profile of periodontitis-affected (PA) parents and their offspring to periodontally healthy (PH) dyads in the pursuit of possible biomarkers for early diagnosis of this disease. MATERIALS AND METHODS Unstimulated saliva samples collected from 17 pairs of PA or PH individuals and their children were submitted to mass spectrometric analyses followed by proteomic analyses. Primary PA fibroblasts were triggered towards having an inflammatory response, and an immunoenzymatic assay of its supernatant was performed to validate the obtained data. RESULTS ANXA1, KRT4, GSTP1, HPX, A2M and KRT13 were lower in PA parents and their children, and IGHG1, CSTB, KRT9, SMR3B, IGHG4 and SERPINA1 were higher. ANXA1 presented the highest fold change, 7.1 times less produced in children of PA parents, and was selected as a potential biomarker for periodontitis. The in vitro assay also showed lower ANXA1 production by cells of PA patients. CONCLUSION Before any clinical sign of periodontal loss, descendants of PA patients have an altered proteomic profile compared to PH individuals, presenting a lower abundance of ANXA1. This protein is suggested as a potential biomarker for periodontitis.
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Affiliation(s)
- Renato C V Casarin
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - Cristiane R Salmon
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - Camila S Stolf
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - Hélvis E S Paz
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - Thiago P Rangel
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - Romênia R Domingues
- Laboratory of Mass Spectrometry, Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Bianca A Pauletti
- Laboratory of Mass Spectrometry, Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Adriana F Paes-Leme
- Laboratory of Mass Spectrometry, Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Cassia Araújo
- Periodontics Division, Department of Diagnosis and Surgery, São José dos Campos School of Dentistry, São Paulo State University, São Paulo, Brazil
| | - Mauro P Santamaria
- Periodontics Division, Department of Diagnosis and Surgery, São José dos Campos School of Dentistry, São Paulo State University, São Paulo, Brazil
| | - Karina S Ruiz
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - Mabelle F Monteiro
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
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Lee J, Chang DS, Kim J, Hwang YS. Alpha-Defensin 1: An Emerging Periodontitis Biomarker. Diagnostics (Basel) 2023; 13:2143. [PMID: 37443537 DOI: 10.3390/diagnostics13132143] [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: 05/13/2023] [Revised: 06/08/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Background: Research on the development of reliable diagnostic targets is being conducted to overcome the high prevalence and difficulty in managing periodontitis. However, despite the development of various periodontitis target markers, their practical application has been limited due to poor diagnostic accuracy. In this study, we present an improved periodontitis diagnostic target and explore its role in periodontitis. Methods: Gingival crevicular fluid (GCF) was collected from healthy individuals and periodontitis patients, and proteomic analysis was performed. The target marker levels for periodontitis were quantified in GCF samples by enzyme-linked immunosorbent assay (ELISA). Mouse bone marrow-derived macrophages (BMMs) were used for the osteoclast formation assay. Results: LC-MS/MS analysis of whole GCF showed that the level of alpha-defensin 1 (DEFA-1) was higher in periodontitis GCF than in healthy GCF. The comparison of periodontitis target proteins galactin-10, ODAM, and azurocidin proposed in other studies found that the difference in DEFA-1 levels was the largest between healthy and periodontitis GCF, and periodontitis was more effectively distinguished. The differentiation of RANKL-induced BMMs into osteoclasts was significantly reduced by recombinant DEFA-1 (rDEFA-1). Conclusions: These results suggest the regulatory role of DEFA-1 in the periodontitis process and the relevance of DEFA-1 as a diagnostic target for periodontitis.
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Affiliation(s)
- Jisuk Lee
- Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Seongnam 13135, Republic of Korea
| | - Dong Sik Chang
- Department of Otorhinolaryngology, Eulji University Hospital, Eulji University, Daejeon 35233, Republic of Korea
| | - Junsu Kim
- Seoul Hana Dental Clinic, Seongnam 13636, Republic of Korea
| | - Young Sun Hwang
- Department of Dental Hygiene, College of Health Science, Eulji University, Seongnam 13135, Republic of Korea
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Xiao X, Xiao X, Liu Y, Sun H, Liu X, Guo Z, Li Q, Sun W. Metaproteomics Characterizes the Human Gingival Crevicular Fluid Microbiome Function in Periodontitis. J Proteome Res 2023. [PMID: 37327455 DOI: 10.1021/acs.jproteome.3c00143] [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: 06/18/2023]
Abstract
Periodontitis is the leading cause of tooth loss in adults worldwide. The human proteome and metaproteome characterization of periodontitis is not clearly understood. Gingival crevicular fluid samples were collected from eight periodontitis and eight healthy subjects. Both the human and microbial proteins were characterized by liquid chromatography coupled with high-resolution mass spectrometry. A total of 570 human proteins were found differentially expressed, which were primarily associated with inflammatory response, cell death, cellular junction, and fatty acid metabolism. For the metaproteome, 51 genera were identified, and 10 genera were found highly expressed in periodontitis, while 11 genera were downregulated. The analysis showed that microbial proteins related to butyrate metabolism were upregulated in periodontitis cases. In particular, correlation analysis showed that the expression of host proteins related to inflammatory response, cell death, cellular junction, and lipid metabolism correlates with the alteration of metaproteins, which reflect the changes of molecular function during the occurrence of periodontitis. This study showed that the gingival crevicular fluid human proteome and metaproteome could reflect the characteristics of periodontitis. This might benefit the understanding of the periodontitis mechanism.
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Affiliation(s)
- Xiaolian Xiao
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials, Xiamen Institute of Rare Earth Materials, Haixi Institute, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiaoping Xiao
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yaoran Liu
- Department of Stomatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Haidan Sun
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Xiaoyan Liu
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Zhengguang Guo
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Qian Li
- Department of Stomatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Wei Sun
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
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Bostanci N, Bao K. Proteome Analysis of Oral Biofluids in Periodontal Health and Disease Using Mass Spectrometry. Methods Mol Biol 2023; 2588:13-23. [PMID: 36418679 DOI: 10.1007/978-1-0716-2780-8_2] [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: 11/24/2022]
Abstract
Mass spectrometry-based proteomic approaches permit the high-throughput assessment of proteins from oral biofluids, therefore, allowing a deeper insight into the mechanistic study of periodontal disease. Here we describe an entire experimental design of proteomic workflow for oral biofluids, exemplified by saliva and gingival crevicular fluid collected from periodontal health or disease subjects and using a label-free quantification strategy for mass spectrometric data acquisition.
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Affiliation(s)
- Nagihan Bostanci
- Section of Oral Health and Periodontology, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Kai Bao
- Section of Oral Health and Periodontology, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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Toomey CE, Heywood WE, Evans JR, Lachica J, Pressey SN, Foti SC, Al Shahrani M, D’Sa K, Hargreaves IP, Heales S, Orford M, Troakes C, Attems J, Gelpi E, Palkovits M, Lashley T, Gentleman SM, Revesz T, Mills K, Gandhi S. Mitochondrial dysfunction is a key pathological driver of early stage Parkinson's. Acta Neuropathol Commun 2022; 10:134. [PMID: 36076304 PMCID: PMC9461181 DOI: 10.1186/s40478-022-01424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The molecular drivers of early sporadic Parkinson's disease (PD) remain unclear, and the presence of widespread end stage pathology in late disease masks the distinction between primary or causal disease-specific events and late secondary consequences in stressed or dying cells. However, early and mid-stage Parkinson's brains (Braak stages 3 and 4) exhibit alpha-synuclein inclusions and neuronal loss along a regional gradient of severity, from unaffected-mild-moderate-severe. Here, we exploited this spatial pathological gradient to investigate the molecular drivers of sporadic PD. METHODS We combined high precision tissue sampling with unbiased large-scale profiling of protein expression across 9 brain regions in Braak stage 3 and 4 PD brains, and controls, and verified these results using targeted proteomic and functional analyses. RESULTS We demonstrate that the spatio-temporal pathology gradient in early-mid PD brains is mirrored by a biochemical gradient of a changing proteome. Importantly, we identify two key events that occur early in the disease, prior to the occurrence of alpha-synuclein inclusions and neuronal loss: (i) a metabolic switch in the utilisation of energy substrates and energy production in the brain, and (ii) perturbation of the mitochondrial redox state. These changes may contribute to the regional vulnerability of developing alpha-synuclein pathology. Later in the disease, mitochondrial function is affected more severely, whilst mitochondrial metabolism, fatty acid oxidation, and mitochondrial respiration are affected across all brain regions. CONCLUSIONS Our study provides an in-depth regional profile of the proteome at different stages of PD, and highlights that mitochondrial dysfunction is detectable prior to neuronal loss, and alpha-synuclein fibril deposition, suggesting that mitochondrial dysfunction is one of the key drivers of early disease.
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Affiliation(s)
- Christina E. Toomey
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
| | - Wendy E. Heywood
- Translational Mass Spectrometry Research Group, Genetic & Genomic Medicine, Institute of Child Health, UCL, London, UK
| | - James R. Evans
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
| | - Joanne Lachica
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Sarah N. Pressey
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Sandrine C. Foti
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Mesfer Al Shahrani
- National Hospital for Neurology and Neurosurgery & Neurometabolic Unit, UCL Great Ormond Street Institute of Child Health, London, UK
- College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Karishma D’Sa
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
| | - Iain P. Hargreaves
- National Hospital for Neurology and Neurosurgery & Neurometabolic Unit, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Simon Heales
- National Hospital for Neurology and Neurosurgery & Neurometabolic Unit, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Michael Orford
- National Hospital for Neurology and Neurosurgery & Neurometabolic Unit, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
| | - Johannes Attems
- Newcastle Brain Tissue Resource, Institute of Neuroscience and Newcastle University Institute for Ageing, Newcastle upon Tyne, UK
| | - Ellen Gelpi
- Neurological Tissue Bank, University of Barcelona, Barcelona, Spain
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Miklos Palkovits
- Human Brain Tissue Bank, Budapest, Semmelweis University, Budapest, Hungary
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | | | - Tamas Revesz
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Kevin Mills
- Translational Mass Spectrometry Research Group, Genetic & Genomic Medicine, Institute of Child Health, UCL, London, UK
| | - Sonia Gandhi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
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11
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Proteomics Disclose the Potential of Gingival Crevicular Fluid (GCF) as a Source of Biomarkers for Severe Periodontitis. MATERIALS 2022; 15:ma15062161. [PMID: 35329612 PMCID: PMC8950923 DOI: 10.3390/ma15062161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/04/2022] [Accepted: 03/11/2022] [Indexed: 01/27/2023]
Abstract
Periodontal disease is a widespread disorder comprising gingivitis, a mild early gum inflammation, and periodontitis, a more severe multifactorial inflammatory disease that, if left untreated, can lead to the gradual destruction of the tooth-supporting apparatus. To date, effective etiopathogenetic models fully explaining the clinical features of periodontal disease are not available. Obviously, a better understanding of periodontal disease could facilitate its diagnosis and improve its treatment. The purpose of this study was to employ a proteomic approach to analyze the gingival crevicular fluid (GCF) of patients with severe periodontitis, in search of potential biomarkers. GCF samples, collected from both periodontally healthy sites (H-GCF) and the periodontal pocket (D-GCF), were subjected to a comparison analysis using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). A total of 26 significantly different proteins, 14 up-regulated and 12 down-regulated in D-GCF vs. H-GCF, were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The main expressed proteins were inflammatory molecules, immune responders, and host enzymes. Most of these proteins were functionally connected using the STRING analysis database. Once validated in a large scale-study, these proteins could represent a cluster of promising biomarkers capable of making a valuable contribution for a better assessment of periodontitis.
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12
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A comparative proteomic analysis to define the influencing factors on gingival crevicular fluid using LC-MS/MS. J Proteomics 2022; 252:104421. [PMID: 34801745 DOI: 10.1016/j.jprot.2021.104421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 12/18/2022]
Abstract
Gingival crevicular fluid (GCF) is a promising biofluid for disease identification and biomarker searching in periodontology. This study aimed to investigate the possible influencing factors, including tooth site, sex and age, on the normal GCF proteome. Forty periodontal healthy adults were randomly divided into a training group and a testing group. In the training group, GCF samples from 12 adults were analyzed using the iTRAQ 2D LC-MS/MS method. The influencing factors, tooth site (including periodontitis-susceptible and -insusceptible tooth sites), sex and age, and related differential proteins were defined and functionally annotated. The important differential proteins from 28 adults in the testing group were then validated by PRM analysis. An average of approximately 5 differential proteins were found between tooth sites of periodontitis-susceptible and -insusceptible sites. Eighty-five differentially expressed proteins were obtained between sexes in the young group, while only 7 sex-associated proteins were found in the old group. A total of 203 and 235 age-associated proteins were found in the male and female groups, respectively. The differential protein functional annotation showed that sex-related proteins were mainly related to immune function and metabolism, and age-related proteins were primarily associated with inflammation, lipid metabolism and immune function. In the testing group, a total of 4 sex-related proteins and 12 age-related proteins were validated by PRM analysis. SIGNIFICANCE: The influences of tooth site, sex and age in GCF proteomics in periodontal health were firstly analyzed using LC-MS/MS. Tooth site showed a small influence on the GCF proteome. The sex effect was significant in young adults, but its influence in old adults is small. Age is an important impact factor for the GCF proteome. These findings enrich the knowledge about the normal GCF proteome and might benefit future disease analyses.
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13
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Simancas Escorcia V, Guillou C, Abbad L, Derrien L, Rodrigues Rezende Costa C, Cannaya V, Benassarou M, Chatziantoniou C, Berdal A, Acevedo AC, Cases O, Cosette P, Kozyraki R. Pathogenesis of Enamel-Renal Syndrome Associated Gingival Fibromatosis: A Proteomic Approach. Front Endocrinol (Lausanne) 2021; 12:752568. [PMID: 34777248 PMCID: PMC8586505 DOI: 10.3389/fendo.2021.752568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/06/2021] [Indexed: 12/24/2022] Open
Abstract
The enamel renal syndrome (ERS) is a rare disorder featured by amelogenesis imperfecta, gingival fibromatosis and nephrocalcinosis. ERS is caused by bi-allelic mutations in the secretory pathway pseudokinase FAM20A. How mutations in FAM20A may modify the gingival connective tissue homeostasis and cause fibromatosis is currently unknown. We here analyzed conditioned media of gingival fibroblasts (GFs) obtained from four unrelated ERS patients carrying distinct mutations and control subjects. Secretomic analysis identified 109 dysregulated proteins whose abundance had increased (69 proteins) or decreased (40 proteins) at least 1.5-fold compared to control GFs. Proteins over-represented were mainly involved in extracellular matrix organization, collagen fibril assembly, and biomineralization whereas those under-represented were extracellular matrix-associated proteins. More specifically, transforming growth factor-beta 2, a member of the TGFβ family involved in both mineralization and fibrosis was strongly increased in samples from GFs of ERS patients and so were various known targets of the TGFβ signaling pathway including Collagens, Matrix metallopeptidase 2 and Fibronectin. For the over-expressed proteins quantitative RT-PCR analysis showed increased transcript levels, suggesting increased synthesis and this was further confirmed at the tissue level. Additional immunohistochemical and western blot analyses showed activation and nuclear localization of the classical TGFβ effector phospho-Smad3 in both ERS gingival tissue and ERS GFs. Exposure of the mutant cells to TGFB1 further upregulated the expression of TGFβ targets suggesting that this pathway could be a central player in the pathogenesis of the ERS gingival fibromatosis. In conclusion our data strongly suggest that TGFβ -induced modifications of the extracellular matrix contribute to the pathogenesis of ERS. To our knowledge this is the first proteomic-based analysis of FAM20A-associated modifications.
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Affiliation(s)
- Victor Simancas Escorcia
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Oral Molecular Pathophysiology, Paris, France
| | - Clément Guillou
- Normandie Université, PISSARO Proteomic Facility, Institute for Research and Innovation in Biomedicine (IRIB), Mont-Saint-Aignan, France
- Normandie Université, UMR670 Centre National de la Recherche Scientifique (CNRS), Mont-Saint-Aignan, France
| | - Lilia Abbad
- UMRS1155, INSERM, Sorbonne Université, Paris, France
| | - Louise Derrien
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Oral Molecular Pathophysiology, Paris, France
| | - Claudio Rodrigues Rezende Costa
- Oral Center for Inherited Diseases, University Hospital of Brasília, Oral Histopathology Laboratory, Department of Dentistry, Health Sciences Faculty, University of Brasília (UnB), Brasília, Brazil
| | - Vidjea Cannaya
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Oral Molecular Pathophysiology, Paris, France
| | - Mourad Benassarou
- Service de Chirurgie Maxillo-faciale et Stomatologie, Hôpital De la Pitié Salpétrière, Sorbonne Université, Paris, France
| | | | - Ariane Berdal
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Oral Molecular Pathophysiology, Paris, France
- Centre de Référence Maladies Rares (CRMR) O-RARES, Hôpital Rothshild, Unité de Formation et de Recherche (UFR) d’Odontologie-Garancière, Université de Paris, Paris, France
| | - Ana Carolina Acevedo
- Oral Center for Inherited Diseases, University Hospital of Brasília, Oral Histopathology Laboratory, Department of Dentistry, Health Sciences Faculty, University of Brasília (UnB), Brasília, Brazil
| | - Olivier Cases
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Oral Molecular Pathophysiology, Paris, France
| | - Pascal Cosette
- Normandie Université, PISSARO Proteomic Facility, Institute for Research and Innovation in Biomedicine (IRIB), Mont-Saint-Aignan, France
- Normandie Université, UMR670 Centre National de la Recherche Scientifique (CNRS), Mont-Saint-Aignan, France
| | - Renata Kozyraki
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Oral Molecular Pathophysiology, Paris, France
- Centre de Référence Maladies Rares (CRMR) O-RARES, Hôpital Rothshild, Unité de Formation et de Recherche (UFR) d’Odontologie-Garancière, Université de Paris, Paris, France
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14
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Xiao X, Song T, Xiao X, Liu Y, Sun H, Guo Z, Liu X, Shao C, Li Q, Sun W. A qualitative and quantitative analysis of the human gingival crevicular fluid proteome and metaproteome. Proteomics 2021; 21:e2000321. [PMID: 34464030 DOI: 10.1002/pmic.202000321] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 08/02/2021] [Accepted: 08/20/2021] [Indexed: 11/08/2022]
Abstract
Gingival crevicular fluid (GCF) is an integral part of oral fluid that plays a special role in maintaining the structure of junctional epithelium and defending against bacterial infection. In this study, we comprehensively analysed the composition of the human GCF proteome and metaproteome simultaneously to obtain multidimensional information about GCF. A total of 3680 human proteins (2540 with at least two unique peptides) were identified in the normal GCF sample, and their functions were mainly associated with immune function and inflammation. Among these proteins, 1874 proteins could be quantified by the iBAQ algorithm, and their abundances spanned a dynamic range of six orders of magnitude. For the GCF metaproteome, a total of 3082 proteins and 69 genera were found. In addition, 16 genera were not identified by GCF metagenomic analysis. Compared to the saliva metaproteome, 32 genera were found to be in common. The protein quantitative analysis showed that the abundance of GCF metaproteome contributed to approximately 4.17% of the total GCF proteome. The top three most abundant genera were Fusobacterium, Corynebacterium, and Leptotrichia. The above data will be useful for future research on GCF-related diseases.
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Affiliation(s)
- Xiaoping Xiao
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.,Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Tingting Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, China
| | - Xiaolian Xiao
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yaoran Liu
- Department of Dentistry, Chinese Academy of Medical Sciences Peking Union Medical College Hospital, Beijing, China
| | - Haidan Sun
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Zhengguang Guo
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiaoyan Liu
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Chen Shao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, China
| | - Qian Li
- Department of Dentistry, Chinese Academy of Medical Sciences Peking Union Medical College Hospital, Beijing, China
| | - Wei Sun
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
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15
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Pyruvate Kinase, Inflammation and Periodontal Disease. Pathogens 2021; 10:pathogens10070784. [PMID: 34206267 PMCID: PMC8308603 DOI: 10.3390/pathogens10070784] [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: 05/01/2021] [Revised: 06/08/2021] [Accepted: 06/20/2021] [Indexed: 11/17/2022] Open
Abstract
Pyruvate kinase (PK) is the final and rate-limiting enzyme in glycolysis. It has four isoforms PKM1, PKM2, PKL and PKR. PK can form homo tetramers, dimers or monomers. The tetrameric form has the most catalytic activity; however, the dimeric form has non-canonical functions that contribute to the inflammatory response, wound healing and cellular crosstalk. This brief review explores these functions and speculates on their role in periodontal disease.
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16
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Millard AR, Annis RG, Caffell AC, Dodd LL, Fischer R, Gerrard CM, Graves CP, Hendy J, Mackenzie L, Montgomery J, Nowell GM, Radini A, Beaumont J, Koon HEC, Speller CF. Scottish soldiers from the Battle of Dunbar 1650: A prosopographical approach to a skeletal assemblage. PLoS One 2020; 15:e0243369. [PMID: 33347451 PMCID: PMC7751964 DOI: 10.1371/journal.pone.0243369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 11/20/2020] [Indexed: 11/18/2022] Open
Abstract
After the Battle Dunbar between English and Scottish forces in 1650, captured Scottish soldiers were imprisoned in Durham and many hundreds died there within a few weeks. The partial skeletal remains of 28 of these men were discovered in 2013. Building on previous osteological work, here we report wide-ranging scientific studies of the remains to address the following questions: Did they have comparable diet, health and disease throughout their lives? Did they have common histories of movement (or lack of movement) during their childhoods? Can we create a collective biography of these men? Strontium and oxygen isotope analysis of tooth enamel investigated childhood movement. Carbon and nitrogen isotope analysis of incrementally sampled dentine addressed childhood diet and nutrition. Metaproteomic analysis of dental calculus investigated oral microbiomes and food residues; this was complemented by microscopic analysis of debris in calculus from ingested materials. Selected individuals were examined for dental microwear. The extent of hydroxylation of proline in collagen was examined as a potential biomarker for scurvy. An osteobiography for each man was created using the full range of data generated about him, and these were synthesised using an approach based on the historical method for a collective biography or prosopography. The childhood residences of the men were primarily within the Midland Valley of Scotland, though some spent parts of their childhood outside the British Isles. This is concordant with the known recruitment areas of the Scottish army in 1650. Their diets included oats, brassicas and milk but little seafood, as expected for lowland rather than highland diets of the period. Childhood periods of starvation or illness were almost ubiquitous, but not simultaneous, suggesting regionally variable food shortages in the 1620s and 1630s. It is likely there was widespread low-level scurvy, ameliorating in later years of life, which suggests historically unrecorded shortages of fruit and vegetables in the early 1640s. Almost all men were exposed to burnt plant matter, probably as inhaled soot, and this may relate to the high proportion of them with of sinusitis. Interpersonal violence causing skeletal trauma was rare. Based on commonalities in their osteobiographies, we argue that these men were drawn from the same stratum of society. This study is perhaps the most extensive to date of individuals from 17th century Scotland. Combined with a precise historical context it allows the lives of these men to be investigated and compared to the historical record with unprecedented precision. It illustrates the power of archaeological science methods to confirm, challenge and complement historical evidence.
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Affiliation(s)
- Andrew R. Millard
- Department of Archaeology, Durham University, Durham, United Kingdom
- * E-mail:
| | - Richard G. Annis
- Archaeological Services, Durham University, Durham, United Kingdom
| | - Anwen C. Caffell
- Department of Archaeology, Durham University, Durham, United Kingdom
| | - Laura L. Dodd
- Department of Archaeology, Durham University, Durham, United Kingdom
- KDK Archaeology Ltd, Leighton Buzzard, United Kingdom
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | | | - C. Pamela Graves
- Department of Archaeology, Durham University, Durham, United Kingdom
| | - Jessica Hendy
- Department of Archaeology, University of York, York, United Kingdom
| | - Lisa Mackenzie
- Department of Archaeology, University of York, York, United Kingdom
| | - Janet Montgomery
- Department of Archaeology, Durham University, Durham, United Kingdom
| | - Geoff M. Nowell
- Department of Earth Sciences, Durham University, Durham, United Kingdom
| | - Anita Radini
- Department of Archaeology, University of York, York, United Kingdom
| | - Julia Beaumont
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom
| | - Hannah E. C. Koon
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom
| | - Camilla F. Speller
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
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17
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Bostanci N, Grant M, Bao K, Silbereisen A, Hetrodt F, Manoil D, Belibasakis GN. Metaproteome and metabolome of oral microbial communities. Periodontol 2000 2020; 85:46-81. [PMID: 33226703 DOI: 10.1111/prd.12351] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The emergence of high-throughput technologies for the comprehensive measurement of biomolecules, also referred to as "omics" technologies, has helped us gather "big data" and characterize microbial communities. In this article, we focus on metaproteomic and metabolomic approaches that support hypothesis-driven investigations on various oral biologic samples. Proteomics reveals the working units of the oral milieu and metabolomics unveils the reactions taking place; and so these complementary techniques can unravel the functionality and underlying regulatory processes within various oral microbial communities. Current knowledge of the proteomic interplay and metabolic interactions of microorganisms within oral biofilm and salivary microbiome communities is presented and discussed, from both clinical and basic research perspectives. Communities indicative of, or from, health, caries, periodontal diseases, and endodontic lesions are represented. Challenges, future prospects, and examples of best practice are given.
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Affiliation(s)
- Nagihan Bostanci
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Melissa Grant
- Biological Sciences, School of Dentistry, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Kai Bao
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Angelika Silbereisen
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Franziska Hetrodt
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Manoil
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Georgios N Belibasakis
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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18
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Bostanci N, Silbereisen A, Bao K, Grossmann J, Nanni P, Fernandez C, Nascimento GG, Belibasakis GN, Lopez R. Salivary proteotypes of gingivitis tolerance and resilience. J Clin Periodontol 2020; 47:1304-1316. [PMID: 32777086 PMCID: PMC7692908 DOI: 10.1111/jcpe.13358] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 07/19/2020] [Accepted: 08/05/2020] [Indexed: 12/18/2022]
Abstract
Aim This study aimed to characterize the salivary proteome during the induction and resolution of gingival inflammation in the course of human experimental gingivitis (EG), and to cluster the proteomic profiles based on the clinically defined “slow” and “fast” response patterns. Materials and Methods A total of 50 unstimulated whole saliva were obtained from the EG model which was induced over 21 days (days 0, 7, 14 and 21), followed by a two‐week resolution phase (day 35). Label‐free quantitative proteomics using liquid chromatography–tandem mass spectrometry was applied. Regulated proteins were subject to Gene Ontology enrichment analysis. Results A total of 804 human proteins were quantified by ≥ 2 peptides. Principal component analysis depicted significant differences between “fast” and “slow” responders. Despite gingival and plaque scores being similar at baseline among the two groups, “fast” responders presented with 48 proteins that were at > 4‐fold higher levels than “slow” responders. These up‐regulated proteins showed enrichment in “antigen presentation” and “proteolysis.” Conclusions Together, these findings highlight the utility of integrative systems‐level quantitative proteomic approaches to unravel the molecular basis of “salivary proteotypes” associated with gingivitis dubbed as “fast” and “slow” responders. Hence, these differential responses may help prognosticate individual susceptibility to gingival inflammation.
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Affiliation(s)
- Nagihan Bostanci
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Angelika Silbereisen
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kai Bao
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Grossmann
- Functional Genomic Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Paolo Nanni
- Functional Genomic Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Claudia Fernandez
- Functional Genomic Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Gustavo G Nascimento
- Section of Periodontology, Department of Dentistry and Oral Health, Aarhus University, Aarhus, Denmark
| | - Georgios N Belibasakis
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rodrigo Lopez
- Section of Periodontology, Department of Dentistry and Oral Health, Aarhus University, Aarhus, Denmark
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19
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Mohd Nasri FA, Zainal Ariffin SH, Karsani SA, Megat Abdul Wahab R. Label-free quantitative proteomic analysis of gingival crevicular fluid to identify potential early markers for root resorption. BMC Oral Health 2020; 20:256. [PMID: 32917196 PMCID: PMC7488717 DOI: 10.1186/s12903-020-01246-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/03/2020] [Indexed: 12/24/2022] Open
Abstract
Background Orthodontically-induced root resorption is an iatrogenic effect and it cannot be examined regularly due to the harmful effects of sequential doses of radiation with more frequent radiography. This study aims to compare protein abundance (PA) of pre-treatment and during orthodontic treatment for root resorption and to determine potential early markers for root resorption. Methods Ten subjects (n = 10) who had upper and lower fixed appliances (MBT, 3 M Unitek, 0.022″ × 0.028″) were recruited for this study. Human gingival crevicular fluid (GCF) was obtained using periopaper strips at pre-treatment (T0), 1 month (T1), 3 months (T3), and 6 months (T6) of orthodontic treatment. Periapical radiographs of the upper permanent central incisors were taken at T0 and T6 to measure the amount of root resorption. Identification of changes in PA was performed using liquid chromatography-tandem mass spectrometry. Student’s t-test was then performed to determine the significance of the differences in protein abundance before and after orthodontic treatment. Results Our findings showed that all ten subjects had mild root resorption, with an average resorption length of 0.56 ± 0.30 mm. A total of 186 proteins were found to be commonly present at T0, T1, T3, and T6. There were significant changes in the abundance of 16 proteins (student’s t-test, p ≤ 0.05). The increased PA of S100A9, immunoglobulin J chain, heat shock protein 1A, immunoglobulin heavy variable 4–34 and vitronectin at T1 suggested a response to stress that involved inflammation during the early phase of orthodontic treatment. On the other hand, the increased PA of thymidine phosphorylase at T3 suggested growth promotion and, angiogenic and chemotactic activities. Conclusions The identified proteins can be potential early markers for root resorption based on the increase in their respective PA and predicted roles during the early phase of orthodontic treatment. Non-invasive detection of root resorption using protein markers as early as possible is extremely important as it can aid orthodontists in successful orthodontic treatment.
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Affiliation(s)
- Farah Amirah Mohd Nasri
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Shahrul Hisham Zainal Ariffin
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.,Malaysia Genome Institute (MGI), National Institute of Biotechnology Malaysia (NIBM), Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Saiful Anuar Karsani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Rohaya Megat Abdul Wahab
- Department of Family Oral Health, Faculty of Dentistry, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300, Kuala Lumpur, Malaysia.
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20
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Gingival Crevicular Fluid Peptidome Profiling in Healthy and in Periodontal Diseases. Int J Mol Sci 2020; 21:ijms21155270. [PMID: 32722327 PMCID: PMC7432128 DOI: 10.3390/ijms21155270] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/09/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
Given its intrinsic nature, gingival crevicular fluid (GCF) is an attractive source for the discovery of novel biomarkers of periodontal diseases. GCF contains antimicrobial peptides and small proteins which could play a role in specific immune-inflammatory responses to guarantee healthy gingival status and to prevent periodontal diseases. Presently, several proteomics studies have been performed leading to increased coverage of the GCF proteome, however fewer efforts have been done to explore its natural peptides. To fill such gap, this review provides an overview of the mass spectrometric platforms and experimental designs aimed at GCF peptidome profiling, including our own data and experiences gathered from over several years of matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI-TOF MS) based approach in this field. These tools might be useful for capturing snapshots containing diagnostic clinical information on an individual and population scale, which may be used as a specific code not only for the diagnosis of the nature or the stage of the inflammatory process in periodontal disease, but more importantly, for its prognosis, which is still an unmet medical need. As a matter of fact, current peptidomics investigations suffer from a lack of standardized procedures, posing a serious problem for data interpretation. Descriptions of the efforts to address such concerns will be highlighted.
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Proteome Analysis of Molecular Events in Oral Pathogenesis and Virus: A Review with a Particular Focus on Periodontitis. Int J Mol Sci 2020; 21:ijms21155184. [PMID: 32707841 PMCID: PMC7432693 DOI: 10.3390/ijms21155184] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/11/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Some systemic diseases are unquestionably related to periodontal health, as periodontal disease can be an extension or manifestation of the primary disease process. One example is spontaneous gingival bleeding, resulting from anticoagulant treatment for cardiac diseases. One important aspect of periodontal therapy is the care of patients with poorly controlled disease who require surgery, such as patients with uncontrolled diabetes. We reviewed research on biomarkers and molecular events for various diseases, as well as candidate markers of periodontal disease. Content of this review: (1) Introduction, (2) Periodontal disease, (3) Bacterial and viral pathogens associated with periodontal disease, (4) Stem cells in periodontal tissue, (5) Clinical applications of mass spectrometry using MALDI-TOF-MS and LC-MS/MS-based proteomic analyses, (6) Proteome analysis of molecular events in oral pathogenesis of virus in GCF, saliva, and other oral Components in periodontal disease, (7) Outlook for the future and (8) Conclusions. This review discusses proteome analysis of molecular events in the pathogenesis of oral diseases and viruses, and has a particular focus on periodontitis.
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Schaffner-Reckinger E, Machado RAC. The actin-bundling protein L-plastin-A double-edged sword: Beneficial for the immune response, maleficent in cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 355:109-154. [PMID: 32859369 DOI: 10.1016/bs.ircmb.2020.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The dynamic organization of the actin cytoskeleton into bundles and networks is orchestrated by a large variety of actin-binding proteins. Among them, the actin-bundling protein L-plastin is normally expressed in hematopoietic cells, where it is involved in the immune response. However, L-plastin is also often ectopically expressed in malignant cancer cells of non-hematopoietic origin and is even considered as a marker for cancer progression. Post-translational modification modulates L-plastin activity. In particular, L-plastin Ser5 phosphorylation has been shown to be important for the immune response in leukocytes as well as for invasion and metastasis formation of carcinoma cells. This chapter discusses the physiological and pathological role of L-plastin with a special focus on the importance of L-plastin Ser5 phosphorylation for the protein functions. The potential use of Ser5 phosphorylated L-plastin as a biomarker and/or therapeutic target will be evoked.
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Affiliation(s)
- Elisabeth Schaffner-Reckinger
- Cancer Cell Biology and Drug Discovery Group, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Raquel A C Machado
- Cancer Cell Biology and Drug Discovery Group, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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Rizal MI, Soeroso Y, Sulijaya B, Assiddiq BF, Bachtiar EW, Bachtiar BM. Proteomics approach for biomarkers and diagnosis of periodontitis: systematic review. Heliyon 2020; 6:e04022. [PMID: 32529063 PMCID: PMC7276445 DOI: 10.1016/j.heliyon.2020.e04022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/12/2020] [Accepted: 05/15/2020] [Indexed: 01/03/2023] Open
Abstract
Quantitative proteomic workflow based on mass spectrometry (MS) is recently developed by the researchers to screen for biomarkers in periodontal diseases comprising periodontitis. Periodontitis is known for chronic inflammatory disease characterized by progressive destruction of the tooth-supporting apparatus, yet has a lack of clear pathobiology based on a discrepancy between specified categories and diagnostic vagueness. The objective of this review was to outlined the accessible information related to proteomics studies on periodontitis. The Preferred Reporting Items for Systematical Reviews and Meta-Analysis (PRISMA) statement guides to acquaint proteomic analysis on periodontal diseases was applied. Three databases were used in this study, such as Pubmed, ScienceDirect and Biomed Central from 2009 up to November 2019. Proteomics analysis platforms that used in the studies were outlined. Upregulated and downregulated proteins findings data were found, in which could be suitable as candidate biomarkers for this disease.
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Affiliation(s)
- Muhammad Ihsan Rizal
- Oral Science Research Center, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia
| | - Yuniarti Soeroso
- Department of Periodontology, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia
| | - Benso Sulijaya
- Department of Periodontology, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia
| | | | - Endang W. Bachtiar
- Oral Science Research Center, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia
- Department of Oral Biology, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia
| | - Boy M. Bachtiar
- Oral Science Research Center, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia
- Department of Oral Biology, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia
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An Evidence-Based Update on the Molecular Mechanisms Underlying Periodontal Diseases. Int J Mol Sci 2020; 21:ijms21113829. [PMID: 32481582 PMCID: PMC7312805 DOI: 10.3390/ijms21113829] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/15/2022] Open
Abstract
Several investigators have reported about the intricate molecular mechanism underlying periodontal diseases (PD). Nevertheless, the role of specific genes, cells, or cellular mechanisms involved in the pathogenesis of periodontitis are still unclear. Although periodontitis is one of the most prevalent oral diseases globally, there are no pre-diagnostic markers or therapeutic targets available for such inflammatory lesions. A pivotal role is played by pro- and anti-inflammatory markers in modulating pathophysiological and physiological processes in repairing damaged tissues. In addition, effects on osteoimmunology is ever evolving due to the ongoing research in understanding the molecular mechanism lying beneath periodontal diseases. The aim of the current review is to deliver an evidence-based update on the molecular mechanism of periodontitis with a particular focus on recent developments. Reports regarding the molecular mechanism of these diseases have revealed unforeseen results indicative of the fact that significant advances have been made to the periodontal medicine over the past decade. There is integrated hypothesis-driven research going on. Although a wide picture of association of periodontal diseases with immune response has been further clarified with present ongoing research, small parts of the puzzle remain a mystery and require further investigations.
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Nguyen T, Sedghi L, Ganther S, Malone E, Kamarajan P, Kapila YL. Host-microbe interactions: Profiles in the transcriptome, the proteome, and the metabolome. Periodontol 2000 2020; 82:115-128. [PMID: 31850641 DOI: 10.1111/prd.12316] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Periodontal studies using transcriptomics, proteomics, and metabolomics encompass the collection of mRNA transcripts, proteins, and small-molecule chemicals in the context of periodontal health and disease. The number of studies using these approaches has significantly increased in the last decade and they have provided new insight into the pathogenesis and host-microbe interactions that define periodontal diseases. This review provides an overview of current molecular findings using -omic approaches that underlie periodontal disease, including modulation of the host immune response, tissue homeostasis, and complex metabolic processes of the host and the oral microbiome. Integration of these -omic approaches will broaden our perspective of the molecular mechanisms involved in periodontal disease, advancing and improving the diagnosis and treatment of various stages and forms of periodontal disease.
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Affiliation(s)
- Trang Nguyen
- School of Dentistry, University of California San Francisco, San Francisco, California, USA
| | - Lea Sedghi
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, California, USA
| | - Sean Ganther
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, California, USA
| | - Erin Malone
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, California, USA
| | - Pachiyappan Kamarajan
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, California, USA
| | - Yvonne L Kapila
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, California, USA
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Rosa N, Campos B, Esteves AC, Duarte AS, Correia MJ, Silva RM, Barros M. Tracking the functional meaning of the human oral-microbiome protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 121:199-235. [PMID: 32312422 DOI: 10.1016/bs.apcsb.2019.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The interactome - the network of protein-protein interactions (PPIs) within a cell or organism - is technically difficult to assess. Bioinformatic tools can, not only, identify potential PPIs that can be later experimentally validated, but also be used to assign functional meaning to PPIs. Saliva's potential as a non-invasive diagnostic fluid is currently being explored by several research groups. But, in order to fully attain its potential, it is necessary to achieve the full characterization of the mechanisms that take place within this ecosystem. The onset of omics technologies, and specifically of proteomics, delivered a huge set of data that is largely underexplored. Quantitative information relative to proteins within a given context (for example a given disease) can be used by computational algorithms to generate information regarding PPIs. These PPIs can be further analyzed concerning their functional meaning and used to identify potential biomarkers, therapeutic targets, defense and pathogenicity mechanisms. We describe a computational pipeline that can be used to identify and analyze PPIs between human and microbial proteins. The pipeline was tested within the scenario of human PPIs of systemic (Zika Virus infection) and of oral conditions (Periodontal disease) and also in the context of microbial interactions (Candida-Streptococcus) and showed to successfully predict functionally relevant PPIs. The pipeline can be applied to different scientific areas, such as pharmacological research, since a functional meaningful PPI network can provide insights on potential drug targets, and even new uses for existing drugs on the market.
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Affiliation(s)
- Nuno Rosa
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Bruno Campos
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Ana Cristina Esteves
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Ana Sofia Duarte
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Maria José Correia
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Raquel M Silva
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Marlene Barros
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
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Silbereisen A, Alassiri S, Bao K, Grossmann J, Nanni P, Fernandez C, Tervahartiala T, Nascimento GG, Belibasakis GN, Heikkinen A, Lopez R, Sorsa T, Bostanci N. Label‐Free Quantitative Proteomics versus Antibody‐Based Assays to Measure Neutrophil‐Derived Enzymes in Saliva. Proteomics Clin Appl 2020; 14:e1900050. [DOI: 10.1002/prca.201900050] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/20/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Angelika Silbereisen
- Section of Periodontology and Dental Prevention Division of Oral Diseases Department of Dental Medicine Karolinska Institutet Alfred Nobels allé 8 14152 Huddinge Stockholm Sweden
| | - Saeed Alassiri
- Department of Oral and Maxillofacial Diseases University of Helsinki Helsinki University Central Hospital P.O. Box 41 (Mannerheimintie 172) 00014 Helsinki Finland
| | - Kai Bao
- Section of Periodontology and Dental Prevention Division of Oral Diseases Department of Dental Medicine Karolinska Institutet Alfred Nobels allé 8 14152 Huddinge Stockholm Sweden
| | - Jonas Grossmann
- Functional Genomics Center Zurich ETH Zurich and University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Paolo Nanni
- Functional Genomics Center Zurich ETH Zurich and University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Claudia Fernandez
- Functional Genomics Center Zurich ETH Zurich and University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Taina Tervahartiala
- Department of Oral and Maxillofacial Diseases University of Helsinki Helsinki University Central Hospital P.O. Box 41 (Mannerheimintie 172) 00014 Helsinki Finland
| | - Gustavo G. Nascimento
- Section of Periodontology Department of Dentistry and Oral Health Aarhus University Vennelyst Boulevard 9 8000 Aarhus C Denmark
| | - Georgios N. Belibasakis
- Section of Periodontology and Dental Prevention Division of Oral Diseases Department of Dental Medicine Karolinska Institutet Alfred Nobels allé 8 14152 Huddinge Stockholm Sweden
| | - Anna‐Maria Heikkinen
- Department of Oral and Maxillofacial Diseases University of Helsinki Helsinki University Central Hospital P.O. Box 41 (Mannerheimintie 172) 00014 Helsinki Finland
| | - Rodrigo Lopez
- Section of Periodontology Department of Dentistry and Oral Health Aarhus University Vennelyst Boulevard 9 8000 Aarhus C Denmark
| | - Timo Sorsa
- Section of Periodontology and Dental Prevention Division of Oral Diseases Department of Dental Medicine Karolinska Institutet Alfred Nobels allé 8 14152 Huddinge Stockholm Sweden
- Department of Oral and Maxillofacial Diseases University of Helsinki Helsinki University Central Hospital P.O. Box 41 (Mannerheimintie 172) 00014 Helsinki Finland
| | - Nagihan Bostanci
- Section of Periodontology and Dental Prevention Division of Oral Diseases Department of Dental Medicine Karolinska Institutet Alfred Nobels allé 8 14152 Huddinge Stockholm Sweden
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Nalmpantis D, Gatou A, Fragkioudakis I, Margariti A, Skoura L, Sakellari D. Azurocidin in gingival crevicular fluid as a potential biomarker of chronic periodontitis. J Periodontal Res 2019; 55:209-214. [PMID: 31608993 DOI: 10.1111/jre.12703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/30/2019] [Accepted: 09/18/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Azurocidin is a neutrophil-derived protein in gingival crevicular fluid (GCF) which, according to relevant studies, might correlate with periodontal disease. The aim of the present study was to evaluate azurocidin as a potential biomarker for chronic periodontitis. MATERIAL AND METHODS One hundred and one patients participated in the study, divided into two groups. Forty-eight were included in the periodontally healthy group (HP) and fifty-three in the chronic periodontitis group (CP). Clinical indices included probing depth (PD), recession (REC), clinical attachment level (CAL), bleeding on probing (BOP) and plaque (PL). Pooled GCF samples were collected with paper strips, freezed in liquid nitrogen (-196°C), stored at -80°C, and the levels of azurocidin were analyzed with ELISA. Values were transformed and expressed for comparisons in pg/30 s sample. Statistical comparisons were performed using non-parametric tests (Mann-Whitney) at the 0.05 level. Furthermore, the diagnostic accuracy of the procedure was assessed with receiver operator characteristic curves (ROC), areas under the curve (AUC), and the Youden's J Index calculated. RESULTS Demographic data were comparable between the two groups. Clinical parameters and the levels of azurocidin were statistically significantly higher in the CP group when compared to the HP group (Mann-Whitney test, P < .05). Quantitative data from ELISA demonstrated a high diagnostic accuracy of azurocidin, with AUC calculated higher than 0.9 at the 0.000 level. CONCLUSION Azurocidin in GCF is a promising biomarker for periodontal disease. The results of the present study agree with previous studies in the literature showing an up-regulated trend in the levels of azurocidin in periodontitis patients.
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Affiliation(s)
- Dimitrios Nalmpantis
- Department of Preventive Dentistry, Periodontology and Implant Biology, Dental School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Asimina Gatou
- Department of Preventive Dentistry, Periodontology and Implant Biology, Dental School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Fragkioudakis
- Department of Preventive Dentistry, Periodontology and Implant Biology, Dental School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Apostolia Margariti
- Department of Microbiology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Lemonia Skoura
- Department of Microbiology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Sakellari
- Department of Preventive Dentistry, Periodontology and Implant Biology, Dental School, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Jiang R, Rong C, Ke R, Meng S, Yan X, Ke H, Wu S. Differential proteomic analysis of serum exosomes reveals alterations in progression of Parkinson disease. Medicine (Baltimore) 2019; 98:e17478. [PMID: 31593110 PMCID: PMC6799836 DOI: 10.1097/md.0000000000017478] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Exosomes are nanometer-sized vesicles with intercellular communication functions, and their encapsulated proteins may participate in the pathological process of neurodegenerative disorders. The aim of this study was to identify the protein changes of serum exosomes in Parkinson disease (PD) patients with different disease progress types, and to identify potential biomarkers. The exosomes of PD patients with different severity and healthy control group were isolated from serum. The exosome proteins were analyzed by mass spectrometry with label-free quantitative proteomics. A total of 429 proteins were identified, of which 14 were significantly different in mild and severe PD patients. The expression levels of 7 proteins, including pigmented epithelium-derived factor, afamin, apolipoprotein D and J, were significantly increased in PD patients. The expression levels of 7 proteins, including complement C1q and protein Immunoglobulin Lambda Variable 1-33 (IGLV1-33)Cluster -33, were decreased in PD patients. These differentially expressed proteins were analyzed by gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, which confirmed that the interaction between prion diseases and ECM receptors was the most significant pathways of enrichment. The changes of proteins and pathways may be related to the pathophysiological mechanism of PD. Therefore, some of these proteins could be considered as potential biomarkers for early PD diagnosis.
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Affiliation(s)
- Ruilai Jiang
- Department of Emergency, the Second People's Hospital of Lishui, Lishui, Zhejiang Province
| | - Chunjiao Rong
- Department of Emergency, the Second People's Hospital of Lishui, Lishui, Zhejiang Province
| | - Ronghu Ke
- Department of Plastic and Reconstructive Surgery
| | - Shuiyan Meng
- Department of Emergency, the Second People's Hospital of Lishui, Lishui, Zhejiang Province
| | - Xiumei Yan
- Department of Emergency, the Second People's Hospital of Lishui, Lishui, Zhejiang Province
| | - Honglin Ke
- Department of Emergency, Huashan Hospital, Fudan University School of Medicine, Shanghai, China
| | - Shaochang Wu
- Department of Emergency, the Second People's Hospital of Lishui, Lishui, Zhejiang Province
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Bostanci N, Bao K, Greenwood D, Silbereisen A, Belibasakis GN. Periodontal disease: From the lenses of light microscopy to the specs of proteomics and next-generation sequencing. Adv Clin Chem 2019; 93:263-290. [PMID: 31655732 DOI: 10.1016/bs.acc.2019.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Periodontal disease entails the inflammatory destruction of the tooth supporting (periodontal) tissues as a result of polymicrobial colonization of the tooth surface in the form of biofilms. Extensive data collected over the past decades on this chronic disease demonstrate that its progression is infrequent and episodic, and the susceptibility to it can vary among individuals. Physical assessments of previously occurring damage to periodontal tissues remain the cornerstone of detection and diagnosis, whereas traditionally used diagnostic procedures do neither identify susceptible individuals nor distinguish between disease-active and disease-inactive periodontal sites. Thus, more sensitive and accurate "measurable biological indicators" of periodontal diseases are needed in order to place diagnosis (e.g., the presence or stage) and management of the disease on a more rational less empirical basis. Contemporary "omics" technologies may help unlock the path to this quest. High throughput nucleic acid sequencing technologies have enabled us to examine the taxonomic distribution of microbial communities in oral health and disease, whereas proteomic technologies allowed us to decipher the molecular state of the host in disease, as well as the interactive cross-talk of the host with the microbiome. The newly established field of metaproteomics has enabled the identification of the repertoire of proteins that oral microorganisms use to compete or co-operate with each other. Vast such data is derived from oral biological fluids, including gingival crevicular fluid and saliva, which is progressively completed and catalogued as the analytical technologies and bioinformatics tools progressively advance. This chapter covers the current "omics"-derived knowledge on the microbiome, the host and their "interactome" with regard to periodontal diseases, and addresses challenges and opportunities ahead.
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Affiliation(s)
- Nagihan Bostanci
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Kai Bao
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David Greenwood
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Angelika Silbereisen
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Georgios N Belibasakis
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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Wen X, Franchi L, Chen F, Gu Y. Proteomic analysis of gingival crevicular fluid for novel biomarkers of pubertal growth peak. Eur J Orthod 2019; 40:414-422. [PMID: 29092020 DOI: 10.1093/ejo/cjx082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Detection of pubertal growth peak is vital in orthodontic treatment timing and planning. Gingival crevicular fluid (GCF) contains abundant proteins from different sources and is an ideal source of biomarkers. The aim of this research is to detect candidate GCF biomarkers of pubertal growth by tandem mass tags (TMT) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to help diagnosis and treatment planning of functional treatment. Methods Forty subjects were recruited and were divided into pubertal and post-pubertal groups according to cervical vertebral maturation method. GCF samples were collected by paper points. GCF proteome of pubertal and post-pubertal subjects was compared by TMT labelling coupled with LC-MS/MS. Results A total of 537 proteins were detected in GCF samples, with 183 proteins detected in GCF for the first time. These proteins were involved in processes of immune response, ion transport, and signal transduction. The GCF concentration of vitamin D binding protein (DBP) and seroserotransferrin (Tf) was significantly higher in pubertal than that in post-pubertal subjects. DBP and Tf, therefore, were considered to be candidate biomarkers of pubertal growth. This result was validated using GCF samples from new subjects (P < 0.05). Conclusion Our results indicate that TMT labelling coupled with LC-MS/MS were proved to be a useful method for proteomic analysis of GCF with high accuracy. The expression of DBP and Tf was increased in children at circumpubertal stage and can be considered candidate biomarkers of pubertal growth.
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Affiliation(s)
- Xi Wen
- Department of orthodontics, Peking University School and Hospital of Stomatology, Haidian District, PR. China.,National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Haidian District, PR. China
| | | | - Feng Chen
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Haidian District, PR. China.,Central Laboratory, Peking University School and Hospital of Stomatology, Haidian District, PR. China
| | - Yan Gu
- Department of orthodontics, Peking University School and Hospital of Stomatology, Haidian District, PR. China.,National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Haidian District, PR. China
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Acioglu C, Tuzuner MB, Serhatli M, Acilan C, Sahin B, Akgun E, Adiguzel Z, Gurel B, Baykal AT. A Proteomic Analysis of Mitochondrial Complex III Inhibition in SH-SY5Y Human Neuroblastoma Cell Line. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164615666180713110139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background and Objective: Antimycin A (AntA) is a potent Electron Transport System (ETS) inhibitor exerting its effect through inhibiting the transfer of the electrons by binding to the quinone reduction site of the cytochrome bc1 complex (Complex III), which is known to be impaired in Huntington’s Disease (HD). The current studies were undertaken to investigate the effect of complex III inhibition in the SH-SY5Y cell line to delineate the molecular and cellular processes, which may play a role in the pathogenesis of HD.
Methods:
We treated SH-SY5Y neuroblastoma cells with AntA in order to establish an in vitro mitochondrial dysfunction model for HD. Differential proteome analysis was performed by the nLCMS/ MS system. Protein expression was assessed by western blot analysis.
Results:
Thirty five differentially expressed proteins as compared to the vehicle-treated controls were detected. Functional pathway analysis indicated that proteins involved in ubiquitin-proteasomal pathway were up-regulated in AntA-treated SH-SY5Y neuroblastoma cells and the ubiquitinated protein accumulation was confirmed by immunoblotting. We found that Prothymosin α (ProT α) was downregulated. Furthermore, we demonstrated that nuclear factor erythroid 2-related factor 2 (Nrf2) protein expression was co-regulated with ProT α expression, hence knockdown of ProT α in SH-SY5Y cells decreased Nrf2 protein level.
Conclusion:
Our findings suggest that complex III impairment might downregulate ubiquitinproteasome function and NRF2/Keap1 antioxidant response. In addition, it is likely that downregulation of Nrf2 is due to the decreased expression of ProT α in AntA-treated SH-SY5Y cells. Our results could advance the understanding of mechanisms involved in neurodegenerative diseases.
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Affiliation(s)
- Cigdem Acioglu
- Department of Neurological Surgery, Reynolds Family Spine Laboratory, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, United States
| | - Mete Bora Tuzuner
- Research and Development Center, Acibadem Labmed Medical Laboratories, Istanbul, Turkey
| | - Muge Serhatli
- TUBITAK, Marmara Research Center, Genetic Engineering and Biotechnology Institute, 41470, Gebze, Kocaeli, Turkey
| | - Ceyda Acilan
- School of Medicine, Research Center for Translational Medicine, Koc University, Istanbul, Turkey
| | - Betul Sahin
- Research and Development Center, Acibadem Labmed Medical Laboratories, Istanbul, Turkey
| | - Emel Akgun
- Research and Development Center, Acibadem Labmed Medical Laboratories, Istanbul, Turkey
| | - Zelal Adiguzel
- TUBITAK, Marmara Research Center, Genetic Engineering and Biotechnology Institute, 41470, Gebze, Kocaeli, Turkey
| | - Busra Gurel
- Department of Medical Biochemistry, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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Tsuchida S, Satoh M, Takiwaki M, Nomura F. Current Status of Proteomic Technologies for Discovering and Identifying Gingival Crevicular Fluid Biomarkers for Periodontal Disease. Int J Mol Sci 2018; 20:ijms20010086. [PMID: 30587811 PMCID: PMC6337088 DOI: 10.3390/ijms20010086] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022] Open
Abstract
Periodontal disease is caused by bacteria in dental biofilms. To eliminate the bacteria, immune system cells release substances that inflame and damage the gums, periodontal ligament, or alveolar bone, leading to swollen bleeding gums, which is a sign of gingivitis. Damage from periodontal disease can cause teeth to loosen also. Studies have demonstrated the proteomic approach to be a promising tool for the discovery and identification of biochemical markers of periodontal diseases. Recently, many studies have applied expression proteomics to identify proteins whose expression levels are altered by disease. As a fluid lying in close proximity to the periodontal tissue, the gingival crevicular fluid (GCF) is the principal target in the search for periodontal disease biomarkers because its protein composition may reflect the disease pathophysiology. Biochemical marker analysis of GCF is effective for objective diagnosis in the early and advanced stages of periodontal disease. Periodontal diseases are also promising targets for proteomics, and several groups, including ours, have applied proteomics in the search for GCF biomarkers of periodontal diseases. This search is of continuing interest in the field of experimental and clinical periodontal disease research. In this article, we summarize the current situation of proteomic technologies to discover and identify GCF biomarkers for periodontal diseases.
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Affiliation(s)
- Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8677, Japan.
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8677, Japan.
| | - Masaki Takiwaki
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8677, Japan.
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8677, Japan.
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Marinho MC, Pacheco ABF, Costa GCV, Ortiz ND, Zajdenverg L, Sansone C. Quantitative gingival crevicular fluid proteome in type 2 diabetes mellitus and chronic periodontitis. Oral Dis 2018; 25:588-595. [PMID: 30362201 DOI: 10.1111/odi.12996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/01/2018] [Accepted: 10/16/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The aim of this study was to investigate the proteome of the gingival crevicular fluid comparing the relative abundance of proteins from type 2 diabetes mellitus (2DM) individuals and chronic periodontitis (CP) affected sites, subjects affected by both conditions and healthy individuals. MATERIAL AND METHODS Twenty individuals were equally allocated in four groups, 2DM with CP, 2DM periodontally healthy, CP without 2DM, and periodontally healthy without 2DM. The relative quantification of proteins was accessed with iTRAQ labeling and mass spectrometry. RESULTS AND CONCLUSION A total of 104 proteins showed significant differences in abundance in pairwise comparisons. Some presented different levels in all diseased groups as compared to control, either increasing (rap guanine nucleotide exchange factor, S100A8, S100A9, and immunoglobulins) or decreasing (actins, myristoylated alanine-rich C-kinase substrate, and glutathione S-transferase). Other differences were specific for a given condition: Titin, neutrophil elastase, and myeloperoxidase levels were higher in the DP group, cathelicidin antimicrobial peptide decreased in CP, and annexin decreased in DH. These differences in the proteome can provide clues for further studies that will validate the variation in their levels and their role in both diseases.
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Affiliation(s)
- Marcelo C Marinho
- Department of Dental Clinic, Division of Periodontology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Beatriz F Pacheco
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Giovani C V Costa
- Brazilian Doping Control Laboratory (LBCD/LADETEC/IQ), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nina D Ortiz
- Brazilian Doping Control Laboratory (LBCD/LADETEC/IQ), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lenita Zajdenverg
- Department of Internal Medicine, Section of Diabetes and Nutrology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carmelo Sansone
- Department of Dental Clinic, Division of Periodontology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Abstract
Ultrahigh performance liquid chromatography (UHPLC) uses small stationary-phase particle size (<2 μm) and high pressure in order to achieve rapid and efficient separations. The speed and high resolution of this method has made it a valuable tool for analyzing the complex glycosylation patterns found in post-translationally modified proteins. This article highlights the differences between UHPLC and HPLC and reviews recent UHPLC applications and developments for detecting glycosylated proteins (e.g., glycomics studies) and characterizing glycosylated pharmaceuticals (e.g., monoclonal antibodies).
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Bostanci N, Bao K, Li X, Maekawa T, Grossmann J, Panse C, Briones RA, Resuello RRG, Tuplano JV, Garcia CAG, Reis ES, Lambris JD, Hajishengallis G. Gingival Exudatome Dynamics Implicate Inhibition of the Alternative Complement Pathway in the Protective Action of the C3 Inhibitor Cp40 in Nonhuman Primate Periodontitis. J Proteome Res 2018; 17:3153-3175. [PMID: 30111112 DOI: 10.1021/acs.jproteome.8b00263] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Periodontitis is a prevalent chronic inflammatory disease associated with dysbiosis. Although complement inhibition has been successfully used to treat periodontitis in animal models, studies globally analyzing inflamed tissue proteins to glean insight into possible mechanisms of action are missing. Using quantitative shotgun proteomics, we aimed to investigate differences in composition of inflammatory gingival tissue exudate ("gingival crevicular fluid"; GCF), before and after local administration of an inhibitor of the central complement component, C3, in nonhuman primates. The C3 inhibitor, Cp40 (also known as AMY-101) was administered locally in the maxillary gingival tissue of cynomolgus monkeys with established periodontitis, either once a week (1×-treatment; n = 5 animals) or three times per week (3×-treatment; n = 10 animals), for 6 weeks followed by another 6 weeks of observation in the absence of treatment. 45 GCF samples were processed for FASP digestion and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Data were processed using the ProgenesisQI software. The statistical significance of differences between the groups was determined by RM-ANOVA, and a protein expression change was considered as a true regulation at >2-fold and p < 0.05. The human orthologues were subjected to Gene Ontology analyses using PANTHER. Data are available via ProteomeXchange with identifier PXD009502. 573 proteins with >2 peptides were longitudinally quantified. Both 3× and 1× administration of Cp40 resulted in significant down-regulation of dozens of proteins during the 6-week course of treatment as compared to baseline. Following drug withdrawal at 6 weeks, more than 50% of the down-regulated proteins showed increased levels at week 12. The top scored pathway was "complement activation, alternative pathway", and several proteins involved in this pathway were down-regulated at 6 weeks. We mapped the proteomic fingerprint changes in local tissue exudate of cynomolgus monkey periodontitis in response to C3 inhibition and identified the alternative pathway of complement activation and leukocyte degranulation as main targets, which are thus likely to play significant roles in periodontal disease pathogenesis. Label-free quantitative proteomics strategies utilizing GCF are powerful tools for the identification of treatment targets and providing insights into disease mechanisms.
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Affiliation(s)
- Nagihan Bostanci
- Division of Oral Diseases, Department of Dental Medicine , Karolinska Institutet , SE-171 77 Stockholm , Sweden
| | - Kai Bao
- Division of Oral Diseases, Department of Dental Medicine , Karolinska Institutet , SE-171 77 Stockholm , Sweden
| | - Xiaofei Li
- Department of Microbiology, School of Dental Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Tomoki Maekawa
- Department of Microbiology, School of Dental Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Jonas Grossmann
- Functional Genomics Centre Zurich , University of Zurich/ETH Zurich , 8006 Zurich , Switzerland
| | - Christian Panse
- Functional Genomics Centre Zurich , University of Zurich/ETH Zurich , 8006 Zurich , Switzerland
| | - Ruel A Briones
- Manila Central University , College of Dentistry , Caloocan City , 1400 Metro Manila , Philippines
| | - Ranillo R G Resuello
- Simian Conservation Breeding and Research Center (SICONBREC) , Makati City , 1213 Metro Manila , Philippines
| | - Joel V Tuplano
- Simian Conservation Breeding and Research Center (SICONBREC) , Makati City , 1213 Metro Manila , Philippines
| | - Cristina A G Garcia
- Manila Central University , College of Dentistry , Caloocan City , 1400 Metro Manila , Philippines
| | - Edimara S Reis
- Department of Pathology and Laboratory Medicine , University of Pennsylvania School of Medicine , Philadelphia , Pennsylvania 19104 , United States
| | - John D Lambris
- Department of Pathology and Laboratory Medicine , University of Pennsylvania School of Medicine , Philadelphia , Pennsylvania 19104 , United States
| | - George Hajishengallis
- Department of Microbiology, School of Dental Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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Hassan MN, Belibasakis GN, Gumus P, Öztürk VÖ, Emingil G, Bostanci N. Annexin-1 as a salivary biomarker for gingivitis during pregnancy. J Periodontol 2018; 89:875-882. [DOI: 10.1002/jper.17-0557] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/02/2018] [Accepted: 01/02/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Manar N. Hassan
- Center of Dental Medicine; University of Zürich; Zürich Switzerland
| | - Georgios N. Belibasakis
- Center of Dental Medicine; University of Zürich; Zürich Switzerland
- Department of Dental Medicine; Karolinska Institute; Stockholm Sweden
| | - Pinar Gumus
- Department of Periodontology; School of Dentistry; Ege University; IZMIR Turkey
| | - Veli Özgen Öztürk
- Department of Periodontology; School of Dentistry; Adnan Menderes University; Aydın Turkey
| | - Gulnur Emingil
- Department of Periodontology; School of Dentistry; Ege University; IZMIR Turkey
| | - Nagihan Bostanci
- Center of Dental Medicine; University of Zürich; Zürich Switzerland
- Department of Dental Medicine; Karolinska Institute; Stockholm Sweden
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Guzman YA, Sakellari D, Papadimitriou K, Floudas CA. High-throughput proteomic analysis of candidate biomarker changes in gingival crevicular fluid after treatment of chronic periodontitis. J Periodontal Res 2018; 53:853-860. [PMID: 29900535 DOI: 10.1111/jre.12575] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND AND OBJECTIVE Untargeted, high-throughput proteomics methodologies have great potential to aid in identifying biomarkers for the diagnosis of periodontal disease. The application of such methods to the discovery of candidate biomarkers for the resolution of periodontal inflammation after periodontal therapy has been investigated. MATERIAL AND METHODS Gingival crevicular fluid samples were collected from 10 patients diagnosed with chronic periodontitis at baseline and 1, 5, 9 and 13 weeks after completion of mechanical periodontal treatment. Clinical indices of periodontal disease, including probing depth, recession, clinical attachment level and bleeding on probing, were recorded at baseline and 13 weeks. Samples were analyzed using an online liquid chromatography-nanoelectrospray-hybrid ion trap-Orbitrap mass spectrometer. Spectra were processed with the PILOT_PROTEIN proteomics software suite. RESULTS Clinical parameters were significantly improved 13 weeks after treatment (Wilcoxon signed ranks test, P < .05). From the substantial number of identified proteins, a small subset was extracted by filter methods that included temporal pattern matching, logistic function fitting and mixed-integer linear optimization. This subset includes azurocidin, lysozyme C and myosin-9 as candidate biomarkers prominent at baseline and alpha-smooth muscle actin as prominent 13 weeks after treatment. Cross-validation studies yielded average predictive accuracy and area under the curve of 0.900 and 0.930, respectively. CONCLUSION High-throughput proteomic analysis can contribute to identifying endpoints of periodontal therapy. These candidate biomarkers should be evaluated for clinical efficacy.
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Affiliation(s)
- Y A Guzman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, USA.,Department of Chemical and Biological Engineering, Princeton University, Princeton, USA
| | - D Sakellari
- Department of Preventive Dentistry, Periodontology and Implant Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - K Papadimitriou
- Department of Preventive Dentistry, Periodontology and Implant Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - C A Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, USA
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Castagnola M, Scarano E, Passali GC, Messana I, Cabras T, Iavarone F, Di Cintio G, Fiorita A, De Corso E, Paludetti G. Salivary biomarkers and proteomics: future diagnostic and clinical utilities. ACTA OTORHINOLARYNGOLOGICA ITALICA 2018; 37:94-101. [PMID: 28516971 PMCID: PMC5463528 DOI: 10.14639/0392-100x-1598] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/12/2016] [Indexed: 12/16/2022]
Abstract
Saliva testing is a non-invasive and inexpensive test that can serve as a source of information useful for diagnosis of disease. As we enter the era of genomic technologies and -omic research, collection of saliva has increased. Recent proteomic platforms have analysed the human salivary proteome and characterised about 3000 differentially expressed proteins and peptides: in saliva, more than 90% of proteins in weight are derived from the secretion of three couples of "major" glands; all the other components are derived from minor glands, gingival crevicular fluid, mucosal exudates and oral microflora. The most common aim of proteomic analysis is to discriminate between physiological and pathological conditions. A proteomic protocol to analyze the whole saliva proteome is not currently available. It is possible distinguish two type of proteomic platforms: top-down proteomics investigates intact naturally-occurring structure of a protein under examination; bottom-up proteomics analyses peptide fragments after pre-digestion (typically with trypsin). Because of this heterogeneity, many different biomarkers may be proposed for the same pathology. The salivary proteome has been characterised in several diseases: oral squamous cell carcinoma and oral leukoplakia, chronic graft-versus-host disease Sjögren's syndrome and other autoimmune disorders such as SAPHO, schizophrenia and bipolar disorder, and genetic diseases like Down's Syndrome and Wilson disease. The results of research reported herein suggest that in the near future human saliva will be a relevant diagnostic fluid for clinical diagnosis and prognosis.
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Affiliation(s)
- M Castagnola
- Institute of Biochemistry and Clinical Biochemistry, Catholic University, Rome, Istituto di Chimica del Riconoscimento Molecolare C.N.R. Rome, Italy
| | - E Scarano
- Department of Head and Neck Surgery, "A. Gemelli" Hospital Foundation, Catholic University, Rome, Italy
| | - G C Passali
- Department of Head and Neck Surgery, "A. Gemelli" Hospital Foundation, Catholic University, Rome, Italy
| | - I Messana
- Life and Enviromental Sciences Department, University of Cagliari, and Istituto di Chimica del Riconoscimento Molecolare C.N.R. Rome, Italy
| | - T Cabras
- Life and Enviromental Sciences Department, University of Cagliari, Italy
| | - F Iavarone
- Institute of Biochemistry and Clinical Biochemistry, Catholic University, Rome, Italy
| | - G Di Cintio
- Department of Head and Neck Surgery, "A. Gemelli" Hospital Foundation, Catholic University, Rome, Italy
| | - A Fiorita
- Department of Head and Neck Surgery, "A. Gemelli" Hospital Foundation, Catholic University, Rome, Italy
| | - E De Corso
- Department of Head and Neck Surgery, "A. Gemelli" Hospital Foundation, Catholic University, Rome, Italy
| | - G Paludetti
- Department of Head and Neck Surgery, "A. Gemelli" Hospital Foundation, Catholic University, Rome, Italy
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Preianò M, Maggisano G, Murfuni MS, Villella C, Pelaia C, Montalcini T, Lombardo N, Pelaia G, Savino R, Terracciano R. An Analytical Method for Assessing Optimal Storage Conditions of Gingival Crevicular Fluid and Disclosing a Peptide Biomarker Signature of Gingivitis by MALDI-TOF MS. Proteomics Clin Appl 2018; 12:e1800005. [DOI: 10.1002/prca.201800005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/27/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Mariaimmacolata Preianò
- Department of Health Sciences; Laboratory of Mass Spectrometry and Proteomics; University “Magna Graecia”; Catanzaro 88100 Italy
| | - Giuseppina Maggisano
- Department of Health Sciences; Laboratory of Mass Spectrometry and Proteomics; University “Magna Graecia”; Catanzaro 88100 Italy
| | - Maria Stella Murfuni
- Department of Health Sciences; Laboratory of Mass Spectrometry and Proteomics; University “Magna Graecia”; Catanzaro 88100 Italy
| | - Chiara Villella
- Department of Health Sciences; Laboratory of Mass Spectrometry and Proteomics; University “Magna Graecia”; Catanzaro 88100 Italy
| | - Corrado Pelaia
- Department of Medical and Surgical Sciences; University “Magna Graecia”; Catanzaro 88100 Italy
| | - Tiziana Montalcini
- Department of Experimental and Clinical Medicine; University “Magna Graecia”; Catanzaro 88100 Italy
| | - Nicola Lombardo
- Department of Medical and Surgical Sciences; University “Magna Graecia”; Catanzaro 88100 Italy
| | - Girolamo Pelaia
- Department of Medical and Surgical Sciences; University “Magna Graecia”; Catanzaro 88100 Italy
| | - Rocco Savino
- Department of Health Sciences; Laboratory of Mass Spectrometry and Proteomics; University “Magna Graecia”; Catanzaro 88100 Italy
| | - Rosa Terracciano
- Department of Health Sciences; Laboratory of Mass Spectrometry and Proteomics; University “Magna Graecia”; Catanzaro 88100 Italy
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Bostanci N, Selevsek N, Wolski W, Grossmann J, Bao K, Wahlander A, Trachsel C, Schlapbach R, Öztürk VÖ, Afacan B, Emingil G, Belibasakis GN. Targeted Proteomics Guided by Label-free Quantitative Proteome Analysis in Saliva Reveal Transition Signatures from Health to Periodontal Disease. Mol Cell Proteomics 2018; 17:1392-1409. [PMID: 29610270 DOI: 10.1074/mcp.ra118.000718] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 03/28/2018] [Indexed: 12/18/2022] Open
Abstract
Periodontal diseases are among the most prevalent worldwide, but largely silent, chronic diseases. They affect the tooth-supporting tissues with multiple ramifications on life quality. Their early diagnosis is still challenging, due to lack of appropriate molecular diagnostic methods. Saliva offers a non-invasively collectable reservoir of clinically relevant biomarkers, which, if utilized efficiently, could facilitate early diagnosis and monitoring of ongoing disease. Despite several novel protein markers being recently enlisted by discovery proteomics, their routine diagnostic application is hampered by the lack of validation platforms that allow for rapid, accurate and simultaneous quantification of multiple proteins in large cohorts. Here we carried out a pipeline of two proteomic platforms; firstly, we applied open ended label-free quantitative (LFQ) proteomics for discovery in saliva (n = 67, including individuals with health, gingivitis, and periodontitis), followed by selected-reaction monitoring (SRM)-targeted proteomics for validation in an independent cohort (n = 82). The LFQ platform led to the discovery of 119 proteins with at least 2-fold significant difference between health and disease. The 65 proteins chosen for the subsequent SRM platform included 50 functionally related proteins derived from the significantly enriched processes of the LFQ data, 11 from literature-mining, and four house-keeping ones. Among those, 60 were reproducibly quantifiable proteins (92% success rate), represented by a total of 143 peptides. Machine-learning modeling led to a narrowed-down panel of five proteins of high predictive value for periodontal diseases with maximum area under the receiver operating curve >0.97 (higher in disease: Matrix metalloproteinase-9, Ras-related protein-1, Actin-related protein 2/3 complex subunit 5; lower in disease: Clusterin, Deleted in Malignant Brain Tumors 1). This panel enriches the pool of credible clinical biomarker candidates for diagnostic assay development. Yet, the quantum leap brought into the field of periodontal diagnostics by this study is the application of the biomarker discovery-through-verification pipeline, which can be used for validation in further cohorts.
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Affiliation(s)
- Nagihan Bostanci
- From the ‡Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden;
| | - Nathalie Selevsek
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Witold Wolski
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Jonas Grossmann
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Kai Bao
- From the ‡Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Asa Wahlander
- ¶AstraZeneca Translational Biomarkers and Bioanalysis, Drug Safety and Metabolism, Innovative Medicines, Mölndal, Sweden
| | - Christian Trachsel
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Ralph Schlapbach
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Veli Özgen Öztürk
- ‖Department of Periodontology, School of Dentistry, Adnan Menderes University, Aydin, Turkey
| | - Beral Afacan
- ‖Department of Periodontology, School of Dentistry, Adnan Menderes University, Aydin, Turkey
| | - Gulnur Emingil
- **Department of Periodontology, School of Dentistry, Ege University, Izmir, Turkey
| | - Georgios N Belibasakis
- From the ‡Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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Ghallab NA. Diagnostic potential and future directions of biomarkers in gingival crevicular fluid and saliva of periodontal diseases: Review of the current evidence. Arch Oral Biol 2018; 87:115-124. [DOI: 10.1016/j.archoralbio.2017.12.022] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 12/04/2017] [Accepted: 12/21/2017] [Indexed: 11/25/2022]
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Lira-Junior R, Öztürk VÖ, Emingil G, Bostanci N, Boström EA. Salivary and Serum Markers Related to Innate Immunity in Generalized Aggressive Periodontitis. J Periodontol 2017; 88:1339-1347. [DOI: 10.1902/jop.2017.170287] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ronaldo Lira-Junior
- Department of Dental Medicine, Division of Periodontology, Karolinska Institute, Stockholm, Sweden
- Department of Periodontology, Faculty of Odontology, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Veli Özgen Öztürk
- Department of Periodontology, School of Dentistry, Adnan Menderes University, Aydın, Turkey
| | - Gulnur Emingil
- Department of Periodontology, School of Dentistry, Ege University, Izmir, Turkey
| | - Nagihan Bostanci
- Department of Dental Medicine, Division of Periodontology, Karolinska Institute, Stockholm, Sweden
| | - Elisabeth A. Boström
- Department of Dental Medicine, Division of Periodontology, Karolinska Institute, Stockholm, Sweden
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Bostanci N, Belibasakis GN. Gingival crevicular fluid and its immune mediators in the proteomic era. Periodontol 2000 2017; 76:68-84. [DOI: 10.1111/prd.12154] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2016] [Indexed: 12/11/2022]
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45
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Batschkus S, Cingoez G, Urlaub H, Miosge N, Kirschneck C, Meyer-Marcotty P, Lenz C. A new albumin-depletion strategy improves proteomic research of gingival crevicular fluid from periodontitis patients. Clin Oral Investig 2017; 22:1375-1384. [DOI: 10.1007/s00784-017-2213-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 09/12/2017] [Indexed: 01/17/2023]
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46
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Mackie M, Hendy J, Lowe AD, Sperduti A, Holst M, Collins MJ, Speller CF. Preservation of the metaproteome: variability of protein preservation in ancient dental calculus. SCIENCE AND TECHNOLOGY OF ARCHAEOLOGICAL RESEARCH 2017; 3:74-86. [PMID: 29098079 PMCID: PMC5633013 DOI: 10.1080/20548923.2017.1361629] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/16/2017] [Indexed: 05/25/2023]
Abstract
Proteomic analysis of dental calculus is emerging as a powerful tool for disease and dietary characterisation of archaeological populations. To better understand the variability in protein results from dental calculus, we analysed 21 samples from three Roman-period populations to compare: 1) the quantity of extracted protein; 2) the number of mass spectral queries; and 3) the number of peptide spectral matches and protein identifications. We found little correlation between the quantity of calculus analysed and total protein identifications, as well as no systematic trends between site location and protein preservation. We identified a wide range of individual variability, which may be associated with the mechanisms of calculus formation and/or post-depositional contamination, in addition to taphonomic factors. Our results suggest dental calculus is indeed a stable, long-term reservoir of proteins as previously reported, but further systematic studies are needed to identify mechanisms associated with protein entrapment and survival in dental calculus.
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Affiliation(s)
- Meaghan Mackie
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Abigail D. Lowe
- BioArCh, Department of Archaeology, University of York, York, UK
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | - Malin Holst
- BioArCh, Department of Archaeology, University of York, York, UK
- York Osteoarchaeology Ltd
| | - Matthew J. Collins
- BioArCh, Department of Archaeology, University of York, York, UK
- EvoGenomics Section, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Barros SP, Williams R, Offenbacher S, Morelli T. Gingival crevicular fluid as a source of biomarkers for periodontitis. Periodontol 2000 2017; 70:53-64. [PMID: 26662482 DOI: 10.1111/prd.12107] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2015] [Indexed: 12/12/2022]
Abstract
In evaluating the pathogenesis of periodontal diseases, the diagnostic potential of gingival crevicular fluid has been extensively explored during the last twenty years, from initially just confirming health and disease states to more recently investigating it as a potential prognostic tool. As host susceptibility is a critical determinant in periodontal disease pathogenesis, the inflammatory mediator levels present in gingival crevicular fluid represent relevant risk indicators for disease activity. Considerable work has been carried out to identify the many different cytokine inflammatory pathways and microbial stimuli that are associated with periodontal disease pathogenesis. Now, 'omics' approaches aim to summarize how these pathways interact and probably converge to create critical inflammatory networks. More recently, gingival crevicular fluid metabolomics appears promising as an additional diagnostic method. Biofilm structure and the host inflammatory response to the microbial challenge may induce specific inflammatory signatures. Host genetics and epigenetics may also modulate microbial colonization, adding to the multiplicity of potential causal pathways. Omics analyses of gingival crevicular fluid, measuring microbial and host interactions in association with the onset and progression of periodontal diseases, still show the potential to expand the landscape for the discovery of diagnostic, prognostic and therapeutic markers.
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Yaprak E, Kasap M, Akpınar G, Kayaaltı-Yüksek S, Sinanoğlu A, Guzel N, Demirturk Kocasarac H. The prominent proteins expressed in healthy gingiva: a pilot exploratory tissue proteomics study. Odontology 2017; 106:19-28. [DOI: 10.1007/s10266-017-0302-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/09/2017] [Indexed: 12/31/2022]
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Bostanci N, Bao K. Contribution of proteomics to our understanding of periodontal inflammation. Proteomics 2017; 17. [DOI: 10.1002/pmic.201500518] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/15/2016] [Accepted: 12/15/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Nagihan Bostanci
- Department of Dental Medicine; Karolinska Institute; Huddinge Sweden
| | - Kai Bao
- Division of Oral Microbiology and Immunology; Institute of Oral Biology; Center of Dental Medicine; University of Zürich; Zürich Switzerland
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ŞAHİN B, BAYKAL AT. Proteomics analysis of mitochondrial dysfunction triggered by complex specific electron transport chain inhibitors reveals common pathways involving protein misfolding in an SH-SY5Y in vitro cell model. Turk J Biol 2017. [DOI: 10.3906/biy-1702-44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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