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Lieske B, Moszka N, Borof K, Petersen EL, Jagemann B, Ebinghaus M, Beikler T, Heydecke G, Aarabi G, Zyriax BC. Association between an Anti-Inflammatory Dietary Score and Periodontitis-Evidence from the Population-Based Hamburg City Health Study. Nutrients 2023; 15:3235. [PMID: 37513653 PMCID: PMC10386141 DOI: 10.3390/nu15143235] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
While the effects of dietary patterns on cardiovascular risk and diabetes have been well studied, the evidence is scarce as to which diet has the greatest anti-inflammatory potential and how dietary patterns are associated with periodontitis. In the Hamburg City Health Study (HCHS), we developed an anti-inflammatory dietary score using a data-driven approach based on the relationship of relevant selected food groups with inflammatory biomarkers (hsCRP and IL-6). The aim of this cross-sectional study was to evaluate the association between the anti-inflammatory dietary score and the incidence of periodontitis in Hamburg, Germany. A total of n = 5642 participants fit the required inclusion criteria and were selected for analysis. Periodontal disease was assessed using probing depth, gingival recession, and bleeding on probing. Dietary intake was measured using a food frequency questionnaire (FFQ). A self-developed anti-inflammatory dietary score served as the key explanatory variable. Higher scores reflected lower inflammatory processes (measured through the biomarkers hsCRP and IL-6). Several covariates were included in the regression analysis. Regressions revealed that a higher anti-inflammatory dietary score was significantly associated with lower odds to be affected by periodontal disease in an unadjusted model (OR 0.86, 95% CI 0.82-0.89, p < 0.001) and in an adjusted model (age, sex, smoking, diabetes, hypertension, and physical activity) (OR 0.93, 95% CI 0.89-0.98, p = 0.003). Our study demonstrated a significant inverse association between an anti-inflammatory dietary score and periodontitis. Individuals with higher intake of proinflammatory nutrition should be specifically addressed to avoid periodontitis.
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Affiliation(s)
- Berit Lieske
- Department of Periodontics, Preventive and Restorative Dentistry, Center for Dental and Oral Medicine, University Medical Center Hamburg Eppendorf, 20246 Hamburg, Germany
- Midwifery Science-Health Care Research and Prevention, Research Group Preventive Medicine and Nutrition, Institute for Health Service Research in Dermatology and Nursing (IVDP), University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Nina Moszka
- Department of Periodontics, Preventive and Restorative Dentistry, Center for Dental and Oral Medicine, University Medical Center Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Katrin Borof
- Department of Periodontics, Preventive and Restorative Dentistry, Center for Dental and Oral Medicine, University Medical Center Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Elina Larissa Petersen
- Population Health Research Department, University Heart and Vascular Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Department of Cardiology, University Heart and Vascular Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Bettina Jagemann
- Midwifery Science-Health Care Research and Prevention, Research Group Preventive Medicine and Nutrition, Institute for Health Service Research in Dermatology and Nursing (IVDP), University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Merle Ebinghaus
- Midwifery Science-Health Care Research and Prevention, Research Group Preventive Medicine and Nutrition, Institute for Health Service Research in Dermatology and Nursing (IVDP), University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Thomas Beikler
- Department of Periodontics, Preventive and Restorative Dentistry, Center for Dental and Oral Medicine, University Medical Center Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Guido Heydecke
- Department of Prosthetic Dentistry, Center for Dental and Oral Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Ghazal Aarabi
- Department of Periodontics, Preventive and Restorative Dentistry, Center for Dental and Oral Medicine, University Medical Center Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Birgit-Christiane Zyriax
- Midwifery Science-Health Care Research and Prevention, Research Group Preventive Medicine and Nutrition, Institute for Health Service Research in Dermatology and Nursing (IVDP), University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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Yang B, Chen Z, Huang Y, Han G, Li W. Identification of potential biomarkers and analysis of prognostic values in head and neck squamous cell carcinoma by bioinformatics analysis. Onco Targets Ther 2017; 10:2315-2321. [PMID: 28490889 PMCID: PMC5414612 DOI: 10.2147/ott.s135514] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The purpose of this study was to find disease-associated genes and potential mechanisms in head and neck squamous cell carcinoma (HNSCC) with deoxyribonucleic acid microarrays. The gene expression profiles of GSE6791 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were obtained with packages in R language and STRING constructed protein–protein interaction (PPI) network of the DEGs with combined score >0.8. Subsequently, module analysis of the PPI network was performed by Molecular Complex Detection plugin and functions and pathways of the hub gene in subnetwork were studied. Finally, overall survival analysis of hub genes was verified in TCGA HNSCC cohort. A total of 811 DEGs were obtained, which were mainly enriched in the terms related to extracellular matrix (ECM)–receptor interaction, ECM structural constituent, and ECM organization. A PPI network was constructed, consisting of 401 nodes and 1,254 edges and 15 hub genes with high degrees in the network. High expression of 4 genes of the 15 genes was associated with poor OS of patients in HNSCC, including PSMA7, ITGA6, ITGB4, and APP. Two significant modules were detected from the PPI network, and the enriched functions and pathways included proteasome, ECM organization, and ECM–receptor interaction. In conclusion, we propose that PSMA7, ITGA6, ITGB4, and APP may be further explored as potential biomarkers to aid HNSCC diagnosis and treatment.
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Affiliation(s)
- Bo Yang
- Department of Oral and Maxillofacial Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Zhifeng Chen
- Department of Oral and Maxillofacial Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yu Huang
- Department of Oral and Maxillofacial Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Guoxu Han
- Department of Oral and Maxillofacial Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Weizhong Li
- Department of Oral and Maxillofacial Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
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Fu S, Liu X, Luo M, Xie K, Nice EC, Zhang H, Huang C. Proteogenomic studies on cancer drug resistance: towards biomarker discovery and target identification. Expert Rev Proteomics 2017; 14:351-362. [PMID: 28276747 DOI: 10.1080/14789450.2017.1299006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Chemoresistance is a major obstacle for current cancer treatment. Proteogenomics is a powerful multi-omics research field that uses customized protein sequence databases generated by genomic and transcriptomic information to identify novel genes (e.g. noncoding, mutation and fusion genes) from mass spectrometry-based proteomic data. By identifying aberrations that are differentially expressed between tumor and normal pairs, this approach can also be applied to validate protein variants in cancer, which may reveal the response to drug treatment. Areas covered: In this review, we will present recent advances in proteogenomic investigations of cancer drug resistance with an emphasis on integrative proteogenomic pipelines and the biomarker discovery which contributes to achieving the goal of using precision/personalized medicine for cancer treatment. Expert commentary: The discovery and comprehensive understanding of potential biomarkers help identify the cohort of patients who may benefit from particular treatments, and will assist real-time clinical decision-making to maximize therapeutic efficacy and minimize adverse effects. With the development of MS-based proteomics and NGS-based sequencing, a growing number of proteogenomic tools are being developed specifically to investigate cancer drug resistance.
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Affiliation(s)
- Shuyue Fu
- a State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Xiang Liu
- b Department of Pathology , Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital , Chengdu , P.R. China
| | - Maochao Luo
- c West China School of Public Health, Sichuan University , Chengdu , P.R.China
| | - Ke Xie
- d Department of Oncology , Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital , Chengdu , P.R. China
| | - Edouard C Nice
- e Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- f School of Medicine , Yangtze University , P. R. China
| | - Canhua Huang
- a State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
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Gong C, Sun S, Liu B, Wang J, Chen X. Identification of potential therapeutic target genes, key miRNAs and mechanisms in oral lichen planus by bioinformatics analysis. Arch Oral Biol 2017; 78:122-128. [PMID: 28237528 DOI: 10.1016/j.archoralbio.2017.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 11/16/2022]
Abstract
The study aimed to identify the potential target genes and key miRNAs as well as to explore the underlying mechanisms in the pathogenesis of oral lichen planus (OLP) by bioinformatics analysis. The microarray data of GSE38617 were downloaded from Gene Expression Omnibus (GEO) database. A total of 7 OLP and 7 normal samples were used to identify the differentially expressed genes (DEGs) and miRNAs. The DEGs were then performed functional enrichment analyses. Furthermore, DEG-miRNA network and miRNA-function network were constructed by Cytoscape software. Total 1758 DEGs (598 up- and 1160 down-regulated genes) and 40 miRNAs (17 up- and 23 down-regulated miRNAs) were selected. The up-regulated genes were related to nuclear factor-Kappa B (NF-κB) signaling pathway, while down-regulated genes were mainly enriched in the function of ribosome. Tumor necrosis factor (TNF), caspase recruitment domain family, member 11 (CARD11) and mitochondrial ribosomal protein (MRP) genes were identified in these functions. In addition, miR-302 was a hub node in DEG-miRNA network and regulated cyclin D1 (CCND1). MiR-548a-2 was the key miRNA in miRNA-function network by regulating multiple functions including ribosomal function. The NF-κB signaling pathway and ribosome function may be the pathogenic mechanisms of OLP. The genes such as TNF, CARD11, MRP genes and CCND1 may be potential therapeutic target genes in OLP. MiR-548a-2 and miR-302 may play important roles in OLP development.
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Affiliation(s)
- Cuihua Gong
- Department of General Emergency, Dalian Hospital of Stomatology, Dalian, Liaoning, 116021, China
| | - Shangtong Sun
- Department of Periodontal Mucosa, Dalian Hospital of Stomatology, Dalian, Liaoning, 116021, China
| | - Bing Liu
- Department of Orthopedic Trauma, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, China
| | - Jing Wang
- Department of Cosmetic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, China.
| | - Xiaodong Chen
- Department of Reconstruction Surgery, Dalian Hospital of Stomatology, No. 935 Changjiang Rd, Shahekou District, Dalian, Liaoning, 116021, China.
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Nicolini C, Bragazzi N, Peshkova E. Nanogenomics and nanoproteomics for personalized nanotheranostics for oral and colorectal cancer. Per Med 2015; 13:9-11. [PMID: 29749864 DOI: 10.2217/pme.15.46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Claudio Nicolini
- Fondazione ELBA Nicolini, Pradalunga, Largo Redaelli 7, Bergamo 24100, Italy.,Biophysics & Nanobiotechnologies Laboratory, Via Antonio Pastore 3, Genoa 16132, Italy
| | - Nicola Bragazzi
- Fondazione ELBA Nicolini, Pradalunga, Largo Redaelli 7, Bergamo 24100, Italy.,Biophysics & Nanobiotechnologies Laboratory, Via Antonio Pastore 3, Genoa 16132, Italy
| | - Evgeniya Peshkova
- Fondazione ELBA Nicolini, Pradalunga, Largo Redaelli 7, Bergamo 24100, Italy.,Biophysics & Nanobiotechnologies Laboratory, Via Antonio Pastore 3, Genoa 16132, Italy
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Bragazzi NL, Amicizia D, Panatto D, Tramalloni D, Valle I, Gasparini R. Quartz-Crystal Microbalance (QCM) for Public Health: An Overview of Its Applications. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 101:149-211. [PMID: 26572979 DOI: 10.1016/bs.apcsb.2015.08.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nanobiotechnologies, from the convergence of nanotechnology and molecular biology and postgenomics medicine, play a major role in the field of public health. This overview summarizes the potentiality of piezoelectric sensors, and in particular, of quartz-crystal microbalance (QCM), a physical nanogram-sensitive device. QCM enables the rapid, real time, on-site detection of pathogens with an enormous burden in public health, such as influenza and other respiratory viruses, hepatitis B virus (HBV), and drug-resistant bacteria, among others. Further, it allows to detect food allergens, food-borne pathogens, such as Escherichia coli and Salmonella typhimurium, and food chemical contaminants, as well as water-borne microorganisms and environmental contaminants. Moreover, QCM holds promises in early cancer detection and screening of new antiblastic drugs. Applications for monitoring biohazards, for assuring homeland security, and preventing bioterrorism are also discussed.
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Affiliation(s)
- Nicola Luigi Bragazzi
- Department of Health Sciences (DISSAL), Via Antonio Pastore 1, University of Genoa, Genoa, Italy
| | - Daniela Amicizia
- Department of Health Sciences (DISSAL), Via Antonio Pastore 1, University of Genoa, Genoa, Italy
| | - Donatella Panatto
- Department of Health Sciences (DISSAL), Via Antonio Pastore 1, University of Genoa, Genoa, Italy
| | - Daniela Tramalloni
- Department of Health Sciences (DISSAL), Via Antonio Pastore 1, University of Genoa, Genoa, Italy
| | - Ivana Valle
- SSD "Popolazione a rischio," Health Prevention Department, Local Health Unit ASL3 Genovese, Genoa, Italy
| | - Roberto Gasparini
- Department of Health Sciences (DISSAL), Via Antonio Pastore 1, University of Genoa, Genoa, Italy.
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Quantitative and Systems-Based Approaches for Deciphering Bacterial Membrane Interactome and Gene Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:135-54. [PMID: 26621466 DOI: 10.1007/978-3-319-23603-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
High-throughput genomic and proteomic methods provide a concise description of the molecular constituents of a cell, whereas systems biology strives to understand the way these components function as a whole. Recent developments, such as genome editing technologies and protein epitope-tagging coupled with high-sensitivity mass-spectrometry, allow systemic studies to be performed at an unprecedented scale. Available methods can be successfully applied to various goals, both expanding fundamental knowledge and solving applied problems. In this review, we discuss the present state and future of bacterial cell envelope interactomics, with a specific focus on host-pathogen interactions and drug target discovery. Both experimental and computational methods will be outlined together with examples of their practical implementation.
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Barone A, Toti P, Giuca MR, Derchi G, Covani U. A gene network bioinformatics analysis for pemphigoid autoimmune blistering diseases. Clin Oral Investig 2014; 19:1207-22. [PMID: 25378027 DOI: 10.1007/s00784-014-1349-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 10/27/2014] [Indexed: 11/25/2022]
Abstract
OBJECTIVE In this theoretical study, a text mining search and clustering analysis of data related to genes potentially involved in human pemphigoid autoimmune blistering diseases (PAIBD) was performed using web tools to create a gene/protein interaction network. METHODS The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database was employed to identify a final set of PAIBD-involved genes and to calculate the overall significant interactions among genes: for each gene, the weighted number of links, or WNL, was registered and a clustering procedure was performed using the WNL analysis. Genes were ranked in class (leader, B, C, D and so on, up to orphans). An ontological analysis was performed for the set of 'leader' genes. RESULTS Using the above-mentioned data network, 115 genes represented the final set; leader genes numbered 7 (intercellular adhesion molecule 1 (ICAM-1), interferon gamma (IFNG), interleukin (IL)-2, IL-4, IL-6, IL-8 and tumour necrosis factor (TNF)), class B genes were 13, whereas the orphans were 24. The ontological analysis attested that the molecular action was focused on extracellular space and cell surface, whereas the activation and regulation of the immunity system was widely involved. CONCLUSIONS Despite the limited knowledge of the present pathologic phenomenon, attested by the presence of 24 genes revealing no protein-protein direct or indirect interactions, the network showed significant pathways gathered in several subgroups: cellular components, molecular functions, biological processes and the pathologic phenomenon obtained from the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database. CLINICAL RELEVANCE The molecular basis for PAIBD was summarised and expanded, which will perhaps give researchers promising directions for the identification of new therapeutic targets.
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Affiliation(s)
- Antonio Barone
- Department of Surgery, Medical, Molecular and Critical Area Pathology, University of Pisa, Via Paradisa 2, 56124, Pisa, Italy,
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